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Conserved domains on  [gi|29126228|ref|NP_803432|]
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splicing factor U2AF 35 kDa subunit [Danio rerio]

Protein Classification

splicing factor SR family protein( domain architecture ID 10457999)

splicing factor SR (serine/arginine-rich) family protein containing the CCCH-type zinc finger domain, similar to Homo sapiens splicing factor U2AF 26 kDa subunit and splicing factor U2AF 35 kDa subunit

Gene Ontology:  GO:0008270|GO:0003723|GO:0000398
PubMed:  19061484

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_U2AF35 cd12538
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...
 43-145 1.94e-71

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain.


:

Pssm-ID: 409954 [Multi-domain]  Cd Length: 104  Bit Score: 213.76  E-value: 1.94e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228  43 SQTIALLNIYRNPQNTAQSADGL-NAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREED 121
Cdd:cd12538   1 SQTILLQNLYQNPQNTPQSADGLkVKVSDVELQEHFDEFYEDVFVELEEKYGEIEEMNVCDNLGDHLVGNVYVKFRREED 80

                        90       100
                ....*....|....*....|....
gi 29126228 122 AEKAVINLNNRWFNGQPIHAELSP 145
Cdd:cd12538  81 AEKAVNDLNNRWFNGQPIYAELSP 104
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
148-174 8.62e-05

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


:

Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 38.71  E-value: 8.62e-05
                          10        20
                  ....*....|....*....|....*..
gi 29126228   148 DFREACCRQYEMGECTRGGFCNFMHLK 174
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAHGQ 27
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
13-39 1.69e-04

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


:

Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 37.94  E-value: 1.69e-04
                          10        20
                  ....*....|....*....|....*..
gi 29126228    13 KDKVNCSFYFKIGACRHGDRCSRLHNK 39
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAHGQ 27
 
Name Accession Description Interval E-value
RRM_U2AF35 cd12538
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...
 43-145 1.94e-71

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain.


Pssm-ID: 409954 [Multi-domain]  Cd Length: 104  Bit Score: 213.76  E-value: 1.94e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228  43 SQTIALLNIYRNPQNTAQSADGL-NAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREED 121
Cdd:cd12538   1 SQTILLQNLYQNPQNTPQSADGLkVKVSDVELQEHFDEFYEDVFVELEEKYGEIEEMNVCDNLGDHLVGNVYVKFRREED 80

                        90       100
                ....*....|....*....|....
gi 29126228 122 AEKAVINLNNRWFNGQPIHAELSP 145
Cdd:cd12538  81 AEKAVNDLNNRWFNGQPIYAELSP 104
RRM_1 smart00361
RNA recognition motif;
77-142 4.61e-17

RNA recognition motif;


Pssm-ID: 214637 [Multi-domain]  Cd Length: 70  Bit Score: 73.21  E-value: 4.61e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228     77 YDEFFEEVFTEMEEKYGEVEEMN--VCDNLG--DHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAE 142
Cdd:smart00361   1 KDEDFERELKEEEEYFGEVGKINkiYIDDVGyeNHKRGNVYITFERSEDAARAIVDLNGRYFDGRLVKAE 70
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 90-140 4.68e-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: 43.38  E-value: 4.68e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 29126228    90 EKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIH 140
Cdd:pfam00076  20 SKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
148-174 8.62e-05

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 38.71  E-value: 8.62e-05
                          10        20
                  ....*....|....*....|....*..
gi 29126228   148 DFREACCRQYEMGECTRGGFCNFMHLK 174
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAHGQ 27
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 69-153 9.93e-05

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: 42.98  E-value: 9.93e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228    69 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDhlvGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAELSPVTD 148
Cdd:TIGR01622 410 PATEEEPNWDKEIEDDVREECSKYGGVVHIYVDDKNSA---GDIYLKFDSVQAAEAAIKALNGRYFGGKMITAAFVVDAV 486


                  ....*
gi 29126228   149 FREAC 153
Cdd:TIGR01622 487 YSKSR 491
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
13-39 1.69e-04

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 37.94  E-value: 1.69e-04
                          10        20
                  ....*....|....*....|....*..
gi 29126228    13 KDKVNCSFYFKIGACRHGDRCSRLHNK 39
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAHGQ 27
ZnF_C3H1 smart00356
zinc finger;
148-172 3.58e-04

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 36.84  E-value: 3.58e-04
                           10        20
                   ....*....|....*....|....*
gi 29126228    148 DFREACCRQYEMGECTRGGFCNFMH 172
Cdd:smart00356   1 KYKTELCKFFKRGYCPRGDRCKFAH 25
 
Name Accession Description Interval E-value
RRM_U2AF35 cd12538
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...
 43-145 1.94e-71

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35); This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain.


Pssm-ID: 409954 [Multi-domain]  Cd Length: 104  Bit Score: 213.76  E-value: 1.94e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228  43 SQTIALLNIYRNPQNTAQSADGL-NAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREED 121
Cdd:cd12538   1 SQTILLQNLYQNPQNTPQSADGLkVKVSDVELQEHFDEFYEDVFVELEEKYGEIEEMNVCDNLGDHLVGNVYVKFRREED 80

                        90       100
                ....*....|....*....|....
gi 29126228 122 AEKAVINLNNRWFNGQPIHAELSP 145
Cdd:cd12538  81 AEKAVNDLNNRWFNGQPIYAELSP 104
RRM_U2AF35_like cd12287
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...
 45-145 1.99e-43

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins; This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR) -rich segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.


Pssm-ID: 409729 [Multi-domain]  Cd Length: 101  Bit Score: 142.40  E-value: 1.99e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228  45 TIALLNIYRNPQNTAQSADGLN-AVSDVEMQEHYDEFFEEVFTEMEeKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAE 123
Cdd:cd12287   1 TLLLKNMYPNPDNFISSLDDGSlTLSEEEIQEHFDEFYEDVFLELS-RFGEIEDLVVCSNLNDHLLGNVYVKFESEEDAE 79

                        90       100
                ....*....|....*....|..
gi 29126228 124 KAVINLNNRWFNGQPIHAELSP 145
Cdd:cd12287  80 AALQALNGRYYAGRPLYPELSP 101
RRM_U2AF35B cd12539
RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B); This ...
 44-145 4.57e-40

RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B); This subgroup corresponds to the RRM of U2AF35B, also termed zinc finger CCCH domain-containing protein 60 (C3H60), which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. Members in this family are mainly found in plant. They show high sequence homology to vertebrates U2AF35 that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. U2AF35B contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.


Pssm-ID: 409955 [Multi-domain]  Cd Length: 102  Bit Score: 133.68  E-value: 4.57e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228  44 QTIALLNIYRNPQNTAQSADGLN-AVSDVEMQEHYDEFFEEVFTEMEeKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDA 122
Cdd:cd12539   1 PTILLSNMYQNPIMNAPLGAAQGiPLDPRELQEHFEDFYEDVFEELS-KFGEVEALNVCDNLGDHMVGNVYVKFRDEEHA 79

                        90       100
                ....*....|....*....|...
gi 29126228 123 EKAVINLNNRWFNGQPIHAELSP 145
Cdd:cd12539  80 AAALKALQGRFYAGRPIIVEFSP 102
RRM_U2AFBPL cd12540
RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 ...
 56-145 7.42e-19

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins; This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain.


Pssm-ID: 409956 [Multi-domain]  Cd Length: 105  Bit Score: 78.85  E-value: 7.42e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228  56 QNTAQSADGLNAVSDVEMQEHYDEFFEEVFTEMEeKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFN 135
Cdd:cd12540  17 KRDDYDTDAGLEYSEEDLYSDFLEFYEDVLPEFK-KFGKVVQFKVCCNSEPHLRGNVYVQYQSEEEALKAFTSFNGRWYA 95

                        90
                ....*....|
gi 29126228 136 GQPIHAELSP 145
Cdd:cd12540  96 GKQLQCEFSP 105
RRM_1 smart00361
RNA recognition motif;
77-142 4.61e-17

RNA recognition motif;


Pssm-ID: 214637 [Multi-domain]  Cd Length: 70  Bit Score: 73.21  E-value: 4.61e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228     77 YDEFFEEVFTEMEEKYGEVEEMN--VCDNLG--DHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAE 142
Cdd:smart00361   1 KDEDFERELKEEEEYFGEVGKINkiYIDDVGyeNHKRGNVYITFERSEDAARAIVDLNGRYFDGRLVKAE 70
RRM3_RBM39_like cd12285
RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...
 78-145 2.08e-12

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia 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. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs.


Pssm-ID: 409727 [Multi-domain]  Cd Length: 85  Bit Score: 61.02  E-value: 2.08e-12
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29126228  78 DEFFEEVFTEMEE---KYGEVEEMNVCDNLGDhlvGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAELSP 145
Cdd:cd12285  18 DNWDDEIKEDVIEecsKYGPVLHIYVDKNSPQ---GNVYVKFKTIEAAQKCVQAMNGRWFDGRQITAAYVP 85
RRM3_U2AF65 cd12232
RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor ...
 65-142 1.12e-10

RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.


Pssm-ID: 409679 [Multi-domain]  Cd Length: 89  Bit Score: 56.44  E-value: 1.12e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228  65 LNAVS--DVEMQEHYDEFFEEVFTEMEeKYGEVEEMNV----CDNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQP 138
Cdd:cd12232   7 LNMVTpeELEDDEEYEEILEDVKEECS-KYGKVLSVVIprpeAEGVDVPGVGKVFVEFEDVEDAQKAQKALAGRKFDGRT 85


                ....
gi 29126228 139 IHAE 142
Cdd:cd12232  86 VVAS 89
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 82-142 6.95e-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: 53.83  E-value: 6.95e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29126228  82 EEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAE 142
Cdd:cd00590  12 EEDLRELFSKFGEVVSVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM2_TatSF1_like cd12282
RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar ...
 70-149 4.70e-08

RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins; This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well.


Pssm-ID: 409724 [Multi-domain]  Cd Length: 91  Bit Score: 49.54  E-value: 4.70e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228  70 DVEMQEHYDEFFEEVFTEME---EKYGEVEEMNVCDnlgDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAEL-SP 145
Cdd:cd12282  11 HPKEFEEDPELINEIKEDLReecEKFGQVKKVVVFD---RHPDGVASVKFKEPEEADKCIQALNGRWFAGRKLEAETwDG 87


                ....
gi 29126228 146 VTDF 149
Cdd:cd12282  88 KTDY 91
RRM smart00360
RNA recognition motif;
82-140 4.24e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.43  E-value: 4.24e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228     82 EEVFTEMEEKYGEVEEMNVC-DNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIH 140
Cdd:smart00360  13 EEELRELFSKFGKVESVRLVrDKETGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLK 72
RRM3_UHM_PUF60 cd12648
RNA recognition motif 3 (RRM3) found in UHM domain of poly(U)-binding-splicing factor PUF60 ...
 75-149 4.51e-07

RNA recognition motif 3 (RRM3) found in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins; This subgroup corresponds to the RRM3 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), 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. The 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: 410052 [Multi-domain]  Cd Length: 98  Bit Score: 47.02  E-value: 4.51e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228  75 EHYDEFFEEVFTEMEEKYGEVE------EMNVCDNLGDHLVgNVYVKFRREEDAEKAVINLNNRWFNGQPIHAELSPVTD 148
Cdd:cd12648  13 EDIDDDLEGEVTEECGKFGAVNrviiyqEKQGEEEDAEIIV-KIFVEFSMPSEAEKAIQALNGRWFGGRKVVAELYDQTR 91


                .
gi 29126228 149 F 149
Cdd:cd12648  92 F 92
RRM_UHM_SPF45_PUF60 cd12374
RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar ...
 78-145 3.82e-06

RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. 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 RRMs and a C-terminal UHM domain.


Pssm-ID: 409809 [Multi-domain]  Cd Length: 85  Bit Score: 44.13  E-value: 3.82e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 29126228  78 DEFFEEVFTEMEE---KYGEVEEMNVC--DNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAELSP 145
Cdd:cd12374  13 GEIDEDLKDEIKEecsKYGKVLNVIIHevASSEADDAVRVFVEFEDADEAIKAFRALNGRFFGGRKVKARFYD 85
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 90-140 4.68e-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: 43.38  E-value: 4.68e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 29126228    90 EKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIH 140
Cdd:pfam00076  20 SKFGPIKSIRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70
RRM_UHM_SPF45 cd12647
RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar ...
 78-150 8.33e-06

RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subgroup corresponds to the RRM of SPF45, also termed RNA-binding motif protein 17 (RBM17), an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155.


Pssm-ID: 410051 [Multi-domain]  Cd Length: 95  Bit Score: 43.43  E-value: 8.33e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 29126228  78 DEFFEEVFTEMEeKYGEVEEMNV--CDNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAELSPVTDFR 150
Cdd:cd12647  18 EDLEPEVKEECE-KYGKVTKVVIfeIPGAPDDEAVRIFVEFERVESAIKAVVDLNGRFFGGRTVKASFYDLDRFR 91
RRM1_2_CoAA_like cd12343
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator ...
 90-142 2.36e-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: 41.06  E-value: 2.36e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 29126228  90 EKYGEVEEMNVCDNLGdhlvgnvYVKFRREEDAEKAVINLNNRWFNGQPIHAE 142
Cdd:cd12343  21 EKYGKVTECDIVKNYA-------FVHMEKEEDAEDAIKALNGYEFMGSRINVE 66
RRM_Aly_REF_like cd12418
RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM ...
 76-143 3.00e-05

RNA recognition motif (RRM) found in the Aly/REF family; This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion.


Pssm-ID: 409852 [Multi-domain]  Cd Length: 75  Bit Score: 41.02  E-value: 3.00e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 29126228  76 HYD---EFFEEVFtemeEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAEL 143
Cdd:cd12418   9 HPDvteEDLRELF----GRVGPVKSVKINYDRSGRSTGTAYVVFERPEDAEKAIKQFDGVLLDGQPMKVEL 75
RRM_Set1B cd12549
RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B); This ...
 78-152 3.60e-05

RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B); This subgroup corresponds to the RRM of Setd1B, also termed SET domain-containing protein 1B (Set1B), or lysine N-methyltransferase 2G, a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1B is localized to euchromatic nuclear speckles and associates with a complex containing six human homologs of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). Set1B complex is a histone methyltransferase that produces trimethylated histone H3 at Lys4. Set1B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain.


Pssm-ID: 409965 [Multi-domain]  Cd Length: 93  Bit Score: 41.48  E-value: 3.60e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 29126228  78 DEFFEEVFTEMEEKYGEVEEMNVCDNLGD--HLvGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAELSPVTDFREA 152
Cdd:cd12549  12 DNIRENFLRDMCKKYGEVEEVEILYNPKNkkHL-GIAKVVFATVKGAKDAVQHLHNTSVMGNIIHVELDTKGETRMR 87
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
148-174 8.62e-05

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 38.71  E-value: 8.62e-05
                          10        20
                  ....*....|....*....|....*..
gi 29126228   148 DFREACCRQYEMGECTRGGFCNFMHLK 174
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAHGQ 27
SF-CC1 TIGR01622
splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...
 69-153 9.93e-05

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: 42.98  E-value: 9.93e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228    69 SDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDhlvGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAELSPVTD 148
Cdd:TIGR01622 410 PATEEEPNWDKEIEDDVREECSKYGGVVHIYVDDKNSA---GDIYLKFDSVQAAEAAIKALNGRYFGGKMITAAFVVDAV 486


                  ....*
gi 29126228   149 FREAC 153
Cdd:TIGR01622 487 YSKSR 491
RRM3_I_PABPs cd12380
RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...
 78-141 1.11e-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: 39.85  E-value: 1.11e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 29126228  78 DEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIHA 141
Cdd:cd12380  11 EDVDDDELKELFEKYGKITSAKVMKDDSGKSKGFGFVNFENHEAAQKAVEELNGKELNGKKLYV 74
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 78-143 1.32e-04

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: 39.50  E-value: 1.32e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 29126228  78 DEFFEEVFTEmeekYGEVEE-MNVCDNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAEL 143
Cdd:cd12413  13 DEQLEELFSD----VGPVKRcFVVKDKGKDKCRGFGYVTFALAEDAQRALEEVKGKKFGGRKIKVEL 75
zf-CCCH pfam00642
Zinc finger C-x8-C-x5-C-x3-H type (and similar);
13-39 1.69e-04

Zinc finger C-x8-C-x5-C-x3-H type (and similar);


Pssm-ID: 459885 [Multi-domain]  Cd Length: 27  Bit Score: 37.94  E-value: 1.69e-04
                          10        20
                  ....*....|....*....|....*..
gi 29126228    13 KDKVNCSFYFKIGACRHGDRCSRLHNK 39
Cdd:pfam00642   1 YKTELCRFFLRTGYCKYGDRCKFAHGQ 27
U2AF_lg TIGR01642
U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...
 75-139 3.36e-04

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.


Pssm-ID: 273727 [Multi-domain]  Cd Length: 509  Bit Score: 41.42  E-value: 3.36e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 29126228    75 EHYDEFFEEVFTEMEeKYGEVEEMNVCDNLGDHL----VGNVYVKFRREEDAEKAVINLNNRWFNGQPI 139
Cdd:TIGR01642 427 EEYEEIYEDVKTEFS-KYGPLINIVIPRPNGDRNstpgVGKVFLEYADVRSAEKAMEGMNGRKFNDRVV 494
ZnF_C3H1 smart00356
zinc finger;
148-172 3.58e-04

zinc finger;


Pssm-ID: 214632 [Multi-domain]  Cd Length: 27  Bit Score: 36.84  E-value: 3.58e-04
                           10        20
                   ....*....|....*....|....*
gi 29126228    148 DFREACCRQYEMGECTRGGFCNFMH 172
Cdd:smart00356   1 KYKTELCKFFKRGYCPRGDRCKFAH 25
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
 82-143 4.81e-04

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: 37.76  E-value: 4.81e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 29126228  82 EEVFTEMEEKYGEVEEmnvCDNLGDHLVGnvYVKFRREEDAEKAVINLNNRWFNGQPIHAEL 143
Cdd:cd12340  13 ESAIREIFSPYGPVKE---VKMLSDSNFA--FVEFEELEDAIRAKDSVHGRVLNNEPLYVTY 69
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
 90-144 1.54e-03

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: 36.26  E-value: 1.54e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 29126228  90 EKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAELS 144
Cdd:cd12447  21 EKYGGVISARViTDRGSGRSKGYGYVDFATPEAAQKALAAMSGKEIDGRQINVDFS 76
RRM_Set1 cd12304
RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases; This ...
 87-158 1.72e-03

RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases; This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo.


Pssm-ID: 409745 [Multi-domain]  Cd Length: 93  Bit Score: 36.56  E-value: 1.72e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 29126228  87 EMEEKYGEVEEMNVC--DNLGDHLvGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAELSPvtdFREACCRQYE 158
Cdd:cd12304  21 DMCKKYGEVEEVKIYfhPKTGKHL-GLARVVFDTTKGAKDCVEKLNQTSVMGNIIHVFLDP---KGRIIARLYE 90
RRM3_RBM19_RRM2_MRD1 cd12316
RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...
 82-140 1.95e-03

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: 36.17  E-value: 1.95e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 29126228  82 EEVFTEMEEKYGEVEEMNV-CDNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPIH 140
Cdd:cd12316  13 EDELRELFEAFGKISEVHIpLDKQTKRSKGFAFVLFVIPEDAVKAYQELDGSIFQGRLLH 72
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 82-143 2.08e-03

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: 36.08  E-value: 2.08e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 29126228  82 EEVFTEMEEKYGEVEEMNVC----DNLGDHLVGNVYVKFRREEDAEKAvINLNNRWFNGQPIHAEL 143
Cdd:cd12298  14 EEALRGIFEKFGEIESINIPkkqkNRKGRHNNGFAFVTFEDADSAESA-LQLNGTLLDNRKISVSL 78
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 90-139 2.35e-03

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: 35.99  E-value: 2.35e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 29126228  90 EKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVINLNNRWFNGQPI 139
Cdd:cd12414  21 SKFGKVLEVTIPKKPDGKLRGFAFVQFTNVADAAKAIKGMNGKKIKGRPV 70
RRM_Set1A cd12548
RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A); This ...
 78-143 2.92e-03

RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A); This subgroup corresponds to the RRM of Setd1A, also termed SET domain-containing protein 1A (Set1A), or lysine N-methyltransferase 2F, or Set1/Ash2 histone methyltransferase complex subunit Set1, a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1A is localized to euchromatic nuclear speckles and associates with a complex containing six human homologs of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). Set1A contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo.


Pssm-ID: 409964 [Multi-domain]  Cd Length: 95  Bit Score: 36.10  E-value: 2.92e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 29126228  78 DEFFEEVFTEMEEKYGEVEEMNVC--DNLGDHLvGNVYVKFRREEDAEKAVINLNNRWFNGQPIHAEL 143
Cdd:cd12548  12 DNVREPFLADMCRKFGEVEEVEILlhPKTRKHL-GLAKVLFTSTRGAKDTVKHLHNTSVMGNIIHAQL 78
RRM_CNOT4 cd12438
RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) ...
 91-141 9.27e-03

RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins; This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T


Pssm-ID: 409872 [Multi-domain]  Cd Length: 98  Bit Score: 34.81  E-value: 9.27e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 29126228  91 KYGEVE--EMNVCDNLGDHLVGN--VYVKFRREEDAEKAVINLNNRWFNGQPIHA 141
Cdd:cd12438  31 QYGKIKkiVINRSTSYAGSQGPSasAYVTYSRKEDALRAIQAVDGFVLDGRTLKA 85
 
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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