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Conserved domains on  [gi|260898763|ref|NP_001159607|]
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RNA-binding protein 28 isoform 2 [Homo sapiens]

Protein Classification

RNA-binding protein( domain architecture ID 13116135)

RNA-binding protein containing an RNA recognition motif (RRM)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM4_RBM28_like cd12416
RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 346-440 2.35e-50

RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


:

Pssm-ID: 409850 [Multi-domain]  Cd Length: 98  Bit Score: 169.32  E-value: 2.35e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 346 TRLCLHNLPKAVDDKQLRKLLLSATSG---EKGVRIKECRVMRDLKGVHGNMKGQSLGYAFAEFQEHEHALKALRLINNN 422
Cdd:cd12416    1 TRLCVRNLPKSVDDKKLKKLFLKAVKErakKKGVKIKEVKVMRDKKRLNSDGKGRSKGYGFVEFTEHEHALKALRALNNN 80

                         90
                 ....*....|....*...
gi 260898763 423 PEIFGPLKRPIVEFSLED 440
Cdd:cd12416   81 PEIFGPDKRPIVEFALEN 98
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 194-276 9.52e-35

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


:

Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 126.18  E-value: 9.52e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 194 KTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLAASPENEAGGLKLDGRQLKV 273
Cdd:cd12415    1 KTVFIRNLSFDTTEEDLKEFFSKFGEVKYARIVLDKDTGHSKGTAFVQFKTKESADKCIEAANDESEDGGLVLDGRKLIV 80


                 ...
gi 260898763 274 DLA 276
Cdd:cd12415   81 SLA 83
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 5-40 5.82e-15

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


The actual alignment was detected with superfamily member cd12413:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 79  Bit Score: 69.93  E-value: 5.82e-15
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEKG 40
Cdd:cd12413    1 TLFVRNLPYDTTDEQLEELFSDVGPVKRCFVVKDKG 36
PABP-1234 super family cl31127
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 187-580 6.97e-08

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


The actual alignment was detected with superfamily member TIGR01628:

Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 55.58  E-value: 6.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  187 PSDVNEGKT-VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEhSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLK 265
Cdd:TIGR01628  81 PSLRRSGVGnIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGK-SRGYGFVHFEKEESAKAAI------QKVNGML 153

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  266 LDGRQLKVDLAVTRDEAAklqTTKVKKPTgtrNLYLAR------EGLIR------------------------------- 308
Cdd:TIGR01628 154 LNDKEVYVGRFIKKHERE---AAPLKKFT---NLYVKNldpsvnEDKLRelfakfgeitsaavmkdgsgrsrgfafvnfe 227

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  309 ---AGTKAAE-------GVSAADM--------AKRERFELL--KHQKLKDQNIFVSR-TRLCLHNLPKAVDDKQLRKLLl 367
Cdd:TIGR01628 228 kheDAAKAVEemngkkiGLAKEGKklyvgraqKRAEREAELrrKFEELQQERKMKAQgVNLYVKNLDDTVTDEKLRELF- 306

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  368 sATSGEkgvrIKECRVMRDlkgvhgnMKGQSLGYAFAEFQEHEHALKALRLINNnpEIFGPlkRPIVeFSLEDRRKLKMK 447
Cdd:TIGR01628 307 -SECGE----ITSAKVMLD-------EKGVSRGFGFVCFSNPEEANRAVTEMHG--RMLGG--KPLY-VALAQRKEQRRA 369

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  448 ELRIQRSLQKMRSK---------PATGEPQKGQPEPAKDQQQKAAQHhtEEQSKVPPEQKRKAGSTSwtgfQTKAEVEQV 518
Cdd:TIGR01628 370 HLQDQFMQLQPRMRqlpmgspmgGAMGQPPYYGQGPQQQFNGQPLGW--PRMSMMPTPMGPGGPLRP----NGLAPMNAV 443

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 260898763  519 ELPDGKKRRKV--LALPSHRGPKIRLRDKGKVKPVHPKKPKPQINQWKQEKQQLSSEQVSRKKA 580
Cdd:TIGR01628 444 RAPSRNAQNAAqkPPMQPVMYPPNYQSLPLSQDLPQPQSTASQGGQNKKLAQVLASATPQMQKQ 507
 
Name Accession Description Interval E-value
RRM4_RBM28_like cd12416
RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 346-440 2.35e-50

RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409850 [Multi-domain]  Cd Length: 98  Bit Score: 169.32  E-value: 2.35e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 346 TRLCLHNLPKAVDDKQLRKLLLSATSG---EKGVRIKECRVMRDLKGVHGNMKGQSLGYAFAEFQEHEHALKALRLINNN 422
Cdd:cd12416    1 TRLCVRNLPKSVDDKKLKKLFLKAVKErakKKGVKIKEVKVMRDKKRLNSDGKGRSKGYGFVEFTEHEHALKALRALNNN 80

                         90
                 ....*....|....*...
gi 260898763 423 PEIFGPLKRPIVEFSLED 440
Cdd:cd12416   81 PEIFGPDKRPIVEFALEN 98
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 194-276 9.52e-35

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 126.18  E-value: 9.52e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 194 KTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLAASPENEAGGLKLDGRQLKV 273
Cdd:cd12415    1 KTVFIRNLSFDTTEEDLKEFFSKFGEVKYARIVLDKDTGHSKGTAFVQFKTKESADKCIEAANDESEDGGLVLDGRKLIV 80


                 ...
gi 260898763 274 DLA 276
Cdd:cd12415   81 SLA 83
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 5-40 5.82e-15

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 69.93  E-value: 5.82e-15
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEKG 40
Cdd:cd12413    1 TLFVRNLPYDTTDEQLEELFSDVGPVKRCFVVKDKG 36
RRM smart00360
RNA recognition motif;
195-273 5.61e-13

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 64.15  E-value: 5.61e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 260898763   195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKV 273
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKAL------EALNGKELDGRPLKV 73
RRM smart00360
RNA recognition motif;
340-427 1.23e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 51.83  E-value: 1.23e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763   340 NIFVSrtrlclhNLPKAVDDKQLRKLLlsatsgEKGVRIKECRVMRDlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLi 419
Cdd:smart00360   1 TLFVG-------NLPPDTTEEELRELF------SKFGKVESVRLVRD------KETGKSKGFAFVEFESEEDAEKALEA- 60


                   ....*...
gi 260898763   420 NNNPEIFG 427
Cdd:smart00360  61 LNGKELDG 68
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 187-580 6.97e-08

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 55.58  E-value: 6.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  187 PSDVNEGKT-VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEhSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLK 265
Cdd:TIGR01628  81 PSLRRSGVGnIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGK-SRGYGFVHFEKEESAKAAI------QKVNGML 153

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  266 LDGRQLKVDLAVTRDEAAklqTTKVKKPTgtrNLYLAR------EGLIR------------------------------- 308
Cdd:TIGR01628 154 LNDKEVYVGRFIKKHERE---AAPLKKFT---NLYVKNldpsvnEDKLRelfakfgeitsaavmkdgsgrsrgfafvnfe 227

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  309 ---AGTKAAE-------GVSAADM--------AKRERFELL--KHQKLKDQNIFVSR-TRLCLHNLPKAVDDKQLRKLLl 367
Cdd:TIGR01628 228 kheDAAKAVEemngkkiGLAKEGKklyvgraqKRAEREAELrrKFEELQQERKMKAQgVNLYVKNLDDTVTDEKLRELF- 306

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  368 sATSGEkgvrIKECRVMRDlkgvhgnMKGQSLGYAFAEFQEHEHALKALRLINNnpEIFGPlkRPIVeFSLEDRRKLKMK 447
Cdd:TIGR01628 307 -SECGE----ITSAKVMLD-------EKGVSRGFGFVCFSNPEEANRAVTEMHG--RMLGG--KPLY-VALAQRKEQRRA 369

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  448 ELRIQRSLQKMRSK---------PATGEPQKGQPEPAKDQQQKAAQHhtEEQSKVPPEQKRKAGSTSwtgfQTKAEVEQV 518
Cdd:TIGR01628 370 HLQDQFMQLQPRMRqlpmgspmgGAMGQPPYYGQGPQQQFNGQPLGW--PRMSMMPTPMGPGGPLRP----NGLAPMNAV 443

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 260898763  519 ELPDGKKRRKV--LALPSHRGPKIRLRDKGKVKPVHPKKPKPQINQWKQEKQQLSSEQVSRKKA 580
Cdd:TIGR01628 444 RAPSRNAQNAAqkPPMQPVMYPPNYQSLPLSQDLPQPQSTASQGGQNKKLAQVLASATPQMQKQ 507
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
193-281 2.52e-07

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 48.56  E-value: 2.52e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 193 GKTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKcllAASPENeagGLKLDGRQLK 272
Cdd:COG0724    1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDRETGRSRGFGFVEMPDDEEAQA---AIEALN---GAELMGRTLK 74


                 ....*....
gi 260898763 273 VDLAVTRDE 281
Cdd:COG0724   75 VNEARPREE 83
RRM smart00360
RNA recognition motif;
5-39 4.37e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 47.59  E-value: 4.37e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 260898763     5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEK 39
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDK 35
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 341-421 7.67e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 46.84  E-value: 7.67e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  341 IFVSrtrlclhNLPKAVDDKQLRKLLlsatsGEKGvRIKECRVMRDLKGvhgnmkgQSLGYAFAEFQEHEHALKALRLIN 420
Cdd:pfam00076   1 LFVG-------NLPPDTTEEDLKDLF-----SKFG-PIKSIRLVRDETG-------RSKGFAFVEFEDEEDAEKAIEALN 60


                  .
gi 260898763  421 N 421
Cdd:pfam00076  61 G 61
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 196-272 1.11e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 46.46  E-value: 1.11e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763  196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVlHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLK 272
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLV-RDETGRSKGFAFVEFEDEEDAEKAI------EALNGKELGGRELK 70
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
5-41 3.97e-06

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 45.09  E-value: 3.97e-06
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEK--GR 41
Cdd:COG0724    3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDRetGR 41
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 6-37 6.25e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 44.15  E-value: 6.25e-06
                          10        20        30
                  ....*....|....*....|....*....|..
gi 260898763    6 LFVGRLPPSARSEQLEELFSQVGPVKQCFVVT 37
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVR 32
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
 344-420 9.07e-05

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 44.93  E-value: 9.07e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763  344 SRTRLCLHNLPKAVDDKQLRKLLLSAtsGEkgvrIKECRVMRDlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLIN 420
Cdd:TIGR01661   2 SKTNLIVNYLPQTMTQEEIRSLFTSI--GE----IESCKLVRD------KVTGQSLGYGFVNYVRPEDAEKAVNSLN 66
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 167-276 7.76e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 42.21  E-value: 7.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  167 STEEQEDKAVQVSNKKKRKLPSDVNEGKtVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQE 246
Cdd:TIGR01622 189 LSEAEKNRAARAATETSGHHPNSIPFHR-LYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDPETGRSKGYGFIQFRDAE 267

                          90       100       110
                  ....*....|....*....|....*....|
gi 260898763  247 AAQKCLLAASpeneagGLKLDGRQLKVDLA 276
Cdd:TIGR01622 268 QAKEALEKMN------GFELAGRPIKVGLG 291
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
 196-284 1.06e-03

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 40.02  E-value: 1.06e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKVDL 275
Cdd:PLN03134  37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI------SEMDGKELNGRHIRVNP 110


                 ....*....
gi 260898763 276 AVTRDEAAK 284
Cdd:PLN03134 111 ANDRPSAPR 119
 
Name Accession Description Interval E-value
RRM4_RBM28_like cd12416
RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 346-440 2.35e-50

RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409850 [Multi-domain]  Cd Length: 98  Bit Score: 169.32  E-value: 2.35e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 346 TRLCLHNLPKAVDDKQLRKLLLSATSG---EKGVRIKECRVMRDLKGVHGNMKGQSLGYAFAEFQEHEHALKALRLINNN 422
Cdd:cd12416    1 TRLCVRNLPKSVDDKKLKKLFLKAVKErakKKGVKIKEVKVMRDKKRLNSDGKGRSKGYGFVEFTEHEHALKALRALNNN 80

                         90
                 ....*....|....*...
gi 260898763 423 PEIFGPLKRPIVEFSLED 440
Cdd:cd12416   81 PEIFGPDKRPIVEFALEN 98
RRM3_RBM28_like cd12415
RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 194-276 9.52e-35

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409849 [Multi-domain]  Cd Length: 83  Bit Score: 126.18  E-value: 9.52e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 194 KTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLAASPENEAGGLKLDGRQLKV 273
Cdd:cd12415    1 KTVFIRNLSFDTTEEDLKEFFSKFGEVKYARIVLDKDTGHSKGTAFVQFKTKESADKCIEAANDESEDGGLVLDGRKLIV 80


                 ...
gi 260898763 274 DLA 276
Cdd:cd12415   81 SLA 83
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
 193-282 3.51e-20

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410077 [Multi-domain]  Cd Length: 107  Bit Score: 85.94  E-value: 3.51e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 193 GKTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLAAS-PENE----------- 260
Cdd:cd12676    1 GRTLFVRNLPFDATEDELYSHFSQFGPLKYARVVKDPATGRSKGTAFVKFKNKEDADNCLSAAPeAQSTsllekysleqd 80

                         90       100
                 ....*....|....*....|....*..
gi 260898763 261 -----AGGLKLDGRQLKVDLAVTRDEA 282
Cdd:cd12676   81 itddvSAKFTLDGRVLQVTPAVSREEA 107
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 5-40 5.82e-15

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 69.93  E-value: 5.82e-15
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEKG 40
Cdd:cd12413    1 TLFVRNLPYDTTDEQLEELFSDVGPVKRCFVVKDKG 36
RRM smart00360
RNA recognition motif;
195-273 5.61e-13

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 64.15  E-value: 5.61e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 260898763   195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKV 273
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDKETGKSKGFAFVEFESEEDAEKAL------EALNGKELDGRPLKV 73
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
 196-274 2.98e-11

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 59.34  E-value: 2.98e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKVD 274
Cdd:cd12448    1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLPTDRETGQPKGFGYVDFSTIDSAEAAI------DALGGEYIDGRPIRLD 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 196-274 1.65e-10

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 57.29  E-value: 1.65e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDtEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKVD 274
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRD-GKSKGFAFVEFESPEDAEKAL------EALNGTELGGRPLKVS 72
RRM1_NUCLs cd12450
RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This ...
 195-279 1.89e-09

RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409884 [Multi-domain]  Cd Length: 78  Bit Score: 54.33  E-value: 1.89e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspenEAGGLKLDGRQLKVD 274
Cdd:cd12450    1 TLFVGNLSWSATQDDLENFFSDCGEVVDVRIAMDRDDGRSKGFGHVEFASAESAQKAL-------EKSGQDLGGREIRLD 73


                 ....*
gi 260898763 275 LAVTR 279
Cdd:cd12450   74 LANER 78
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 348-433 2.95e-09

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 53.83  E-value: 2.95e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 348 LCLHNLPKAVDDKQLRKLLlsatsgEKGVRIKECRVMRDlkgvhgnMKGQSLGYAFAEFQEHEHALKALRLiNNNPEIFG 427
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELF------SKFGEVVSVRIVRD-------RDGKSKGFAFVEFESPEDAEKALEA-LNGTELGG 66


                 ....*.
gi 260898763 428 plkRPI 433
Cdd:cd00590   67 ---RPL 69
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
 5-38 9.39e-09

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 52.47  E-value: 9.39e-09
                         10        20        30
                 ....*....|....*....|....*....|....
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTE 38
Cdd:cd12674    2 TLFVRNLPFDVTLESLTDFFSDIGPVKHAVVVTD 35
RRM smart00360
RNA recognition motif;
340-427 1.23e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 51.83  E-value: 1.23e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763   340 NIFVSrtrlclhNLPKAVDDKQLRKLLlsatsgEKGVRIKECRVMRDlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLi 419
Cdd:smart00360   1 TLFVG-------NLPPDTTEEELRELF------SKFGKVESVRLVRD------KETGKSKGFAFVEFESEEDAEKALEA- 60


                   ....*...
gi 260898763   420 NNNPEIFG 427
Cdd:smart00360  61 LNGKELDG 68
RRM1_Nop4p cd12674
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
 194-279 2.11e-08

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410075 [Multi-domain]  Cd Length: 80  Bit Score: 51.70  E-value: 2.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 194 KTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKV 273
Cdd:cd12674    1 TTLFVRNLPFDVTLESLTDFFSDIGPVKHAVVVTDPETKKSRGYGFVSFSTHDDAEEAL------AKLKNRKLSGHILKL 74


                 ....*.
gi 260898763 274 DLAVTR 279
Cdd:cd12674   75 DFAKPR 80
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
 195-276 4.88e-08

RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409881 [Multi-domain]  Cd Length: 76  Bit Score: 50.51  E-value: 4.88e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLAASpeneagGLKLDGRQLKVD 274
Cdd:cd12447    1 TLFVGGLSWNVDDPWLKKEFEKYGGVISARVITDRGSGRSKGYGYVDFATPEAAQKALAAMS------GKEIDGRQINVD 74


                 ..
gi 260898763 275 LA 276
Cdd:cd12447   75 FS 76
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 187-580 6.97e-08

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 55.58  E-value: 6.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  187 PSDVNEGKT-VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEhSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLK 265
Cdd:TIGR01628  81 PSLRRSGVGnIFVKNLDKSVDNKALFDTFSKFGNILSCKVATDENGK-SRGYGFVHFEKEESAKAAI------QKVNGML 153

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  266 LDGRQLKVDLAVTRDEAAklqTTKVKKPTgtrNLYLAR------EGLIR------------------------------- 308
Cdd:TIGR01628 154 LNDKEVYVGRFIKKHERE---AAPLKKFT---NLYVKNldpsvnEDKLRelfakfgeitsaavmkdgsgrsrgfafvnfe 227

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  309 ---AGTKAAE-------GVSAADM--------AKRERFELL--KHQKLKDQNIFVSR-TRLCLHNLPKAVDDKQLRKLLl 367
Cdd:TIGR01628 228 kheDAAKAVEemngkkiGLAKEGKklyvgraqKRAEREAELrrKFEELQQERKMKAQgVNLYVKNLDDTVTDEKLRELF- 306

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  368 sATSGEkgvrIKECRVMRDlkgvhgnMKGQSLGYAFAEFQEHEHALKALRLINNnpEIFGPlkRPIVeFSLEDRRKLKMK 447
Cdd:TIGR01628 307 -SECGE----ITSAKVMLD-------EKGVSRGFGFVCFSNPEEANRAVTEMHG--RMLGG--KPLY-VALAQRKEQRRA 369

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  448 ELRIQRSLQKMRSK---------PATGEPQKGQPEPAKDQQQKAAQHhtEEQSKVPPEQKRKAGSTSwtgfQTKAEVEQV 518
Cdd:TIGR01628 370 HLQDQFMQLQPRMRqlpmgspmgGAMGQPPYYGQGPQQQFNGQPLGW--PRMSMMPTPMGPGGPLRP----NGLAPMNAV 443

                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 260898763  519 ELPDGKKRRKV--LALPSHRGPKIRLRDKGKVKPVHPKKPKPQINQWKQEKQQLSSEQVSRKKA 580
Cdd:TIGR01628 444 RAPSRNAQNAAqkPPMQPVMYPPNYQSLPLSQDLPQPQSTASQGGQNKKLAQVLASATPQMQKQ 507
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
193-281 2.52e-07

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 48.56  E-value: 2.52e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 193 GKTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKcllAASPENeagGLKLDGRQLK 272
Cdd:COG0724    1 SMKIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDRETGRSRGFGFVEMPDDEEAQA---AIEALN---GAELMGRTLK 74


                 ....*....
gi 260898763 273 VDLAVTRDE 281
Cdd:COG0724   75 VNEARPREE 83
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 198-277 3.63e-07

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 47.93  E-value: 3.63e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 198 IRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEhSKGCAFAQFMTQEAAQKCLLAASpeneagGLKLDGRQLKVDLAV 277
Cdd:cd12414    4 VRNLPFKCTEDDLKKLFSKFGKVLEVTIPKKPDGK-LRGFAFVQFTNVADAAKAIKGMN------GKKIKGRPVAVDWAV 76
RRM smart00360
RNA recognition motif;
5-39 4.37e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 47.59  E-value: 4.37e-07
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 260898763     5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEK 39
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVRDK 35
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 341-421 7.67e-07

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 46.84  E-value: 7.67e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  341 IFVSrtrlclhNLPKAVDDKQLRKLLlsatsGEKGvRIKECRVMRDLKGvhgnmkgQSLGYAFAEFQEHEHALKALRLIN 420
Cdd:pfam00076   1 LFVG-------NLPPDTTEEDLKDLF-----SKFG-PIKSIRLVRDETG-------RSKGFAFVEFEDEEDAEKAIEALN 60


                  .
gi 260898763  421 N 421
Cdd:pfam00076  61 G 61
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
 346-422 1.02e-06

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 46.40  E-value: 1.02e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763 346 TRLCLHNLPKAVDDKQLRKLLlsatsgEKGVRIKECRVMRdlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLINNN 422
Cdd:cd12565    1 SRIIVKNLPKYVTEKRLKEHF------SKKGEITDVKVMR-------TKDGKSRRFGFIGFKSEEEAQKAVKYFNKT 64
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 196-272 1.11e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 46.46  E-value: 1.11e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763  196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVlHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLK 272
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLV-RDETGRSKGFAFVEFEDEEDAEKAI------EALNGKELGGRELK 70
RRM4_Nop4p cd12677
RNA recognition motif 4 (RRM4) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
 342-440 1.16e-06

RNA recognition motif 4 (RRM4) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM4 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410078 [Multi-domain]  Cd Length: 158  Bit Score: 48.70  E-value: 1.16e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 342 FVSRTRLCLHNLPKAVDDKQLRKLLLSATSG--------------------EKGVRIKECRVMRDLKG-----------V 390
Cdd:cd12677    1 HLSLTRLSIRNIPRHVTDKDLKALARKAIVGfatevkeglrapltkeelarDGDEMDEAEQKKKKKKSgvvrqakiifeK 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 260898763 391 HGNMKGQSLGYAFAEFQEHEHALKALRLINNNpEIFGPL----------------------KRPIVEFSLED 440
Cdd:cd12677   81 AGGGAGRSRGYGFIEYYTHRDALMGLRWLNGH-AVTSKKieeeykeemkdeiendpgkdrkKRLIVEFAIEN 151
RRM_CIRBP_RBM3 cd12449
RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding ...
 196-276 1.44e-06

RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins; This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain.


Pssm-ID: 409883 [Multi-domain]  Cd Length: 80  Bit Score: 46.32  E-value: 1.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLAASpeneagGLKLDGRQLKVDL 275
Cdd:cd12449    3 LFVGGLSFDTNEQSLEEVFSKYGQISEVVVVKDRETQRSRGFGFVTFENPDDAKDAMMAMN------GKSLDGRQIRVDQ 76


                 .
gi 260898763 276 A 276
Cdd:cd12449   77 A 77
RRM1_SXL cd12649
RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
 346-420 1.51e-06

RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 241093 [Multi-domain]  Cd Length: 81  Bit Score: 46.24  E-value: 1.51e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 260898763 346 TRLCLHNLPKAVDDKQLRKLLLSATsgekgvRIKECRVMRDlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLIN 420
Cdd:cd12649    1 TNLIVNYLPQDLTDREFRALFRAIG------PVNTCKIVRD------KKTGYSYGFGFVDFTSEEDAQRAIKTLN 63
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
 196-273 1.59e-06

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409755 [Multi-domain]  Cd Length: 74  Bit Score: 46.18  E-value: 1.59e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKV 273
Cdd:cd12316    2 LFVRNLPFTATEDELRELFEAFGKISEVHIPLDKQTKRSKGFAFVLFVIPEDAVKAY------QELDGSIFQGRLLHV 73
RRM_SNP1_like cd21615
RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ...
 187-274 2.21e-06

RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins; SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410194 [Multi-domain]  Cd Length: 118  Bit Score: 46.92  E-value: 2.21e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 187 PSDVNEG-----KTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLAAspeNEA 261
Cdd:cd21615    7 EEDPHIAdgdpyKTLFVGRLDYSLTELELQKKFSKFGEIEKIRIVRDKETGKSRGYAFIVFKSESDAKNAFKEG---NGL 83

                         90
                 ....*....|...
gi 260898763 262 GGLKLDGRQLKVD 274
Cdd:cd21615   84 RGLKINDRTCIVD 96
RRM2_Nop12p_like cd12670
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar ...
 196-273 2.83e-06

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar proteins; This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410071 [Multi-domain]  Cd Length: 77  Bit Score: 45.51  E-value: 2.83e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLAaspeNEAGGLKldGRQLKV 273
Cdd:cd12670    2 VFVGNLAFEAEEEGLWRYFGKCGAIESVRIVRDPKTNVGKGFAYVQFKDENAVEKALLL----NEKPTMK--GRKLRV 73
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 195-279 3.80e-06

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 44.89  E-value: 3.80e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKVD 274
Cdd:cd12413    1 TLFVRNLPYDTTDEQLEELFSDVGPVKRCFVVKDKGKDKCRGFGYVTFALAEDAQRAL------EEVKGKKFGGRKIKVE 74


                 ....*
gi 260898763 275 LAVTR 279
Cdd:cd12413   75 LAKKK 79
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
5-41 3.97e-06

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 45.09  E-value: 3.97e-06
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEK--GR 41
Cdd:COG0724    3 KIYVGNLPYSVTEEDLRELFSEYGEVTSVKLITDRetGR 41
RRM_DAZL_BOULE cd12412
RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...
 195-277 4.01e-06

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.


Pssm-ID: 409846 [Multi-domain]  Cd Length: 81  Bit Score: 44.91  E-value: 4.01e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDtEHSKGCAFAQFMTQEAAQKCLlaaspENEAgGLKLDGRQLKVD 274
Cdd:cd12412    4 RIFVGGIDWDTTEEELREFFSKFGKVKDVKIIKDRA-GVSKGYGFVTFETQEDAEKIQ-----KWGA-NLVFKGKKLNVG 76


                 ...
gi 260898763 275 LAV 277
Cdd:cd12412   77 PAI 79
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
 195-273 5.19e-06

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.


Pssm-ID: 409827 [Multi-domain]  Cd Length: 76  Bit Score: 44.58  E-value: 5.19e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLAASpeneagGLKLDGRQLKV 273
Cdd:cd12393    3 TVYVSNLPFSLTNNDLHQIFSKYGKVVKVTILKDKETRKSKGVAFVLFLDRESAHNAVRAMN------NKELFGRTLKC 75
RRM2_RBM34 cd12395
RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...
 195-273 5.80e-06

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.


Pssm-ID: 409829 [Multi-domain]  Cd Length: 73  Bit Score: 44.41  E-value: 5.80e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspenEAGGLKLDGRQLKV 273
Cdd:cd12395    1 SVFVGNLPFDIEEEELRKHFEDCGDVEAVRIVRDRETGIGKGFGYVLFKDKDSVDLAL-------KLNGSKLRGRKLRV 72
RRM1_Hu_like cd12375
RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...
 348-420 6.08e-06

RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 409810 [Multi-domain]  Cd Length: 76  Bit Score: 44.32  E-value: 6.08e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 260898763 348 LCLHNLPKAVDDKQLRKLLLSAtsGEkgvrIKECRVMRDLKgvhgnmKGQSLGYAFAEFQEHEHALKALRLIN 420
Cdd:cd12375    2 LIVNYLPQSMTQEELRSLFGAI--GP----IESCKLVRDKI------TGQSLGYGFVNYRDPNDARKAINTLN 62
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 6-41 6.17e-06

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 44.20  E-value: 6.17e-06
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 260898763   6 LFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEKGR 41
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVRDRDG 36
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 6-37 6.25e-06

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 44.15  E-value: 6.25e-06
                          10        20        30
                  ....*....|....*....|....*....|..
gi 260898763    6 LFVGRLPPSARSEQLEELFSQVGPVKQCFVVT 37
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKSIRLVR 32
RRM_Nop6 cd12400
RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and ...
 196-252 6.52e-06

RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins; This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing.


Pssm-ID: 409834 [Multi-domain]  Cd Length: 74  Bit Score: 44.13  E-value: 6.52e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCL 252
Cdd:cd12400    3 LFVGNLPYDTTAEDLKEHFKKAGEPPSVRLLTDKKTGKSKGCAFVEFDNQKALQKAL 59
RRM_RBM22 cd12224
RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This ...
 216-273 6.81e-06

RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins; This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines.


Pssm-ID: 409671 [Multi-domain]  Cd Length: 74  Bit Score: 44.20  E-value: 6.81e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 260898763 216 QFGELKYVRIVlhpdteHSKGCAFAQFMTQEAAQKcllAAspENEAGGLKLDGRQLKV 273
Cdd:cd12224   24 QFGEIRSITVV------ARQQCAFVQFTTRQAAER---AA--ERTFNKLIIKGRRLKV 70
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
 194-276 6.84e-06

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 44.43  E-value: 6.84e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 194 KTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQkclLAASPENeagGLKLDGRQLKV 273
Cdd:cd12398    1 RSVFVGNIPYDATEEQLKEIFSEVGPVVSFRLVTDRETGKPKGYGFCEFRDAETAL---SAVRNLN---GYELNGRPLRV 74


                 ...
gi 260898763 274 DLA 276
Cdd:cd12398   75 DFA 77
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 195-276 8.39e-06

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 44.08  E-value: 8.39e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKVD 274
Cdd:cd21608    1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKVITDRETGRSRGFGFVTFSTAEAAEAAI------DALNGKELDGRSIVVN 74


                 ..
gi 260898763 275 LA 276
Cdd:cd21608   75 EA 76
RRM2_RBM23_RBM39 cd12284
RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and ...
 217-276 1.19e-05

RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins; This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor.


Pssm-ID: 409726 [Multi-domain]  Cd Length: 78  Bit Score: 43.77  E-value: 1.19e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 217 FGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKVDLA 276
Cdd:cd12284   22 FGKIEFVQLQKDPETGRSKGYGFIQFRDAEDAKKAL------EQLNGFELAGRPMKVGHV 75
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
 348-426 1.89e-05

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 43.41  E-value: 1.89e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 260898763 348 LCLHNLPKAVDDKQLRKLLLSATsgekGVRIKECRVMRDLKGvhgnmkGQSLGYAFAEFQEHEHALKALRLINNNPEIF 426
Cdd:cd12313    5 LILRGLDVLTTEEDILSALQAHA----DLPIKDVRLIRDKLT------GTSRGFAFVEFSSLEDATQVMDALQNLLPPF 73
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
 6-36 2.47e-05

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins; This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region.


Pssm-ID: 409779 [Multi-domain]  Cd Length: 66  Bit Score: 42.22  E-value: 2.47e-05
                         10        20        30
                 ....*....|....*....|....*....|.
gi 260898763   6 LFVGRLPPSARSEQLEELFSQVGPVKQCFVV 36
Cdd:cd12343    2 IFVGNLPDAATSEELRALFEKYGKVTECDIV 32
RRM3_TIA1_like cd12354
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...
 195-272 2.81e-05

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.


Pssm-ID: 409790 [Multi-domain]  Cd Length: 71  Bit Score: 42.27  E-value: 2.81e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIvlHPDtehsKGCAFAQFMTQEAAQKCLLAASpeneagGLKLDGRQLK 272
Cdd:cd12354    2 TVYVGNITKGLTEALLQQTFSPFGQILEVRV--FPD----KGYAFIRFDSHEAATHAIVSVN------GTIINGQAVK 67
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
 194-274 3.60e-05

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 42.61  E-value: 3.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 194 KTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQE---AAQKcllaaspenEAGGLKLDGRQ 270
Cdd:cd12236    2 KTLFVARLSYDTTESKLRREFEKYGPIKRVRLVRDKKTGKSRGYAFIEFEHERdmkAAYK---------HADGKKIDGRR 72


                 ....
gi 260898763 271 LKVD 274
Cdd:cd12236   73 VLVD 76
RRM2_MRD1 cd12566
RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 ...
 192-254 4.57e-05

RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409982 [Multi-domain]  Cd Length: 79  Bit Score: 42.02  E-value: 4.57e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 260898763 192 EGKTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLA 254
Cdd:cd12566    1 ETGRLFLRNLPYSTKEDDLQKLFSKFGEVSEVHVPIDKKTKKSKGFAYVLFLDPEDAVQAYNE 63
RRM1_LARP7 cd12290
RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; ...
 217-252 4.86e-05

RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins; This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus.


Pssm-ID: 409732 [Multi-domain]  Cd Length: 79  Bit Score: 41.93  E-value: 4.86e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 260898763 217 FGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCL 252
Cdd:cd12290   23 YGEVVYVSIPRYKSTGDPKGFAFIEFETSESAQKAV 58
RRM_CSTF2_RNA15_like cd12398
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...
 5-39 6.45e-05

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.


Pssm-ID: 409832 [Multi-domain]  Cd Length: 77  Bit Score: 41.35  E-value: 6.45e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEK 39
Cdd:cd12398    2 SVFVGNIPYDATEEQLKEIFSEVGPVVSFRLVTDR 36
RRM_TRA2 cd12363
RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and ...
 216-278 7.30e-05

RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins; This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 409798 [Multi-domain]  Cd Length: 80  Bit Score: 41.45  E-value: 7.30e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 260898763 216 QFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCllaaspENEAGGLKLDGRQLKVDLAVT 278
Cdd:cd12363   24 RYGPIEKVQVVYDQQTGRSRGFGFVYFESVEDAKEA------KERLNGQEIDGRRIRVDYSIT 80
RRM2_NUCLs cd12451
RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This ...
 195-276 8.77e-05

RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants; This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409885 [Multi-domain]  Cd Length: 79  Bit Score: 41.24  E-value: 8.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 195 TVFIRNLSF----DSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspenEAGGLKLDGRQ 270
Cdd:cd12451    1 TIFVKGFDAslgeDTIRDELREHFGECGEVTNVRIPTDRETGELKGFAYIEFSTKEAKEKAL-------ELNGSDIAGGN 73


                 ....*.
gi 260898763 271 LKVDLA 276
Cdd:cd12451   74 LVVDEA 79
ELAV_HUD_SF TIGR01661
ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing ...
 344-420 9.07e-05

ELAV/HuD family splicing factor; This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076).


Pssm-ID: 273741 [Multi-domain]  Cd Length: 352  Bit Score: 44.93  E-value: 9.07e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763  344 SRTRLCLHNLPKAVDDKQLRKLLLSAtsGEkgvrIKECRVMRDlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLIN 420
Cdd:TIGR01661   2 SKTNLIVNYLPQTMTQEEIRSLFTSI--GE----IESCKLVRD------KVTGQSLGYGFVNYVRPEDAEKAVNSLN 66
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 5-41 1.02e-04

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 41.00  E-value: 1.02e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEK--GR 41
Cdd:cd21608    1 KLYVGNLSWDTTEDDLRDLFSEFGEVESAKVITDRetGR 39
RRM_snRNP35 cd12237
RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein ...
 194-279 1.46e-04

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.


Pssm-ID: 409683 [Multi-domain]  Cd Length: 94  Bit Score: 41.16  E-value: 1.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 194 KTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAqkclLAASpeNEAGGLKLDGRQLKV 273
Cdd:cd12237    5 LTLFVGRLSLQTTEEKLKEVFSRYGDIRRLRLVRDIVTGFSKRYAFIEYKEERDA----LHAY--RDAKKLVIDQYEIFV 78


                 ....*.
gi 260898763 274 DLAVTR 279
Cdd:cd12237   79 DFECER 84
sex-lethal TIGR01659
sex-lethal family splicing factor; This model describes the sex-lethal family of splicing ...
 344-420 1.51e-04

sex-lethal family splicing factor; This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661).


Pssm-ID: 273740 [Multi-domain]  Cd Length: 346  Bit Score: 44.24  E-value: 1.51e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763  344 SRTRLCLHNLPKAVDDKQLRKLLlsATSGEkgvrIKECRVMRDLKgvhgnmKGQSLGYAFAEFQEHEHALKALRLIN 420
Cdd:TIGR01659 106 SGTNLIVNYLPQDMTDRELYALF--RTIGP----INTCRIMRDYK------TGYSFGYAFVDFGSEADSQRAIKNLN 170
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
 340-421 1.54e-04

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409814 [Multi-domain]  Cd Length: 80  Bit Score: 40.62  E-value: 1.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 340 NIFVSrtrlclhNLPKAVDDKQLRKLLlsatsgEKGVRIKECRVMRDLkgvhgnmKGQSLGYAFAEFQEHEHALKALRLI 419
Cdd:cd12380    3 NVYVK-------NFGEDVDDDELKELF------EKYGKITSAKVMKDD-------SGKSKGFGFVNFENHEAAQKAVEEL 62


                 ..
gi 260898763 420 NN 421
Cdd:cd12380   63 NG 64
RRM1_HRB1_GBP2 cd21605
RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, ...
 5-41 2.28e-04

RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif.


Pssm-ID: 410184 [Multi-domain]  Cd Length: 77  Bit Score: 39.97  E-value: 2.28e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEKGR 41
Cdd:cd21605    3 SIFVGNLPFDCTWEDLKDHFSQVGEVIRADIVTSRGR 39
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
 195-253 3.38e-04

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 39.52  E-value: 3.38e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPdTEHSKGCAFAQFMTQEAAQKCLL 253
Cdd:cd12391    1 TVFVSNLDYSVPEDKIREIFSGCGEITDVRLVKNY-KGKSKGYCYVEFKDEESAQKALK 58
RRM2_I_PABPs cd12379
RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This ...
 340-421 3.62e-04

RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409813 [Multi-domain]  Cd Length: 77  Bit Score: 39.48  E-value: 3.62e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 340 NIFVSrtrlclhNLPKAVDDKQLRKLLlSATSgekgvRIKECRVMRDLKGvhgnmkgQSLGYAFAEFQEHEHALKALRLI 419
Cdd:cd12379    4 NIFIK-------NLDKSIDNKALYDTF-SAFG-----NILSCKVATDENG-------GSKGYGFVHFETEEAAERAIEKV 63


                 ..
gi 260898763 420 NN 421
Cdd:cd12379   64 NG 65
RRM_SLIRP cd12242
RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and ...
 5-39 3.82e-04

RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins; This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities.


Pssm-ID: 409688 [Multi-domain]  Cd Length: 73  Bit Score: 39.26  E-value: 3.82e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEK 39
Cdd:cd12242    1 KLFVSNLPWTTGSSELKEYFSQFGKVKRCNLPFDK 35
RRM1_p54nrb_like cd12332
RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds ...
 6-40 4.43e-04

RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family; This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members.


Pssm-ID: 409769 [Multi-domain]  Cd Length: 71  Bit Score: 38.82  E-value: 4.43e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 260898763   6 LFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEKG 40
Cdd:cd12332    4 LFVGNLPNDITEEEFKELFQKYGEVSEVFLNKGKG 38
RRM2_Nop13p_fungi cd12397
RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar ...
 196-262 4.48e-04

RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins; This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409831 [Multi-domain]  Cd Length: 76  Bit Score: 38.96  E-value: 4.48e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLAASPENEAG 262
Cdd:cd12397    1 LFVGNLSFETTEEDLRKHFAPAGKIRKVRMATFEDSGKCKGFAFVDFKEIESATNAVKGPINHSLNG 67
RRM1_TIA1_like cd12352
RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and ...
 6-40 4.53e-04

RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409788 [Multi-domain]  Cd Length: 73  Bit Score: 38.93  E-value: 4.53e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 260898763   6 LFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEKG 40
Cdd:cd12352    1 LYVGNLDRQVTEDLILQLFSQIGPCKSCKMITEHG 35
RRM_RBM25 cd12446
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; ...
 346-421 4.73e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor.


Pssm-ID: 409880 [Multi-domain]  Cd Length: 83  Bit Score: 39.43  E-value: 4.73e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763 346 TRLCLHNLPKAVDDKQLRKLLlsatsgEKGVRIKEC-RVMrdlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLINN 421
Cdd:cd12446    1 TTVFVGNIPDDVSDDFIRQLL------EKCGKVLSWkRVQ--------DPSGKLKAFGFCEFEDPEGALRALRLLNG 63
RRM6_RBM19_RRM5_MRD1 cd12320
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA ...
 194-276 4.88e-04

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409759 [Multi-domain]  Cd Length: 76  Bit Score: 39.14  E-value: 4.88e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 194 KTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHsKGCAFAQFMTQEAAQKCLLAaspeneAGGLKLDGRQLKV 273
Cdd:cd12320    1 TKLIVKNVPFEATRKEIRELFSPFGQLKSVRLPKKFDGSH-RGFAFVEFVTKQEAQNAMEA------LKSTHLYGRHLVL 73


                 ...
gi 260898763 274 DLA 276
Cdd:cd12320   74 EYA 76
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
 215-250 4.94e-04

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 39.14  E-value: 4.94e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 260898763 215 QQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQK 250
Cdd:cd12361   21 EQFGNIEEVQILRDKQTGQSKGCAFVTFSTREEALR 56
RRM2_RAVER cd12389
RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
 6-36 6.59e-04

RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409823 [Multi-domain]  Cd Length: 77  Bit Score: 38.84  E-value: 6.59e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 260898763   6 LFVGRLPPSARSEQLEELFSQVGPVKQCFVV 36
Cdd:cd12389    2 LCVTNLPLSFTEEQFEELVRPYGNVERCFLV 32
RRM3_MYEF2 cd12662
RNA recognition motif 3 (RRM3) found in vertebrate myelin expression factor 2 (MEF-2); This ...
 196-275 6.69e-04

RNA recognition motif 3 (RRM3) found in vertebrate myelin expression factor 2 (MEF-2); This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity.


Pssm-ID: 410063 [Multi-domain]  Cd Length: 77  Bit Score: 38.80  E-value: 6.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLhpDTEHSKGCAFAQFMTQEAAQK-CLLaaspeneAGGLKLDGRQLKVD 274
Cdd:cd12662    2 IFVRNLPFDLTWQKLKEKFSQCGHVMFAEIKM--ENGKSKGCGTVRFDSPESAEKaCRL-------MNGIKISGREIDVR 72


                 .
gi 260898763 275 L 275
Cdd:cd12662   73 L 73
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 196-275 6.95e-04

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 38.78  E-value: 6.95e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRI---VLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspenEAGGLKLDGRQLK 272
Cdd:cd12298    3 IRVRNLDFELDEEALRGIFEKFGEIESINIpkkQKNRKGRHNNGFAFVTFEDADSAESAL-------QLNGTLLDNRKIS 75


                 ...
gi 260898763 273 VDL 275
Cdd:cd12298   76 VSL 78
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 167-276 7.76e-04

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.


Pssm-ID: 273721 [Multi-domain]  Cd Length: 494  Bit Score: 42.21  E-value: 7.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763  167 STEEQEDKAVQVSNKKKRKLPSDVNEGKtVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQE 246
Cdd:TIGR01622 189 LSEAEKNRAARAATETSGHHPNSIPFHR-LYVGNLHFNITEQDLRQIFEPFGEIEFVQLQKDPETGRSKGYGFIQFRDAE 267

                          90       100       110
                  ....*....|....*....|....*....|
gi 260898763  247 AAQKCLLAASpeneagGLKLDGRQLKVDLA 276
Cdd:TIGR01622 268 QAKEALEKMN------GFELAGRPIKVGLG 291
RRM1_PHIP1 cd12271
RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting ...
 217-273 7.78e-04

RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins; This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA.


Pssm-ID: 409714 [Multi-domain]  Cd Length: 72  Bit Score: 38.46  E-value: 7.78e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763 217 FGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspenEAGGLKLDGRQLKV 273
Cdd:cd12271   22 CGEVRSVDLMRFPDSGNFRGIAFITFKTEEAAKRAL-------ALDGEMLGNRFLKV 71
RRM1_Hu cd12650
RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to ...
 346-420 7.85e-04

RNA recognition motif 1 (RRM1) found in the Hu proteins family; This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410053 [Multi-domain]  Cd Length: 77  Bit Score: 38.54  E-value: 7.85e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 260898763 346 TRLCLHNLPKAVDDKQLRKLLLSAtsGEkgvrIKECRVMRDlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLIN 420
Cdd:cd12650    1 TNLIVNYLPQNMTQDEIRSLFSSI--GE----IESCKLIRD------KVTGQSLGYGFVNYVDPSDAEKAINTLN 63
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
 6-40 7.92e-04

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 38.27  E-value: 7.92e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 260898763   6 LFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEKG 40
Cdd:cd12399    1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDRE 35
PLN03134 PLN03134
glycine-rich RNA-binding protein 4; Provisional
 196-284 1.06e-03

glycine-rich RNA-binding protein 4; Provisional


Pssm-ID: 178680 [Multi-domain]  Cd Length: 144  Bit Score: 40.02  E-value: 1.06e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKVDL 275
Cdd:PLN03134  37 LFIGGLSWGTDDASLRDAFAHFGDVVDAKVIVDRETGRSRGFGFVNFNDEGAATAAI------SEMDGKELNGRHIRVNP 110


                 ....*....
gi 260898763 276 AVTRDEAAK 284
Cdd:PLN03134 111 ANDRPSAPR 119
RRM_II_PABPs cd12306
RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to ...
 196-273 1.13e-03

RNA recognition motif in type II polyadenylate-binding proteins; This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only.


Pssm-ID: 409747 [Multi-domain]  Cd Length: 73  Bit Score: 38.05  E-value: 1.13e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLAaspeNEAgglKLDGRQLKV 273
Cdd:cd12306    2 IYVGNVDYGTTPEELQAHFKSCGTINRVTILCDKFTGQPKGFAYIEFVDKSSVENALLL----NES---EFRGRQIKV 72
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
 5-30 1.18e-03

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 38.26  E-value: 1.18e-03
                         10        20
                 ....*....|....*....|....*.
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPV 30
Cdd:cd12671    8 SVFVGNIPYEATEEQLKDIFSEVGPV 33
RRM3_RAVER cd12390
RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
 5-49 1.25e-03

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409824 [Multi-domain]  Cd Length: 91  Bit Score: 38.37  E-value: 1.25e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 260898763   5 TLFVGRLPPSAR-SEQLEELFSQVGPVKQCFVVTEKGrtVAVDWAV 49
Cdd:cd12390    4 CLFVDRLPKDFRdGSELRKLFSQVGKPTFCQLAMGNG--VPRGFAF 47
RRM_PPIL4 cd12235
RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and ...
 378-421 1.43e-03

RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins; This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus.


Pssm-ID: 409681 [Multi-domain]  Cd Length: 83  Bit Score: 38.02  E-value: 1.43e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 260898763 378 IKECRVMRDLKgvhgnmKGQSLGYAFAEFQEHEHALKALRLINN 421
Cdd:cd12235   30 IKSCEVIRDKK------TGDSLQYAFIEFETKESCEEAYFKMDN 67
RRM1_SART3 cd12391
RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells ...
 341-418 1.47e-03

RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409825 [Multi-domain]  Cd Length: 72  Bit Score: 37.59  E-value: 1.47e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 260898763 341 IFVSrtrlclhNLPKAVDDKQLRKLLlsATSGEkgvrIKECRVMRdlkgvhgNMKGQSLGYAFAEFQEHEHALKALRL 418
Cdd:cd12391    2 VFVS-------NLDYSVPEDKIREIF--SGCGE----ITDVRLVK-------NYKGKSKGYCYVEFKDEESAQKALKL 59
RRM2_RAVER cd12389
RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
 348-423 1.47e-03

RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409823 [Multi-domain]  Cd Length: 77  Bit Score: 37.68  E-value: 1.47e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 260898763 348 LCLHNLPKAVDDKQLRKLLLSATSgekgvrIKECRVmrdlkgVHGNMKGQSLGYAFAEFQEHEHALKALRLINNNP 423
Cdd:cd12389    2 LCVTNLPLSFTEEQFEELVRPYGN------VERCFL------VYSEVTGESKGYGFVEYTSKESAIRAKNQLHGRQ 65
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
 6-52 1.63e-03

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 37.38  E-value: 1.63e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 260898763   6 LFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEKGRTVAV-----DWAVAKD 52
Cdd:cd12340    2 LFVRPFPPDTSESAIREIFSPYGPVKEVKMLSDSNFAFVEfeeleDAIRAKD 53
RRM1_PUF60 cd12370
RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; ...
 196-273 1.64e-03

RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins; This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.


Pssm-ID: 409805 [Multi-domain]  Cd Length: 76  Bit Score: 37.39  E-value: 1.64e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQkclLAASPENeagGLKLDGRQLKV 273
Cdd:cd12370    3 VYVGSIYFELGEDTIRQAFAPFGPIKSIDMSWDPVTMKHKGFAFVEYEVPEAAQ---LALEQMN---GVMLGGRNIKV 74
RRM1_HuB cd12771
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup ...
 344-420 1.64e-03

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB); This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410164 [Multi-domain]  Cd Length: 83  Bit Score: 37.78  E-value: 1.64e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763 344 SRTRLCLHNLPKAVDDKQLRKLLlsATSGEkgvrIKECRVMRDlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLIN 420
Cdd:cd12771    3 SKTNLIVNYLPQNMTQEELKSLF--GSIGE----IESCKLVRD------KITGQSLGYGFVNYIEPKDAEKAINTLN 67
RRM2_gar2 cd12448
RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This ...
 6-41 1.69e-03

RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins; This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues.


Pssm-ID: 409882 [Multi-domain]  Cd Length: 73  Bit Score: 37.39  E-value: 1.69e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 260898763   6 LFVGRLPPSARSEQLEELFSQVGPVKQCFVVT--EKGR 41
Cdd:cd12448    1 LFVGNLPFSATQDALYEAFSQHGSIVSVRLPTdrETGQ 38
RRM1_RBM4 cd12606
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup ...
 6-40 1.75e-03

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4); This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4.


Pssm-ID: 410018 [Multi-domain]  Cd Length: 67  Bit Score: 37.09  E-value: 1.75e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 260898763   6 LFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEKG 40
Cdd:cd12606    3 LFIGNLPREATEEEIRSLFEQYGKVTECDIIKNYG 37
RRM2_SART3 cd12392
RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells ...
 5-37 1.81e-03

RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins; This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409826 [Multi-domain]  Cd Length: 81  Bit Score: 37.70  E-value: 1.81e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVT 37
Cdd:cd12392    4 KLFVKGLPFSCTKEELEELFKQHGTVKDVRLVT 36
RRM1_hnRNPA_hnRNPD_like cd12325
RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and ...
 196-270 1.87e-03

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins; This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs.


Pssm-ID: 409763 [Multi-domain]  Cd Length: 72  Bit Score: 37.12  E-value: 1.87e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKClLAASPEneagglKLDGRQ 270
Cdd:cd12325    1 LFVGGLSWETTEESLREYFSKYGEVVDCVVMKDPATGRSRGFGFVTFKDPSSVDAV-LAARPH------TLDGRT 68
RRM_eIF3G_like cd12408
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...
 195-252 2.10e-03

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.


Pssm-ID: 409842 [Multi-domain]  Cd Length: 76  Bit Score: 37.10  E-value: 2.10e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCL 252
Cdd:cd12408    1 TIRVTNLSEDATEEDLRELFRPFGPISRVYLAKDKETGQSKGFAFVTFETREDAERAI 58
RRM4_I_PABPs cd12381
RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...
 352-423 2.27e-03

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.


Pssm-ID: 409815 [Multi-domain]  Cd Length: 79  Bit Score: 37.25  E-value: 2.27e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763 352 NLPKAVDDKQLRKLLLSATSgekgvrIKECRVMRDLKGvhgnmkgQSLGYAFAEFQEHEHALKAL-----RLINNNP 423
Cdd:cd12381    8 NLDDTIDDEKLREEFSPFGT------ITSAKVMTDEGG-------RSKGFGFVCFSSPEEATKAVtemngRIIGGKP 71
RRM3_hnRNPM cd12661
RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein M ...
 196-275 2.37e-03

RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M); This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif).


Pssm-ID: 410062 [Multi-domain]  Cd Length: 77  Bit Score: 37.16  E-value: 2.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLhpDTEHSKGCAFAQFMTQEAAQK-CLLaaspeneAGGLKLDGRQLKVD 274
Cdd:cd12661    2 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKM--ENGKSKGCGVVRFESPEVAERaCRM-------MNGIKLNGREIDVR 72


                 .
gi 260898763 275 L 275
Cdd:cd12661   73 I 73
RRM1_HuD cd12770
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup ...
 345-420 2.49e-03

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD); This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410163 [Multi-domain]  Cd Length: 81  Bit Score: 37.40  E-value: 2.49e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 260898763 345 RTRLCLHNLPKAVDDKQLRKLLlsATSGEkgvrIKECRVMRDlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLIN 420
Cdd:cd12770    1 KTNLIVNYLPQNMTQEEFRSLF--GSIGE----IESCKLVRD------KITGQSLGYGFVNYIDPKDAEKAINTLN 64
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
 353-421 2.73e-03

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 36.83  E-value: 2.73e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 260898763 353 LPKAVDDKQLRKLLlsatsgEKGVRIKECRVMRDlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLINN 421
Cdd:cd12361    7 IPKTASEEDVRPLF------EQFGNIEEVQILRD------KQTGQSKGCAFVTFSTREEALRAIEALHN 63
RRM3_Nop4p cd12676
RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...
 3-39 3.06e-03

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 410077 [Multi-domain]  Cd Length: 107  Bit Score: 37.79  E-value: 3.06e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 260898763   3 GLTLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEK 39
Cdd:cd12676    1 GRTLFVRNLPFDATEDELYSHFSQFGPLKYARVVKDP 37
RRM1_HuC cd12772
RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup ...
 344-420 3.24e-03

RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC); This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.


Pssm-ID: 410165 [Multi-domain]  Cd Length: 85  Bit Score: 37.02  E-value: 3.24e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 260898763 344 SRTRLCLHNLPKAVDDKQLRKLLLSATSgekgvrIKECRVMRDlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLIN 420
Cdd:cd12772    3 SKTNLIVNYLPQNMTQEEFKSLFGSIGD------IESCKLVRD------KITGQSLGYGFVNYVDPNDADKAINTLN 67
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
 194-271 3.28e-03

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 36.82  E-value: 3.28e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 194 KTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEH---SKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQ 270
Cdd:cd12318    1 TTLFVKNLNFKTTEEALKKHFEKCGPIRSVTIAKKKDPKGpllSMGYGFVEFKSPEAAQKAL------KQLQGTVLDGHA 74


                 .
gi 260898763 271 L 271
Cdd:cd12318   75 L 75
RRM1_RBM19_MRD1 cd12315
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19), yeast multiple ...
 346-420 3.38e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409754 [Multi-domain]  Cd Length: 81  Bit Score: 36.75  E-value: 3.38e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 260898763 346 TRLCLHNLPKAVDDKQLRKLLLSATSgEKGVRIKECRVMRDLKGVhgnmkgqSLGYAFAEFQEHEHALKALRLIN 420
Cdd:cd12315    1 SRLIVKNLPLSLDEDQFRRLFSQKCK-DIGLTITDCKLLTKSGGV-------SRRFGFVGFKDEEDAQKAKEFFN 67
RRM3_RAVER cd12390
RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
 344-421 3.38e-03

RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409824 [Multi-domain]  Cd Length: 91  Bit Score: 37.22  E-value: 3.38e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 344 SRTrLCLHNLPKA-VDDKQLRKLLlsatsgEKGVRIKECRV-MRDlkgvhgnmkGQSLGYAFAEFQEHEHALKALRLINN 421
Cdd:cd12390    2 SKC-LFVDRLPKDfRDGSELRKLF------SQVGKPTFCQLaMGN---------GVPRGFAFVEFASAEDAEEAQQLLNG 65
RRM_eIF4H cd12401
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and ...
 195-280 3.53e-03

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins; This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation.


Pssm-ID: 409835 [Multi-domain]  Cd Length: 84  Bit Score: 36.88  E-value: 3.53e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFgELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspenEAGGLKLDGRQLKVD 274
Cdd:cd12401    7 TAYVGNLPFNTVQGDLDAIFKDL-KVRSVRLVRDRETDKFKGFCYVEFEDLESLKEAL-------EYDGALFEDRPLRVD 78


                 ....*.
gi 260898763 275 LAVTRD 280
Cdd:cd12401   79 IAEGRK 84
RRM_CSTF2_CSTF2T cd12671
RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage ...
 194-278 3.61e-03

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins; This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64.


Pssm-ID: 410072 [Multi-domain]  Cd Length: 85  Bit Score: 36.72  E-value: 3.61e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 194 KTVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAaqkcllAASPENEAGGLKLDGRQLKV 273
Cdd:cd12671    7 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQET------ALSAMRNLNGYELNGRALRV 80


                 ....*
gi 260898763 274 DLAVT 278
Cdd:cd12671   81 DNAAS 85
RRM2_NCL cd12404
RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to ...
 194-274 3.82e-03

RNA recognition motif 2 (RRM2) found in vertebrate nucleolin; This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop.


Pssm-ID: 409838 [Multi-domain]  Cd Length: 77  Bit Score: 36.64  E-value: 3.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 194 KTVFIRNLSFDSeeeELGELLQQFGELKYVRIVLHpDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKV 273
Cdd:cd12404    4 RTLFVKNLPYST---TQDELKEVFEDAVDIRIPMG-RDGRSKGIAYIEFKSEAEAEKAL------EEKQGTEVDGRSIVV 73


                 .
gi 260898763 274 D 274
Cdd:cd12404   74 D 74
RRM4_MRD1 cd12319
RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 ...
 195-276 3.86e-03

RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409758 [Multi-domain]  Cd Length: 84  Bit Score: 36.69  E-value: 3.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEH-----SKGCAFAQFMTQEAAQKCLLAASpeneagGLKLDGR 269
Cdd:cd12319    2 TLFVKNLNFSTTNQHLTDVFKHLDGFVFARVKTKPDPKRpgktlSMGFGFVGFKTKEQAQAALKAMD------GFVLDGH 75


                 ....*..
gi 260898763 270 QLKVDLA 276
Cdd:cd12319   76 KLEVKFS 82
RRM2_RAVER cd12389
RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
 217-274 4.17e-03

RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409823 [Multi-domain]  Cd Length: 77  Bit Score: 36.53  E-value: 4.17e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 260898763 217 FGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCllaaspENEAGGLKLDGRQLKVD 274
Cdd:cd12389   23 YGNVERCFLVYSEVTGESKGYGFVEYTSKESAIRA------KNQLHGRQIGGRALQVD 74
RRM_snRNP35 cd12237
RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein ...
 4-36 4.37e-03

RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins; This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain.


Pssm-ID: 409683 [Multi-domain]  Cd Length: 94  Bit Score: 36.92  E-value: 4.37e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 260898763   4 LTLFVGRLPPSARSEQLEELFSQVGPVKQCFVV 36
Cdd:cd12237    5 LTLFVGRLSLQTTEEKLKEVFSRYGDIRRLRLV 37
RRM_snRNP70 cd12236
RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and ...
 341-415 4.41e-03

RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins; This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function.


Pssm-ID: 409682 [Multi-domain]  Cd Length: 91  Bit Score: 36.83  E-value: 4.41e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 260898763 341 IFVSRtrlclhnLPKAVDDKQLRKLLlsatsgEKGVRIKECRVMRDLKgvhgnmKGQSLGYAFAEFqEHEHALKA 415
Cdd:cd12236    4 LFVAR-------LSYDTTESKLRREF------EKYGPIKRVRLVRDKK------TGKSRGYAFIEF-EHERDMKA 58
RRM1_SECp43_like cd12344
RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and ...
 369-423 4.73e-03

RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins; This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs.


Pssm-ID: 409780 [Multi-domain]  Cd Length: 82  Bit Score: 36.51  E-value: 4.73e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 260898763 369 ATSGEKGVRIKECRVmrdlkgvhgNMKGQSLGYAFAEFQEHEHALKALRLINNNP 423
Cdd:cd12344   21 AKTGEEVVSVKIIRN---------KQTGKSAGYCFVEFATQEAAEQALEHLNGKP 66
RRM_PPIL4 cd12235
RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and ...
 5-39 5.36e-03

RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins; This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus.


Pssm-ID: 409681 [Multi-domain]  Cd Length: 83  Bit Score: 36.10  E-value: 5.36e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEK 39
Cdd:cd12235    5 VLFVCKLNPVTTDEDLEIIFSRFGKIKSCEVIRDK 39
RRM3_hnRNPM_like cd12387
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) ...
 196-273 5.46e-03

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins; This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity.


Pssm-ID: 409821 [Multi-domain]  Cd Length: 71  Bit Score: 36.03  E-value: 5.46e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLhpDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKV 273
Cdd:cd12387    1 IFVRNLPFDYTWQKLKDKFKDCGHVTFASIKM--ENGKSKGCGTVRFDSPEDAENAC------RMMNGSKQSGREIDV 70
RRM2_TIA1_like cd12353
RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...
 196-274 5.49e-03

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.


Pssm-ID: 409789 [Multi-domain]  Cd Length: 75  Bit Score: 36.22  E-value: 5.49e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKVD 274
Cdd:cd12353    2 IFVGDLSPEIETEDLKEAFAPFGEISDARVVKDTQTGKSKGYGFVSFVKKEDAENAI------QGMNGQWLGGRNIRTN 74
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
 6-35 5.53e-03

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 36.06  E-value: 5.53e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 260898763   6 LFVGRLPPSARSEQLEELFSQVGPVKQCFV 35
Cdd:cd12361    2 LFVGMIPKTASEEDVRPLFEQFGNIEEVQI 31
RRM5_RBM19_like cd12318
RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar ...
 346-417 5.69e-03

RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins; This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409757 [Multi-domain]  Cd Length: 80  Bit Score: 36.05  E-value: 5.69e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 260898763 346 TRLCLHNLPKAVDDKQLRKLLlsatsgEKGVRIKECRVMR--DLKGvhgnmKGQSLGYAFAEFQEHEHALKALR 417
Cdd:cd12318    1 TTLFVKNLNFKTTEEALKKHF------EKCGPIRSVTIAKkkDPKG-----PLLSMGYGFVEFKSPEAAQKALK 63
RRM_eIF4B cd12402
RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and ...
 195-280 5.79e-03

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins; This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation.


Pssm-ID: 409836 [Multi-domain]  Cd Length: 81  Bit Score: 36.04  E-value: 5.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 195 TVFIRNLSFDSeeeELGELLQQFGEL--KYVRIVLHPDTEHSKGCAFAQFMTQEAaqkcLLAASPENEaggLKLDGRQLK 272
Cdd:cd12402    4 TAYLGNLPYDV---TEDDIEDFFRGLniSSVRLPRENGPGRLRGFGYVEFEDRES----LIQALSLNE---ESLKNRRIR 73


                 ....*...
gi 260898763 273 VDLAVTRD 280
Cdd:cd12402   74 VDVAGQAQ 81
RRM1_TDP43 cd12321
RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar ...
 216-276 5.85e-03

RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins; This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity.


Pssm-ID: 409760 [Multi-domain]  Cd Length: 74  Bit Score: 35.84  E-value: 5.85e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 260898763 216 QFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeneAGGLKLDGRQLKVDLA 276
Cdd:cd12321   22 TFGEVLMVQVKKDPKTGRSKGFGFVRFASYETQVKVL--------SQRHMIDGRWCDVKLP 74
RRM3_PES4_MIP6 cd21603
RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 ...
 5-34 6.03e-03

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins; The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.


Pssm-ID: 410182 [Multi-domain]  Cd Length: 73  Bit Score: 35.72  E-value: 6.03e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 260898763   5 TLFVGRLPPSARSEQLEELFSQVGPVKQCF 34
Cdd:cd21603    2 AIFVKNLPLDTNNDEILDFFSKVGPIKSVF 31
RRM2_MRN1 cd12523
RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This ...
 6-40 6.06e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409943 [Multi-domain]  Cd Length: 78  Bit Score: 35.87  E-value: 6.06e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 260898763   6 LFVGRLPPSARSEQLEELFSQVGPVKQCFVVTEKG 40
Cdd:cd12523    6 VYLGNLPESITEEELREDLEKFGPIDQIKIVKEKN 40
RRM_HP0827_like cd12399
RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; ...
 196-276 6.17e-03

RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins; This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827.


Pssm-ID: 409833 [Multi-domain]  Cd Length: 75  Bit Score: 35.96  E-value: 6.17e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 196 VFIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLLaaspenEAGGLKLDGRQLKVDL 275
Cdd:cd12399    1 LYVGNLPYSASEEQLKSLFGQFGAVFDVKLPMDRETKRPRGFGFVELQEEESAEKAIA------KLDGTDFMGRTIRVNE 74


                 .
gi 260898763 276 A 276
Cdd:cd12399   75 A 75
RRM2_SXL cd12651
RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This ...
 337-421 6.27e-03

RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.


Pssm-ID: 410054 [Multi-domain]  Cd Length: 81  Bit Score: 36.02  E-value: 6.27e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 337 KDQNIFVSrtrlclhNLPKAVDDKQLRKLLlsatsgEKGVRIKECRVMRDlkgvhgNMKGQSLGYAFAEFQEHEHALKAL 416
Cdd:cd12651    1 KDTNLYVT-------NLPRTITEDELDTIF------GAYGNIVQKNLLRD------KLTGRPRGVAFVRYDKREEAQAAI 61


                 ....*
gi 260898763 417 RLINN 421
Cdd:cd12651   62 SALNG 66
RRM_TRA2B cd12641
RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and ...
 216-279 6.92e-03

RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins; This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes.


Pssm-ID: 410046 [Multi-domain]  Cd Length: 87  Bit Score: 36.14  E-value: 6.92e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 260898763 216 QFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCllaaspENEAGGLKLDGRQLKVDLAVTR 279
Cdd:cd12641   30 KYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA------KERANGMELDGRRIRVDFSITK 87
RRM3_NGR1_NAM8_like cd12346
RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), ...
 195-252 7.63e-03

RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins; This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs.


Pssm-ID: 409782 [Multi-domain]  Cd Length: 72  Bit Score: 35.38  E-value: 7.63e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 260898763 195 TVFIRNLSFDSEEEELGELLQQFGELKYVRIVLhpdtehSKGCAFAQFMTQEAAQKCL 252
Cdd:cd12346    3 TVFVGGLDPNVTEEDLRVLFGPFGEIVYVKIPP------GKGCGFVQFVNRASAEAAI 54
RRM_ist3_like cd12411
RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ...
 186-274 7.66e-03

RNA recognition motif (RRM) found in ist3 family; This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well.


Pssm-ID: 409845 [Multi-domain]  Cd Length: 89  Bit Score: 36.03  E-value: 7.66e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260898763 186 LPSDVNEGK--TVFirnlsfdseeeelgellQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAaqkCLLAASPENeagG 263
Cdd:cd12411   17 LPYELTEGDilCVF-----------------SQYGEIVDINLVRDKKTGKSKGFAFLAYEDQRS---TILAVDNLN---G 73

                         90
                 ....*....|.
gi 260898763 264 LKLDGRQLKVD 274
Cdd:cd12411   74 IKLLGRTIRVD 84
RRM_TRA2A cd12642
RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and ...
 216-279 8.43e-03

RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins; This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions.


Pssm-ID: 410047 [Multi-domain]  Cd Length: 84  Bit Score: 35.74  E-value: 8.43e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 260898763 216 QFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaaspeNEAGGLKLDGRQLKVDLAVTR 279
Cdd:cd12642   27 RYGPLAGVNVVYDQRTGRSRGFAFVYFERIDDSKEAM------ERANGMELDGRRIRVDYSITK 84
RRM1_MSI cd12576
RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, ...
 197-267 9.01e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins; This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function.


Pssm-ID: 409990 [Multi-domain]  Cd Length: 76  Bit Score: 35.50  E-value: 9.01e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 260898763 197 FIRNLSFDSEEEELGELLQQFGELKYVRIVLHPDTEHSKGCAFAQFMTQEAAQKCLlaASPENEAGGLKLD 267
Cdd:cd12576    3 FIGGLSWQTTPEGLREYFSKFGEITECMVMRDPTTKRSRGFGFVTFSDPASVDKVL--AQGPHELDGKKID 71
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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