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Conserved domains on  [gi|6322550|ref|NP_012624|]
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Jsn1p [Saccharomyces cerevisiae S288C]

Protein Classification

COG5099 family protein( domain architecture ID 11473804)

COG5099 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 58-920 0e+00

RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 604.43  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550    58 KFSNTLSNLLPSISAKLHHSKKNshgkngaefsssnnssqstvasktpraspsrskmmessidgvtmdrPGSLTPPQDME 137
Cdd:COG5099    1 PNSDTMNNLLPSIKSQLHHSKKS----------------------------------------------PPSSTTSQELM 34

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   138 KLVHFPdsSNNFLIPAPRGSSDSFNLPhqisRTRNNTMSSQITSISSIAPKPrtsSGIWSSNASANDPMQQHLLQQLQPT 217
Cdd:COG5099   35 NGNSTP--NSFSPIPSKASSSATFTLN----LPINNSVNHKITSSSSSRRKP---SGSWSVAISSSTSGSQSLLMELPSS 105

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   218 TSNNTTNSNTLNDYST-KTAYFDNMVSTSGS-QMADNKMNTNNLAIPNSVWSNTRQRSQSNASSIYTDAPLYEQPAR-AS 294
Cdd:COG5099  106 SFNPSTSSRNKSNSALsSTQQGNANSSVTLSsSTASSMFNSNKLPLPNPNHSNSATTNQSGSSFINTPASSSSQPLTnLV 185

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   295 ISSHYTIP--TQESPLIADEIDPQSINWVTMDPTVPSINQISNLLPTNTISISNVFPLQHQQPQLNNAINLTSTSLATLC 372
Cdd:COG5099  186 VSSIKRFPylTSLSPFFNYLIDPSSDSATASADTSPSFNPPPNLSPNNLFSTSDLSPLPDTQSVENNIILNSSSSINELT 265

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   373 SKYGEVISARTLRNLNMALVEFSSVESAVKALDSLQGKEVSMIGAPSKISFAKILPMHQQPPqfllnsqglplglennnl 452
Cdd:COG5099  266 SIYGSVPSIRNLRGLNSALVSFLNVSSSSLAFSALNGKEVSPTGSPSTRSFARVLPKSSPNN------------------ 327

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   453 qpqpLLQEQLFNGAVTFQQQGNVSIPVFNQQSqqsqhqnhssgSAGFSNVLHGYNNNNSMHGNNNNSANEKEQCPFPLPP 532
Cdd:COG5099  328 ----LLTEILTTGVNPPQSLPSLLNPVFLSTS-----------TGFSLTNLSGYLNPNKNLKKNTLSSLSNLGYSSNVPS 392

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   533 PNVNE-KEDLLREIIELFEANSDEYQINSLIKKSLNHKGT-SDTQNFGPLPEPLsgrEFDPPKLRELRKSIDSNafSDLE 610
Cdd:COG5099  393 PSSSEsTRNILGNISPNFKTSSNLTNLNSLLKEKLSNSSSvSATDILGPSIIVS---CKDQHGSRFLQKLLDSN--SSPE 467

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   611 IEQLAIAMLDELPELSSDYLGNTIVQKLFEHSSDIIKDIMLRKTSKYLTSMGVHKNGTWACQKMITMAHTPRQIMQVTQG 690
Cdd:COG5099  468 IEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEE 547

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   691 VKDYCTPLINDQFGNYVIQ-CVLKFGFPWNQFIFESIIANFWVIVQNRYGARAVRACLEAHDIVTPEQsivLSAMIVTYA 769
Cdd:COG5099  548 LRPYCLQLIKDQNGNHVIQkCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKEN---LVEEIISNS 624

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   770 EYLSTNSNGALLVTWFLDTSVLPNRHSILAPRLTKRIVELCGHRLASLTILKVLNYRGDDNARKIILDSLFGNVNAHDSs 849
Cdd:COG5099  625 KYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIKYASDSFKRSRILNELTNRGIEKPG- 703

                        810       820       830       840       850       860       870
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6322550   850 ppkELTKLLCETNYGPTFVHKVLAMPLLEDDLRAHIIKQVRKVLTDSTQIQPSRRLLEEVGLASPSSTHNK 920
Cdd:COG5099  704 ---FLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILALLEKVGSSSQSSISNK 771
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 58-920 0e+00

RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis];


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 604.43  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550    58 KFSNTLSNLLPSISAKLHHSKKNshgkngaefsssnnssqstvasktpraspsrskmmessidgvtmdrPGSLTPPQDME 137
Cdd:COG5099    1 PNSDTMNNLLPSIKSQLHHSKKS----------------------------------------------PPSSTTSQELM 34

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   138 KLVHFPdsSNNFLIPAPRGSSDSFNLPhqisRTRNNTMSSQITSISSIAPKPrtsSGIWSSNASANDPMQQHLLQQLQPT 217
Cdd:COG5099   35 NGNSTP--NSFSPIPSKASSSATFTLN----LPINNSVNHKITSSSSSRRKP---SGSWSVAISSSTSGSQSLLMELPSS 105

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   218 TSNNTTNSNTLNDYST-KTAYFDNMVSTSGS-QMADNKMNTNNLAIPNSVWSNTRQRSQSNASSIYTDAPLYEQPAR-AS 294
Cdd:COG5099  106 SFNPSTSSRNKSNSALsSTQQGNANSSVTLSsSTASSMFNSNKLPLPNPNHSNSATTNQSGSSFINTPASSSSQPLTnLV 185

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   295 ISSHYTIP--TQESPLIADEIDPQSINWVTMDPTVPSINQISNLLPTNTISISNVFPLQHQQPQLNNAINLTSTSLATLC 372
Cdd:COG5099  186 VSSIKRFPylTSLSPFFNYLIDPSSDSATASADTSPSFNPPPNLSPNNLFSTSDLSPLPDTQSVENNIILNSSSSINELT 265

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   373 SKYGEVISARTLRNLNMALVEFSSVESAVKALDSLQGKEVSMIGAPSKISFAKILPMHQQPPqfllnsqglplglennnl 452
Cdd:COG5099  266 SIYGSVPSIRNLRGLNSALVSFLNVSSSSLAFSALNGKEVSPTGSPSTRSFARVLPKSSPNN------------------ 327

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   453 qpqpLLQEQLFNGAVTFQQQGNVSIPVFNQQSqqsqhqnhssgSAGFSNVLHGYNNNNSMHGNNNNSANEKEQCPFPLPP 532
Cdd:COG5099  328 ----LLTEILTTGVNPPQSLPSLLNPVFLSTS-----------TGFSLTNLSGYLNPNKNLKKNTLSSLSNLGYSSNVPS 392

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   533 PNVNE-KEDLLREIIELFEANSDEYQINSLIKKSLNHKGT-SDTQNFGPLPEPLsgrEFDPPKLRELRKSIDSNafSDLE 610
Cdd:COG5099  393 PSSSEsTRNILGNISPNFKTSSNLTNLNSLLKEKLSNSSSvSATDILGPSIIVS---CKDQHGSRFLQKLLDSN--SSPE 467

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   611 IEQLAIAMLDELPELSSDYLGNTIVQKLFEHSSDIIKDIMLRKTSKYLTSMGVHKNGTWACQKMITMAHTPRQIMQVTQG 690
Cdd:COG5099  468 IEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEE 547

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   691 VKDYCTPLINDQFGNYVIQ-CVLKFGFPWNQFIFESIIANFWVIVQNRYGARAVRACLEAHDIVTPEQsivLSAMIVTYA 769
Cdd:COG5099  548 LRPYCLQLIKDQNGNHVIQkCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKEN---LVEEIISNS 624

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   770 EYLSTNSNGALLVTWFLDTSVLPNRHSILAPRLTKRIVELCGHRLASLTILKVLNYRGDDNARKIILDSLFGNVNAHDSs 849
Cdd:COG5099  625 KYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIKYASDSFKRSRILNELTNRGIEKPG- 703

                        810       820       830       840       850       860       870
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6322550   850 ppkELTKLLCETNYGPTFVHKVLAMPLLEDDLRAHIIKQVRKVLTDSTQIQPSRRLLEEVGLASPSSTHNK 920
Cdd:COG5099  704 ---FLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILALLEKVGSSSQSSISNK 771
RRM_ScJSN1_like cd21616
RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein JSN1 and similar ...
 311-428 1.10e-62

RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein JSN1 and similar proteins; JSN1, also called Pumilio homology domain family member 1 (PUF1), is a member of the PUF family of proteins. It facilitates association of Arp2/3 complex to yeast mitochondria. It may play a role in mitosis, perhaps by affecting the stability of microtubules. Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410195 [Multi-domain]  Cd Length: 118  Bit Score: 208.46  E-value: 1.10e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   311 DEIDPQSINWVTMDPTVPSINQISNLLPTNTISISNVFPLQHQQPQLNNAINLTSTSLATLCSKYGEVISARTLRNLNMA 390
Cdd:cd21616    1 DDVDPTSINWITTSPYVPPINQVNNLLPTNTILVSNIFPIQQTSPQPPNPINLTSTSLASLCSKFGDIISSRTLRGLNMA 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 6322550   391 LVEFSSVESAVKALDSLQGKEVSMIGAPSKISFAKILP 428
Cdd:cd21616   81 LIEFESVDSAILALESLQGKEISIIGVPSDITFAKILP 118
RRM smart00360
RNA recognition motif;
362-412 3.13e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 48.74  E-value: 3.13e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 6322550      362 NLTSTSLATLCSKYGEVISAR------TLRNLNMALVEFSSVESAVKALDSLQGKEV 412
Cdd:smart00360   10 DTTEEELRELFSKFGKVESVRlvrdkeTGKSKGFAFVEFESEEDAEKALEALNGKEL 66
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 362-412 3.29e-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: 48.38  E-value: 3.29e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 6322550     362 NLTSTSLATLCSKYGEVISAR-----TLRNLNMALVEFSSVESAVKALDSLQGKEV 412
Cdd:pfam00076    9 DTTEEDLKDLFSKFGPIKSIRlvrdeTGRSKGFAFVEFEDEEDAEKAIEALNGKEL 64
 
Name Accession Description Interval E-value
COG5099 COG5099
RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal ...
 58-920 0e+00

RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis];


Pssm-ID: 227430 [Multi-domain]  Cd Length: 777  Bit Score: 604.43  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550    58 KFSNTLSNLLPSISAKLHHSKKNshgkngaefsssnnssqstvasktpraspsrskmmessidgvtmdrPGSLTPPQDME 137
Cdd:COG5099    1 PNSDTMNNLLPSIKSQLHHSKKS----------------------------------------------PPSSTTSQELM 34

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   138 KLVHFPdsSNNFLIPAPRGSSDSFNLPhqisRTRNNTMSSQITSISSIAPKPrtsSGIWSSNASANDPMQQHLLQQLQPT 217
Cdd:COG5099   35 NGNSTP--NSFSPIPSKASSSATFTLN----LPINNSVNHKITSSSSSRRKP---SGSWSVAISSSTSGSQSLLMELPSS 105

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   218 TSNNTTNSNTLNDYST-KTAYFDNMVSTSGS-QMADNKMNTNNLAIPNSVWSNTRQRSQSNASSIYTDAPLYEQPAR-AS 294
Cdd:COG5099  106 SFNPSTSSRNKSNSALsSTQQGNANSSVTLSsSTASSMFNSNKLPLPNPNHSNSATTNQSGSSFINTPASSSSQPLTnLV 185

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   295 ISSHYTIP--TQESPLIADEIDPQSINWVTMDPTVPSINQISNLLPTNTISISNVFPLQHQQPQLNNAINLTSTSLATLC 372
Cdd:COG5099  186 VSSIKRFPylTSLSPFFNYLIDPSSDSATASADTSPSFNPPPNLSPNNLFSTSDLSPLPDTQSVENNIILNSSSSINELT 265

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   373 SKYGEVISARTLRNLNMALVEFSSVESAVKALDSLQGKEVSMIGAPSKISFAKILPMHQQPPqfllnsqglplglennnl 452
Cdd:COG5099  266 SIYGSVPSIRNLRGLNSALVSFLNVSSSSLAFSALNGKEVSPTGSPSTRSFARVLPKSSPNN------------------ 327

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   453 qpqpLLQEQLFNGAVTFQQQGNVSIPVFNQQSqqsqhqnhssgSAGFSNVLHGYNNNNSMHGNNNNSANEKEQCPFPLPP 532
Cdd:COG5099  328 ----LLTEILTTGVNPPQSLPSLLNPVFLSTS-----------TGFSLTNLSGYLNPNKNLKKNTLSSLSNLGYSSNVPS 392

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   533 PNVNE-KEDLLREIIELFEANSDEYQINSLIKKSLNHKGT-SDTQNFGPLPEPLsgrEFDPPKLRELRKSIDSNafSDLE 610
Cdd:COG5099  393 PSSSEsTRNILGNISPNFKTSSNLTNLNSLLKEKLSNSSSvSATDILGPSIIVS---CKDQHGSRFLQKLLDSN--SSPE 467

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   611 IEQLAIAMLDELPELSSDYLGNTIVQKLFEHSSDIIKDIMLRKTSKYLTSMGVHKNGTWACQKMITMAHTPRQIMQVTQG 690
Cdd:COG5099  468 IEVIFNEILDQLVELSSDYFGNYLIQKLFEYGSEIQKSIMLSKSSKHLVSLSVHKYGTRVLQKAIDIVSTDIQISLLVEE 547

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   691 VKDYCTPLINDQFGNYVIQ-CVLKFGFPWNQFIFESIIANFWVIVQNRYGARAVRACLEAHDIVTPEQsivLSAMIVTYA 769
Cdd:COG5099  548 LRPYCLQLIKDQNGNHVIQkCIEKFNKEKNQFIFDSINENLYDLSTHRYGSRVVQRCLENCNSEDKEN---LVEEIISNS 624

                        730       740       750       760       770       780       790       800
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   770 EYLSTNSNGALLVTWFLDTSVLPNRHSILAPRLTKRIVELCGHRLASLTILKVLNYRGDDNARKIILDSLFGNVNAHDSs 849
Cdd:COG5099  625 KYLSQDQYGNYVVQHILDNGAEPNKERIIIKLLSKRVVELSTHKFASNVVEKCIKYASDSFKRSRILNELTNRGIEKPG- 703

                        810       820       830       840       850       860       870
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6322550   850 ppkELTKLLCETNYGPTFVHKVLAMPLLEDDLRAHIIKQVRKVLTDSTQIQPSRRLLEEVGLASPSSTHNK 920
Cdd:COG5099  704 ---FLMLILDDQYANYVIQYLLDVSPEIQRSLLARAIKKVIPSLKKSMYGQHILALLEKVGSSSQSSISNK 771
RRM_ScJSN1_like cd21616
RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein JSN1 and similar ...
 311-428 1.10e-62

RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein JSN1 and similar proteins; JSN1, also called Pumilio homology domain family member 1 (PUF1), is a member of the PUF family of proteins. It facilitates association of Arp2/3 complex to yeast mitochondria. It may play a role in mitosis, perhaps by affecting the stability of microtubules. Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410195 [Multi-domain]  Cd Length: 118  Bit Score: 208.46  E-value: 1.10e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   311 DEIDPQSINWVTMDPTVPSINQISNLLPTNTISISNVFPLQHQQPQLNNAINLTSTSLATLCSKYGEVISARTLRNLNMA 390
Cdd:cd21616    1 DDVDPTSINWITTSPYVPPINQVNNLLPTNTILVSNIFPIQQTSPQPPNPINLTSTSLASLCSKFGDIISSRTLRGLNMA 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 6322550   391 LVEFSSVESAVKALDSLQGKEVSMIGAPSKISFAKILP 428
Cdd:cd21616   81 LIEFESVDSAILALESLQGKEISIIGVPSDITFAKILP 118
Pumilio cd07920
Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology ...
 595-907 2.74e-23

Pumilio-family RNA binding domain; Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats.


Pssm-ID: 153420 [Multi-domain]  Cd Length: 322  Bit Score: 101.90  E-value: 2.74e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   595 RELRKSIDSNAFSDLEIEQLAIamLDELPELSSDYLGNTIVQKLFEHSSDIIKDIMLRKTSKYLTSMGVHKNGTWACQKM 674
Cdd:cd07920   23 RFLQQKLEEATPEEKELIFDEI--LPHVVELMVDPFGNYVIQKLFEHGTEEQRLQLLEKILGHVVRLSLDMYGCRVIQKL 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   675 ITMAHtPRQIMQVTQGVKDYCTPLINDQFGNYVIQ-CVLKFGFPWNQFIFESIIANFWVIVQNRYGARAVRACLEAhdiV 753
Cdd:cd07920  101 LESIS-EEQISLLVKELRGHVVELVKDQNGNHVIQkCIEKFPPEDLQFIIDAFKGNCVALSTHPYGCRVIQRCLEH---C 176

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   754 TPEQSIVLSAMIVTYAEYLSTNSNGALLVTWFLDTSVLPNRHSILApRLTKRIVELCGHRLASLTILKVLNYrGDDNARK 833
Cdd:cd07920  177 SEEQREPLLEEILEHALELVQDQFGNYVVQHVLELGDPDDTSRIIE-KLLGNIVQLSCHKFASNVVEKCLKH-ASKEERE 254

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 6322550   834 IILDSLFGNVNAHDSSPpkeltkLLCETNYGPTFVHKVLAmpLLEDDLRAHIIKQVRKVLTDSTQIQPSRRLLE 907
Cdd:cd07920  255 LIIDEILASGNETSALD------TLMKDQYGNYVIQTALD--VAKEEQRELLVEAIRPHLPSLRKSPYGKHILA 320
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 362-412 2.76e-07

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: 48.82  E-value: 2.76e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 6322550   362 NLTSTSLATLCSKYGEVISARTLRNL-----NMALVEFSSVESAVKALDSLQGKEV 412
Cdd:cd00590    9 DTTEEDLRELFSKFGEVVSVRIVRDRdgkskGFAFVEFESPEDAEKALEALNGTEL 64
RRM smart00360
RNA recognition motif;
362-412 3.13e-07

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 48.74  E-value: 3.13e-07
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 6322550      362 NLTSTSLATLCSKYGEVISAR------TLRNLNMALVEFSSVESAVKALDSLQGKEV 412
Cdd:smart00360   10 DTTEEELRELFSKFGKVESVRlvrdkeTGKSKGFAFVEFESEEDAEKALEALNGKEL 66
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 362-412 3.29e-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: 48.38  E-value: 3.29e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 6322550     362 NLTSTSLATLCSKYGEVISAR-----TLRNLNMALVEFSSVESAVKALDSLQGKEV 412
Cdd:pfam00076    9 DTTEEDLKDLFSKFGPIKSIRlvrdeTGRSKGFAFVEFEDEEDAEKAIEALNGKEL 64
RRM1_U1A_like cd12246
RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily ...
 341-425 2.46e-06

RNA recognition motif 1 (RRM1) found in the U1A/U2B"/SNF protein family; This subfamily corresponds to the RRM1 of U1A/U2B"/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B" (U2 snRNP B" or U2B"), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding.


Pssm-ID: 409692 [Multi-domain]  Cd Length: 78  Bit Score: 46.37  E-value: 2.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   341 TISISNvfplqhqqpqLNNAINLTS--TSLATLCSKYGEVISARTLRNLNM---ALVEFSSVESAVKALDSLQGKEVsmI 415
Cdd:cd12246    1 TLYINN----------LNEKIKKDElkRSLYALFSQFGPVLDIVASKSLKMrgqAFVVFKDVESATNALRALQGFPF--Y 68

                         90
                 ....*....|
gi 6322550   416 GAPSKISFAK 425
Cdd:cd12246   69 GKPMRIQYAK 78
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
 358-425 1.82e-05

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an 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: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 43.93  E-value: 1.82e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6322550   358 NNAINLTSTSLATLCSKYGEVISARTLRNLNMALVEFSSVESAVKALDSLQGKEVSMigAPSKISFAK 425
Cdd:cd12262   10 NLDDSLTEEEIRGILEKYGEIESIKILKEKNCAFVNYLNIANAIKAVQELPIKNPKF--KKVRINYGK 75
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 362-412 6.77e-05

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: 42.16  E-value: 6.77e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 6322550   362 NLTSTSLATLCSKYGEVISAR------TLRNLNMALVEFSSVESAVKALDSLQGKEV 412
Cdd:cd21608   10 DTTEDDLRDLFSEFGEVESAKvitdreTGRSRGFGFVTFSTAEAAEAAIDALNGKEL 66
Pumilio smart00025
Pumilio-like repeats; Pumilio-like repeats that bind RNA.
 691-724 1.20e-04

Pumilio-like repeats; Pumilio-like repeats that bind RNA.


Pssm-ID: 214475 [Multi-domain]  Cd Length: 36  Bit Score: 40.11  E-value: 1.20e-04
                            10        20        30
                    ....*....|....*....|....*....|....*
gi 6322550      691 VKDYCTPLINDQFGNYVIQCVLKFGFP-WNQFIFE 724
Cdd:smart00025    2 IKGHLLELSKDQYGNRVVQKLLEHASEsQREQIID 36
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
 364-413 1.56e-04

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 41.09  E-value: 1.56e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 6322550   364 TSTSLATLCSKYGEVISA------RTLRNLNMALVEFSSVESAVKALDSLQGKEVS 413
Cdd:cd12417   12 KAADLKKIFSKYGKVVSAkvvtsaRTPGSRCYGYVTMASVEEADLCIKSLNKTELH 67
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
 365-410 7.61e-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: 38.92  E-value: 7.61e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 6322550   365 STSLATLCSKYGEVISARTLRNLNMALVEFSSVESAVKALDSLQGK 410
Cdd:cd12340   13 ESAIREIFSPYGPVKEVKMLSDSNFAFVEFEELEDAIRAKDSVHGR 58
RRM_Srp1p_AtRSp31_like cd12233
RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis ...
 359-412 7.72e-04

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.


Pssm-ID: 240679 [Multi-domain]  Cd Length: 70  Bit Score: 38.97  E-value: 7.72e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 6322550   359 NAINLTSTSLATLCSKYGEVISARTLRNLnmALVEFSSVESAVKALDSLQGKEV 412
Cdd:cd12233    8 DPGTTREEDIEKLFEPFGPLVRCDIRKTF--AFVEFEDSEDATKALEALHGSRI 59
RRM3_hnRNPR_like cd12251
RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...
 358-425 8.88e-04

RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409697 [Multi-domain]  Cd Length: 72  Bit Score: 38.77  E-value: 8.88e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6322550   358 NNAINLTSTSLATLCSKYGEVISARTLRNLnmALVEFSSVESAVKALDSLQGKEVSmiGAPSKISFAK 425
Cdd:cd12251    8 NLMLSTTEEKLRELFSEYGKVERVKKIKDY--AFVHFEERDDAVKAMEEMNGKELE--GSEIEVSLAK 71
RRM4_MRN1 cd12522
RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This ...
 363-411 1.61e-03

RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM4 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: 409942 [Multi-domain]  Cd Length: 81  Bit Score: 38.28  E-value: 1.61e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 6322550   363 LTSTSLATLCSKYGEVISARTLRNLNMALVEFSSVESAVKALDSLQGKE 411
Cdd:cd12522   17 LTEERLRHDFSQYGEIEQVNFLREKNCAFVNFTNIANAIKAIDKIKSKP 65
RRM2_hnRNPL_like cd12694
RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) ...
 357-425 1.77e-03

RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins; This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both nuclear and cytoplasmic roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410094 [Multi-domain]  Cd Length: 86  Bit Score: 38.41  E-value: 1.77e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322550   357 LNNAINLTSTSLATLCSKYGEVISARTLR-NLNMALVEFSSVESAVKALDSLQGKEVSMIGAPSKISFAK 425
Cdd:cd12694    9 LNPLYPITVDVIHTICSPYGKVLRIVIFRkNGVQAMVEFDSVESAQRAKAALNGADIYSGCCTLKIEYAK 78
RRM1_MSSP cd12243
RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) ...
 362-414 1.93e-03

RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.


Pssm-ID: 409689 [Multi-domain]  Cd Length: 71  Bit Score: 38.06  E-value: 1.93e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6322550   362 NLTSTSLATLCSKYGEVISARTL--RNLNMA----LVEFSSVESAVKALDSLQGK--EVSM 414
Cdd:cd12243   11 NTTDEDLLLLCQSFGKIISTKAIidKQTNKCkgygFVDFDSPEAALKAIEGLNGRgvQASF 71
RRM1_gar2 cd12447
RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins; This ...
 374-412 3.34e-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: 37.41  E-value: 3.34e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 6322550   374 KYGEVISARTL------RNLNMALVEFSSVESAVKALDSLQGKEV 412
Cdd:cd12447   22 KYGGVISARVItdrgsgRSKGYGYVDFATPEAAQKALAAMSGKEI 66
RRM2_PTBP1_hnRNPL_like cd12422
RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...
 358-410 4.42e-03

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.


Pssm-ID: 409856 [Multi-domain]  Cd Length: 85  Bit Score: 37.17  E-value: 4.42e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 6322550   358 NNAINLTSTSLATLCSKYGEV--ISARTLRNLNMALVEFSSVESAVKALDSLQGK 410
Cdd:cd12422    8 NLLYPVTVDVLHQVFSPYGAVekIVIFEKGTGVQALVQFDSVESAEAAKKALNGR 62
RRM_ALKBH8 cd12431
RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and ...
 363-412 4.98e-03

RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins; This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain.


Pssm-ID: 409865 [Multi-domain]  Cd Length: 80  Bit Score: 37.17  E-value: 4.98e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 6322550   363 LTSTSLATLCSKYGEVISARTLRNLNMALVEFSSVESAVKALDSLQGKEV 412
Cdd:cd12431   15 VSREQLLEVFEKYGTVEDIVMLPGKPYSFVSFKSVEEAAKAYNALNGKEL 64
RRM_Set1 cd12304
RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases; This ...
 356-412 6.96e-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: 36.94  E-value: 6.96e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6322550   356 QLNNAINltSTSLATLCSKYGEV------ISARTLRNLNMALVEFSSVESAVKALDSLQGKEV 412
Cdd:cd12304    9 NLNDNIN--EGFLKDMCKKYGEVeevkiyFHPKTGKHLGLARVVFDTTKGAKDCVEKLNQTSV 69
RRM_ZCRB1 cd12393
RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...
 363-412 8.13e-03

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: 36.11  E-value: 8.13e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 6322550   363 LTSTSLATLCSKYGEVISARTLRNLN------MALVEFSSVESAVKALDSLQGKEV 412
Cdd:cd12393   13 LTNNDLHQIFSKYGKVVKVTILKDKEtrkskgVAFVLFLDRESAHNAVRAMNNKEL 68
 
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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