Citrus Sinensis ID: 002482

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710-------720-------730-------740-------750-------760-------770-------780-------790-------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-------900-------910-------

MTSERRQKSQKAKPKPSEGRMHLTNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYCHAWIRNMPCSVPDCLYLHDFGSQEDSFTKDEIVSAFTRSRVQQIIGATNNMHRRSGNALPPPADEYINSNITSTAKPIAKNSSNIIENPNNGSCADIVAGKSNSLPTAASWVMRVSATLPTNKNLSGPVRPPSNQPKASNGPQVPGTEVVSTTISIQTVQPMEAVATSKVHHKLDPLELGKEYIDALSSTNEEATLDSIPATATSNQYITCRPTSKSSEKDIATPSSRTSSSESTKPFSSPGSVEDESSHIVMDFQGLCCGLSSIGLESQFEKDRSLPVVPNSSISKHVSVNLPGSHGPQEEKSGQFTECKSFQASMAAPTMEDSPDFDDLQFKGLEDMHHLPPISSTPHLPHNLNQSSYLSWQAGDVSNQSNLDGHSGNVPLEHKEVLPSRSENLISNGFITNEASSFFNLDATVQHSSLFSEVGFGSYLGKHDSMVAPLHSNVASDVGESSIISKILSLDADAWEDSLTSPYSFAKLLRESNRQHDSLKMPSLFKESDCRQSRFSFARQEEFSNHASDVEHSLSNIRHSADQHPAPNGLLKNKDIFTDKHQNAFSSSSSMDSDNFLGSHSFISSSVSKAPTSVPPGFAVPNRAPPPGFSPHGTMQKPFDSSASHLRWTSAQAAGNSGPCGDIPFVDPAILEVGKGLQAIGLNNLGCDMRQTPSSQLNPFEHEARLQLLMQQSSSGYQNLRFQDYPMNRFSPPSDTYGISSKVLNQPQPNNLSSFTQSPAQQYRNAHMSTGHLGSLKGVKSINDLGVSDLMTNGGIGFNKFIPSYEDLKCQMSNSSNLYNRGFAM

ccHHHHHHHHccccccccccccccccEEEEEccEEEEccccccccHHHHcccccccccccEEEEEEcccccccccccccccEEEEEEEccHHHHHHHHHHHccccccccEEEEccccHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHcccccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEccccccccHHcccc

ccHHHHHHHHHHHHHHHHHHHHHcccEEEEccEEEEEccccccccHHHHcccHHcccccEEEEEEEEccccccccccccccEEEEEEEccHHHHHHHHHHHccccccccEEEEEccccHHHHHHHccccccccccEEEcccccccccccHHHHHHHccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEccccccccccccccccccccccHHHHHHHcccccccccccccHHHHHHHHccccccccccccccccccccccccEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEcccHHHHEcccccccccccccccccccccccHcccccccHHHHHHccccccccccccccccccccccccccccccccHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccccHHccccc

mtserrqksqkakpkpsegrmhltNVRVIQRNLVYIIGlpinladedLLQRKEYFGQYGKVLKVSISrtatgdiqhsannSCCVYITYSREDDAIRCIQSVHSYildgrplracfgttkychawirnmpcsvpdclylhdfgsqedsftkdEIVSAFTRSRVQQIIGATnnmhrrsgnalpppadeyinsnitstakpiaknssniienpnngscadivagksnslptAASWVMRVsatlptnknlsgpvrppsnqpkasngpqvpgtevVSTTISIQTVQPMEAVAtskvhhkldplelGKEYIDALSstneeatldsipatatsnqyitcrptskssekdiatpssrtsssestkpfsspgsvedesshiVMDFQGlccglssiglesqfekdrslpvvpnssiskhvsvnlpgshgpqeeksgqftecksfqasmaaptmedspdfddlqfkgledmhhlppisstphlphnlnqssylswqagdvsnqsnldghsgnvplehkevlpsrsenlisngfitneassffnldatvqhsslfsevgfgsylgkhdsmvaplhsnvasdvgeSSIISKILSldadawedsltspySFAKLLRESnrqhdslkmpslfkesdcrqsrfsFARQEEFSNHASDVEHSlsnirhsadqhpapngllknkdiftdkhqnafsssssmdsdnflgshsfisssvskaptsvppgfavpnrapppgfsphgtmqkpfdssashLRWTsaqaagnsgpcgdipfvdpAILEVGKGLQAiglnnlgcdmrqtpssqlnpfEHEARLQLLMQQsssgyqnlrfqdypmnrfsppsdtygisskvlnqpqpnnlssftqspaqQYRNAhmstghlgslkgvksindlgvsdlmtnggigfnkfipsyedlkcqmsnssnlynrgfam

mtserrqksqkakpkpsegrmhltnvRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTatgdiqhsannSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYCHAWIRNMPCSVPDCLYLHDFGSQEDSFTKDEIVSAFTRSRVQQIIgatnnmhrrsGNALPPPADEYINSNITSTAKPIAKNSSNIIENPNNGSCADIVAGKSNSLPTAASWVMRVSATLptnknlsgpvrppsnqpkasngpqvpGTEVVSTTISIQTVQPMEAVATSKVHHKLDPLELGKEYIDALSSTNEeatldsipatatsnqyitcrptskssekdiatpssrtsssestkpfsSPGSVEDESSHIVMDFQGLCCGLSSIGLESQFEKDRSLPVVPNSSISKHVSVNLPGSHGPQEEKSGQFTECKSFQASMAAPTMEDSPDFDDLQFKGLEDMHHLPPISSTPHLPHNLNQSSYLSWQAGDVSNQSNLDGHSGNVPLEHKEVLPSRSENLISNGFITNEASSFFNLDATVQHSSLFSEVGFGSYLGKHDSMVAPLHSNVASDVGESSIISKILSLDADAWEDSLTSPYSFAKLLRESNRqhdslkmpslfkesDCRQSRFSFARQEEFSNHASDVEHSLSNIRHSADQHPAPNGLLKNKDIFTDKHQNAFSSSSSMDSDNFLGSHSFISSSVSKAPTSVPPGFAVPNRAPPPGFSPHGTMQKPFDSSASHLRWTSAQAAGNSGPCGDIPFVDPAILEVGKGLQAIGLNNLGCDMRQTPSSQLNPFEHEARLQLLMQQSSSGYQNLRFQDYPMNRFSPPSDTYGISSKVLNQPQPNNLSSFTQSPAQQYRNAHMSTGHLGSLKGVKSINDLGVSDLMTNGGIGFNKFIPSYEDLKCqmsnssnlynrgfam

MTSERRQKSQKAKPKPSEGRMHLTNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYCHAWIRNMPCSVPDCLYLHDFGSQEDSFTKDEIVSAFTRSRVQQIIGATNNMHRRSGNALPPPADEYINSNITSTAKPIAKNSSNIIENPNNGSCADIVAGKSNSLPTAASWVMRVSATLPTNKNLSGPVRPPSNQPKASNGPQVPGTEVVSTTISIQTVQPMEAVATSKVHHKLDPLELGKEYIDALSSTNEEATLDSIPATATSNQYITCRPTSKSSEKDIAtpssrtsssestkpfsspgsVEDESSHIVMDFQGLCCGLSSIGLESQFEKDRSLPVVPNSSISKHVSVNLPGSHGPQEEKSGQFTECKSFQASMAAPTMEDSPDFDDLQFKGLEDMHHLPPISSTPHLPHNLNQSSYLSWQAGDVSNQSNLDGHSGNVPLEHKEVLPSRSENLISNGFITNEASSFFNLDATVQHSSLFSEVGFGSYLGKHDSMVAPLHSNVASDVGESSIISKILSLDADAWEDSLTSPYSFAKLLRESNRQHDSLKMPSLFKESDCRQSRFSFARQEEFSNHASDVEHSLSNIRHSADQHPAPNGLLKNKDIFTDKHQNAFsssssmdsdNFLGSHSFISSSVSKAPTSVPPGFAVPNRAPPPGFSPHGTMQKPFDSSASHLRWTSAQAAGNSGPCGDIPFVDPAILEVGKGLQAIGLNNLGCDMRQTPSSQLNPFEHEARLQLLMQQSSSGYQNLRFQDYPMNRFSPPSDTYGISSKVLNQPQPNNLSSFTQSPAQQYRNAHMSTGHLGSLKGVKSINDLGVSDLMTNGGIGFNKFIPSYEDLKCQMSNSSNLYNRGFAM

*********************HLTNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYCHAWIRNMPCSVPDCLYLHDFGSQEDSFTKDEIVSAFTRSRVQQIIG**************************************************************ASWVMR***************************************ISIQTV**********VHH*LDPLELGKEYI******************************************************************IVMDFQGLCCGLSSIGL********************************************************************************************************************************LISNGFITNEASSFFNLDATVQHSSLFSEVGFGSYLGKHDSMVAPLHSNVASDVGESSIISKILSLDADAWEDSLTSPYSFA********************************************************************************************************************************************************PCGDIPFVDPAILEVGKGLQAIGLNNLGCD***************************************************************************************LKGVKSINDLGVSDLMTNGGIGFNKFIPSYEDLKC***************

**************************RVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSI***************CCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYCHAWIRNMPCSVPDCLYLHDFGSQEDSFT**********************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************************PAI**********************************************************************************************************KGV*************NGGIGFNKFIPSYEDLKCQMSNSSNLYNRGFAM

*******************RMHLTNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYCHAWIRNMPCSVPDCLYLHDFGSQEDSFTKDEIVSAFTRSRVQQIIGATNNMHRRSGNALPPPADEYINSNITSTAKPIAKNSSNIIENPNNGSCADIVAGKSNSLPTAASWVMRVSATLPTNKNLS**********************VVSTTISIQTVQPMEAVATSKVHHKLDPLELGKEYIDALSSTNEEATLDSIPATATSNQYITCR***********************************SSHIVMDFQGLCCGLSSIGLESQFEKDRSLPVVPNSSISKHVSVNLP************FTECKSFQASMAAPTMEDSPDFDDLQFKGLEDMHHLPPISSTPHLPHNLNQSSYLSWQAGDVSNQSNLDGHSGNVPLEHKEVLPSRSENLISNGFITNEASSFFNLDATVQHSSLFSEVGFGSYLGKHDSMVAPLHSNVASDVGESSIISKILSLDADAWEDSLTSPYSFAKLLRESNRQHDSLKMPSLFKESDCRQSRFSFARQEEFSNHASDVEHSLSNIRHSADQHPAPNGLLKNKDIFTDKHQN**********DNFLGSHSFISS*********PPGFAVPNRAPPPGFSPHGTMQKPFDSSASHLRWTSAQAAGNSGPCGDIPFVDPAILEVGKGLQAIGLNNLGCDMRQTPSSQLNPFEHEARLQLLMQQSSSGYQNLRFQDYPMNRFSPPSDTYGISSKVLNQPQPNNLSSFTQSPAQQYRNAHMSTGHLGSLKGVKSINDLGVSDLMTNGGIGFNKFIPSYEDLKCQMSNSSNLYNRGFAM

*****R**SQKAKPKPSEGRMHLTNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATG*****ANNSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYCHAWIRNMPCSVPDCLYLHDFGSQEDSFTKDEIVSAFT******************************************************************************************************************************************************************************************************************************************************************************************************************************NQSSYL***A*DV**********GN************SENLISN******AS****************************SMVAPLHSNVASDVGESSIISKILSLDADAWEDSLTSPYSFAKLLRE*********************SRFSFARQEEFSNHAS*VEHSL*NI*************************************NFLG******SSVSKAPTSVPPGFAVPNRAPPP**********PFDSSASHLRWTSAQAAGNSGPCGDIPFVDPAILEVGKGLQAIGLNNLGCDMRQTPSSQLNPFEHEARLQLLMQQSSSGYQNLRFQDYPMNRFSPPSDTYGISSKVLNQPQPNNLSSFTQSPAQQYRNAHMSTGHLGSLKGVKSINDLGVSDLMTNGGIGFNKFIPSYEDLKCQMSNSSNLYNRGFAM

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

iiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		917	2.2.26 [Sep-21-2011]
O95628		575	CCR4-NOT transcription co	no	no	0.178	0.285	0.433	5e-38
Q8BT14		575	CCR4-NOT transcription co	no	no	0.178	0.285	0.433	5e-38
P34909		587	General negative regulato	yes	no	0.197	0.308	0.354	4e-31
Q09818		489	Putative general negative	yes	no	0.145	0.271	0.467	3e-24
Q66JB7		380	RNA binding protein fox-1	no	no	0.089	0.215	0.266	0.0006

>sp\|O95628\|CNOT4_HUMAN CCR4-NOT transcription complex subunit 4 OS=Homo sapiens GN=CNOT4 PE=1 SV=3	Back alignment and function desciption

 Score =  160 bits (405), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 72/166 (43%), Positives = 113/166 (68%), Gaps = 2/166 (1%)

Query: 1   MTSERRQKSQKAKPKPSEGRMHLTNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGK 60
           + +E++QK  + K K SE R HL +VRV+Q+NLV+++GL   LAD ++L+R EYFG++GK
Sbjct: 78  IKNEKKQKQNERKQKISENRKHLASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGK 137

Query: 61  VLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKY 120
           + KV I+ + +     S   S   Y+TY R +DA+R IQ V++ ++DGR L+A  GTTKY
Sbjct: 138 IHKVVINNSTS--YAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKY 195

Query: 121 CHAWIRNMPCSVPDCLYLHDFGSQEDSFTKDEIVSAFTRSRVQQII 166
           C  +++NM C  PDC+YLH+ G +  SFTK+E+ +   +   Q+++
Sbjct: 196 CSYFLKNMQCPKPDCMYLHELGDEAASFTKEEMQAGKHQEYEQKLL 241

Has E3 ubiquitin ligase activity. The CCR4-NOT complex functions as general transcription regulation complex.
Homo sapiens (taxid: 9606)
EC: 6EC: .EC: 3EC: .EC: 2EC: .EC: -

>sp\|Q8BT14\|CNOT4_MOUSE CCR4-NOT transcription complex subunit 4 OS=Mus musculus GN=Cnot4 PE=1 SV=2	Back alignment and function description

>sp\|P34909\|NOT4_YEAST General negative regulator of transcription subunit 4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MOT2 PE=1 SV=1	Back alignment and function description

>sp\|Q09818\|YAC4_SCHPO Putative general negative regulator of transcription C16C9.04c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC16C9.04c PE=3 SV=1	Back alignment and function description

>sp\|Q66JB7\|RFOX2_XENTR RNA binding protein fox-1 homolog 2 OS=Xenopus tropicalis GN=rbfox2 PE=2 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		917
359478673		1024	PREDICTED: uncharacterized protein LOC10	0.961	0.861	0.432	0.0
297746185		1022	unnamed protein product [Vitis vinifera]	0.959	0.861	0.431	0.0
356542573		1022	PREDICTED: uncharacterized protein LOC10	0.955	0.857	0.408	1e-163
356541279		1023	PREDICTED: uncharacterized protein LOC10	0.966	0.866	0.408	1e-159
356557479		1045	PREDICTED: uncharacterized protein LOC10	0.955	0.838	0.4	1e-151
357472457		1223	CCR4-NOT transcription complex subunit [	0.969	0.726	0.388	1e-151
356550179		1003	PREDICTED: uncharacterized protein LOC10	0.925	0.846	0.393	1e-148
357453719		1007	CCR4-NOT transcription complex subunit [	0.952	0.866	0.391	1e-144
297793573		1001	hypothetical protein ARALYDRAFT_358235 [	0.931	0.853	0.377	1e-131
334188516		987	RNA binding (RRM/RBD/RNP motifs) family	0.921	0.856	0.377	1e-127

>gi\|359478673\|ref\|XP_002281895.2\| PREDICTED: uncharacterized protein LOC100267264 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  677 bits (1746), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 422/975 (43%), Positives = 562/975 (57%), Gaps = 93/975 (9%)

Query: 4    ERRQKSQKAKPKPSEGRMHLTNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLK 63
            ER+ KSQKAK K SEGR  L +VRVIQRNLVYI+GLP+NLADEDLLQRKEYFG YGKVLK
Sbjct: 82   ERKMKSQKAKTKLSEGRKQLGSVRVIQRNLVYIVGLPLNLADEDLLQRKEYFGLYGKVLK 141

Query: 64   VSISRTATGDIQHSANNSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYCHA 123
            VS+SRTA G IQ   NN+C VYITYS+E++A+RCIQ+VH ++LDGRPLRACFGTTKYCH 
Sbjct: 142  VSMSRTAAGVIQQFPNNTCSVYITYSKEEEAVRCIQTVHGFVLDGRPLRACFGTTKYCHQ 201

Query: 124  WIRNMPCSVPDCLYLHDFGSQEDSFTKDEIVSAFTRSRVQQIIGATNNMHRRSGNALPPP 183
            W+RN+PC+ PDCLYLH+ GSQEDSFTKDEI+S++TR+RVQQI GATNN+ RRSGN LPPP
Sbjct: 202  WLRNVPCNNPDCLYLHEIGSQEDSFTKDEIISSYTRNRVQQITGATNNLQRRSGNMLPPP 261

Query: 184  ADEYINSNITSTAKPIAKNSSNIIENPNNGSCADIVAGKSNSLPTAASWVMRVSATLPTN 243
            ADEY N++  S  KPI KN+SN   +   GS  +  +G+SN+LP AASW MR S +    
Sbjct: 262  ADEYCNNSSASMGKPITKNASNNSVSIAKGSPPNSSSGRSNALPAAASWGMRSSNSQTMA 321

Query: 244  KNLSGPVRPPSNQPKASNGPQVPGTEVVSTTISIQTVQPMEAVAT-SKV----------- 291
             +LS    P   +P + +G     + V STT+ + T    +AVA  S+V           
Sbjct: 322  SSLSCGNGPFKQKPDSFSGSVAFSSAVTSTTLPLTT----QAVALHSEVGKKPTLNEENR 377

Query: 292  ----HHKLDPLELGKEYIDALSSTNEEATLDSIPATATSNQYITCRPTSKSSEKDIATPS 347
                  KL+ LE  K++I ++ ++    T D  PA+      ++C PTSK +++ I+   
Sbjct: 378  LINPKGKLESLESMKQHI-SMDTSEGLITPDEAPASLPLGGQLSCPPTSKDNDRGISLSP 436

Query: 348  SRTSSSESTKPFSSPGSVEDESSHIVMDFQGLCCGLSSIGLESQFEKDRSLPVVPNSSIS 407
              T+SS+ T+  +  GS  + +     +   L   +SS+ ++ Q + +    +  N S+S
Sbjct: 437  KVTNSSDFTRQPNCSGSEREGNVATDGNLHNLLSDMSSMSIDRQLKSEHPGVLRSNCSLS 496

Query: 408  KHVSVNLPGSHGPQEEKSGQFTE-----------------C--------KSFQASMAAPT 442
             +     PGS G Q+  + QF E                 C        +S   +   P 
Sbjct: 497  DNGLTQTPGSQGLQQYYAEQFKESLTSPVSRKVSTTINGVCVPDEQNDWRSDSQTQVVPN 556

Query: 443  M-----EDSPDFDDLQFKGLEDMHHLPPISSTPHLPHNLNQSSYLSWQAGDVSNQSNLDG 497
            M     +D   FD+ + K  E +     + ++ HL H+ N     S Q  D+ N  + + 
Sbjct: 557  MCSEMEDDLLSFDNQRLKDSEVVSGTTYLPNSSHLLHHSNDLRGKSSQHNDIHNGVSFNA 616

Query: 498  HSGNVPLEHKE--VLPSRSENLISNGFITNEASSFFNLDATVQHSSLFSEVGFGSYLGKH 555
                V  +  E  +  +   ++ISNGF      +   LD                     
Sbjct: 617  DPIFVGRKFSEGSLTHAPGASVISNGFPEKRVGNSAGLDRA------------------- 657

Query: 556  DSMVAPLHSNVASDVGESSIISKILSLDADAWEDSLTSPYSFAKLLRESNRQHDSLKMPS 615
                   +++   DVGE+SIIS ILSLD DAW+DS+TSP + A+LL E+++QH SLK   
Sbjct: 658  -------NASTTMDVGENSIISNILSLDFDAWDDSITSPQNLAQLLGENDKQHSSLKTSG 710

Query: 616  LFKESDCRQSRFSFARQEEFSNHASDVEHSLSNIRHSADQHPAPNGLLKNKDIFTDKHQN 675
             +K  +  QSRFSFARQEE  N   D+E S SNI             ++++D F DK  N
Sbjct: 711  SWKVQNSNQSRFSFARQEESKNQVFDIEPSFSNIGQVPRNCSFNQNFVESRDPFLDKLGN 770

Query: 676  A--FSSSSSMDSDNFLGSHSFISS---SVSKAPTSVPPGFAVPNRAPPPGFSPHGTMQKP 730
               FSS+   +SDNF   HS ISS   S S+A  S PPGF VP+RAPPPGFS H   ++ 
Sbjct: 771  GSLFSSNIFGESDNFAPGHSVISSNKISASRAQISAPPGFTVPSRAPPPGFSSHERTEQA 830

Query: 731  FDS-SASHLRWTSA-------QAAGNSGPCGDIPFVDPAILEVGKGLQAIGLNNLGCDMR 782
            FD+ S +HL  TS+         +GN    GDI F+DPAIL VGKG    GLNN   DMR
Sbjct: 831  FDAISGNHLLDTSSLLRNPYQTPSGNIASAGDIEFIDPAILAVGKGRLPGGLNNPALDMR 890

Query: 783  QTPSSQLNPFEHEARLQLLMQQSSSGYQNLRFQDYPMNRFSPPSDTYGISSKVLNQPQPN 842
                 QL+ FE+EARLQLLMQ+S S +QNLRF D     FSP  D YGI S+++ Q Q +
Sbjct: 891  SNFHPQLSAFENEARLQLLMQRSLSPHQNLRFADIGEG-FSPLGDAYGIPSRLMEQSQAS 949

Query: 843  NLSSFTQSPAQQYRNAHMSTGHLGSLKGVKSINDLGVSDLMTNGGIGFNKFIPSYEDLKC 902
            N+S F Q   QQ RNA MS GH      ++S NDL +++L+ N  +G+NKF   YED K 
Sbjct: 950  NISPFAQLSLQQSRNAIMSNGHWDGWNEIQSGNDLNMAELLRNERLGYNKFYTGYEDSKF 1009

Query: 903  QMSNSSNLYNRGFAM 917
            +M  S +LYNR F +
Sbjct: 1010 RMPPSGDLYNRTFGI 1024

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|297746185\|emb\|CBI16241.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356542573\|ref\|XP_003539741.1\| PREDICTED: uncharacterized protein LOC100801880 [Glycine max]	Back alignment and taxonomy information

>gi\|356541279\|ref\|XP_003539106.1\| PREDICTED: uncharacterized protein LOC100813427 [Glycine max]	Back alignment and taxonomy information

>gi\|356557479\|ref\|XP_003547043.1\| PREDICTED: uncharacterized protein LOC100796804 [Glycine max]	Back alignment and taxonomy information

>gi\|357472457\|ref\|XP_003606513.1\| CCR4-NOT transcription complex subunit [Medicago truncatula] gi\|355507568\|gb\|AES88710.1\| CCR4-NOT transcription complex subunit [Medicago truncatula]	Back alignment and taxonomy information

>gi\|356550179\|ref\|XP_003543466.1\| PREDICTED: uncharacterized protein LOC100805811 [Glycine max]	Back alignment and taxonomy information

>gi\|357453719\|ref\|XP_003597140.1\| CCR4-NOT transcription complex subunit [Medicago truncatula] gi\|355486188\|gb\|AES67391.1\| CCR4-NOT transcription complex subunit [Medicago truncatula]	Back alignment and taxonomy information

>gi\|297793573\|ref\|XP_002864671.1\| hypothetical protein ARALYDRAFT_358235 [Arabidopsis lyrata subsp. lyrata] gi\|297310506\|gb\|EFH40930.1\| hypothetical protein ARALYDRAFT_358235 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|334188516\|ref\|NP_001190578.1\| RNA binding (RRM/RBD/RNP motifs) family protein [Arabidopsis thaliana] gi\|332009906\|gb\|AED97289.1\| RNA binding (RRM/RBD/RNP motifs) family protein [Arabidopsis thaliana]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		917
TAIR\|locus:2085617		989	AT3G45630 [Arabidopsis thalian	0.943	0.874	0.354	3.1e-106
TAIR\|locus:2056563		960	AT2G28540 [Arabidopsis thalian	0.347	0.332	0.470	1.4e-103
UNIPROTKB\|E2QXU6		572	CNOT4 "Uncharacterized protein	0.223	0.358	0.394	6.3e-36
UNIPROTKB\|I3LC53		304	LOC100622832 "Uncharacterized	0.176	0.532	0.439	2.9e-35
UNIPROTKB\|E1C4B3		765	CNOT4 "Uncharacterized protein	0.334	0.401	0.310	4.5e-35
UNIPROTKB\|Q5ZJC9		762	CNOT4 "Uncharacterized protein	0.333	0.401	0.305	9.7e-35
UNIPROTKB\|E2QXU8		710	CNOT4 "Uncharacterized protein	0.223	0.288	0.394	1.5e-34
MGI\|MGI:1859026		575	Cnot4 "CCR4-NOT transcription	0.176	0.281	0.439	1.9e-34
UNIPROTKB\|D4ADF8		575	Cnot4 "RCG28297" [Rattus norve	0.176	0.281	0.439	1.9e-34
UNIPROTKB\|O95628		575	CNOT4 "CCR4-NOT transcription	0.176	0.281	0.439	1.9e-34

TAIR\|locus:2085617 AT3G45630 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 1051 (375.0 bits), Expect = 3.1e-106, P = 3.1e-106
 Identities = 338/954 (35%), Positives = 487/954 (51%)

Query:     6 RQKSQKAKPKPSEGRMHLTNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVS 65
             R+K QK+KPK S+GR  LT+VRV+QRNLVYI+GLP+NLADEDLLQRKEYFGQYGKVLKVS
Sbjct:    83 RKKIQKSKPKSSDGRKPLTSVRVVQRNLVYIVGLPLNLADEDLLQRKEYFGQYGKVLKVS 142

Query:    66 ISRTATGDIQHSANNSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYCHAWI 125
             +SRTATG IQ   NN+C VYITY +E++AIRCIQSVH +ILDG+ L+ACFGTTKYCHAW+
Sbjct:   143 MSRTATGLIQQFPNNTCSVYITYGKEEEAIRCIQSVHGFILDGKALKACFGTTKYCHAWL 202

Query:   126 RNMPCSVPDCLYLHDFGSQEDSFTKDEIVSAFTRSRVQQIIGATNNMHRRSGNALPPPAD 185
             RN+ C+  DCLYLH+ GSQEDSFTKDEI+SA TR  VQQI GATN M  RSG+ LPPP D
Sbjct:   203 RNVACNNQDCLYLHEVGSQEDSFTKDEIISAHTR--VQQITGATNTMQYRSGSMLPPPLD 260

Query:   186 EYINSNITSTAKPIAK-NSSNIIENPNNGSCADIVAGKSNSLPTAASWVMRVSA--TLPT 242
              Y + +  ST  PIAK  SS  +  P +   +   +GKS +LP AASW  R++   +L T
Sbjct:   261 AYTSDS--STGNPIAKVPSSTSVSAPKSSPPSGS-SGKSTALPAAASWGARLTNQHSLAT 317

Query:   243 NKNLSGPVRPPSNQPKAS-NGPQVPGTEV-------VSTTISIQTV---QPMEAVATSKV 291
             +   +G +    NQ   S NG     T V       VS++ S+Q     + ++++A    
Sbjct:   318 SALSNGSL---DNQRSTSENGTLATSTVVTKAANGPVSSSNSLQKAPLKEEIQSLAEKSK 374

Query:   292 HHKLDPLELGKEYIDALS----STNEEATLDSIPATATS--NQYITCRPTS--KSSE--K 341
                L PL+  K  +D  S    S N + + + I     S  N  +  +P++   S E   
Sbjct:   375 PGVLKPLQQ-KIVLDPESKRTTSPNRDPSSNQISCLVESSYNSRVIDKPSAVENSLEHTS 433

Query:   342 DIAXXXXXXXXXXXXXX-XXXXXXVEDESSHIVMDFQGLCCGLSSIGLESQFEKD-RSLP 399
             +IA                       DE+  + +   G  C L SI   +Q + D ++L 
Sbjct:   434 EIAEDVFDVGKLSADVAWMGITTNSRDETPGVPVVI-GTHCDLGSI---TQSDNDVQNLE 489

Query:   400 VVPNSSISK---HVSVNLPGSHGPQEEKSGQFTECKSFQASMAAPT-MEDSPDFDDLQFK 455
                  S +       ++L G HG + E   + +  +S Q  +  P  + D   F++ + +
Sbjct:   490 QCRKQSPTNTYAEADISLNGIHGSRPEWDWR-SGLQS-QIDVKEPLEVNDFSSFNNNR-R 546

Query:   456 GLEDM--HHLPPISSTPHLPHNLNQSSYLSWQAGDVSNQSNLDGHSGNVPLEHKEVLPSR 513
             G+ +   H     SS+  +  + N  +  S+Q  + S    +D  +G+      E+   R
Sbjct:   547 GIAEAVSHSTSKFSSSISILDS-NHLASRSFQNRETS--CGMDSKTGS----SFEIGSDR 599

Query:   514 SENLISNGFITNEASSFFNLDATVQHSSLFSEVGFGSYLGKHDSMVAPLHSNVAS-DVGE 572
                 + NGF + +A S       ++HS LF+  G  +     D ++    SN+   D  +
Sbjct:   600 LH--LPNGF-SEKAMS------NMEHS-LFANEGRSNIQNTEDDII----SNILDFDPWD 645

Query:   573 SSIISKILSLDADAWEDSLTSPYSFAKLLRESNRQHDSLKMPSLFKESDCRQSRFSFARQ 632
              S+ S+          D   S    + LL++ N Q            S    +R S++  
Sbjct:   646 ESLTSQHNFAKLLGQSDHRASTLESSNLLKQHNDQSRFSFARHEESNSQAYDNR-SYSIY 704

Query:   633 EEFSNHASDVEHSLSNIRHSADQHPAPNGLLKNKDIFTDKHQNAFXXXXXXXXXNFLGSH 692
              + S      E   +   +  D+  + NG   N   ++  ++  F             + 
Sbjct:   705 GQLSRDQPLQEFGANRDMYQ-DKLGSQNGFASN---YSGGYEQ-FATSPGLSSYKSPVAR 759

Query:   693 SFISSSVS-KAPTSVPP-GFAVPNRAPPPGFSPHGTMQKPFDSSASHLR--WTSAQAAGN 748
             + +S+     AP  +PP GF+   R         GT  +  DS A+ LR  +     +GN
Sbjct:   760 TQVSAPPGFSAPNRLPPPGFSSHQRGDLSSDIASGT--RLLDS-ANLLRNAYHVPPPSGN 816

Query:   749 SGPCGDIPFVDPAILEVGKGLQAIGLNNLGCDMRQTPSSQLNPFEHEARLQLLMQQSSSG 808
                 GDI F+DPAIL VG+G    G+     D+R   SSQLN F+++ARLQLL Q+S + 
Sbjct:   817 LNAAGDIEFIDPAILAVGRGRLHNGMETADFDLRSGFSSQLNSFDNDARLQLLAQRSLAA 876

Query:   809 YQNLRFQDYP--MNRFSPP-SDTYGISSKVLNQPQPNNLSSFTQSPAQQYRNAHMSTGHL 865
              Q   F D P  +N FS   SD YGISS+  +Q Q   LS FTQ P Q   N  +S GH 
Sbjct:   877 QQVNGFHD-PRNVNNFSSSFSDPYGISSRPTDQTQGTGLSPFTQLPRQASANPLLSNGHW 935

Query:   866 GSL-KGVKSINDLGVSDLMTNGGIGFNKFIPS-YEDLKCQMSNSSNLYNRGFAM 917
              +     +S N+LG++ L+ N  +GFN  + S +E+ K +     + YNR + +
Sbjct:   936 DNKWNEPQSGNNLGITQLLRNERMGFNDNVYSGFEEPKFRRPGPGDPYNRTYGI 989

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009506 "plasmodesma" evidence=IDA

TAIR\|locus:2056563 AT2G28540 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QXU6 CNOT4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|I3LC53 LOC100622832 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|E1C4B3 CNOT4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|Q5ZJC9 CNOT4 "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QXU8 CNOT4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

MGI\|MGI:1859026 Cnot4 "CCR4-NOT transcription complex, subunit 4" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|D4ADF8 Cnot4 "RCG28297" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|O95628 CNOT4 "CCR4-NOT transcription complex subunit 4" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		917
cd12438		98	cd12438, RRM_CNOT4, RNA recognition motif in Eukar	6e-52
COG5175		480	COG5175, MOT2, Transcriptional repressor [Transcri	2e-42
cd00590		72	cd00590, RRM_SF, RNA recognition motif (RRM) super	9e-13
pfam00076		70	pfam00076, RRM_1, RNA recognition motif	6e-12
smart00360		73	smart00360, RRM, RNA recognition motif	7e-11
smart00361		70	smart00361, RRM_1, RNA recognition motif	3e-10
pfam13893		56	pfam13893, RRM_5, RNA recognition motif	2e-07
pfam14259		69	pfam14259, RRM_6, RNA recognition motif (a	1e-06
cd12393		78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	3e-06
cd12232		89	cd12232, RRM3_U2AF65, RNA recognition motif 3 foun	4e-06
cd12380		80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	3e-05
cd12374		85	cd12374, RRM_UHM_SPF45_PUF60, RNA recognition moti	4e-05
cd12413		79	cd12413, RRM1_RBM28_like, RNA recognition motif 1	4e-05
cd12361		77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	7e-05
cd12414		76	cd12414, RRM2_RBM28_like, RNA recognition motif 2	2e-04
cd12417		74	cd12417, RRM_SAFB_like, RNA recognition motif in t	2e-04
cd12298		78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-04
cd12387		72	cd12387, RRM3_hnRNPM_like, RNA recognition motif 3	2e-04
cd12454		80	cd12454, RRM2_RIM4_like, RNA recognition motif 2 i	3e-04
COG0724		306	COG0724, COG0724, RNA-binding proteins (RRM domain	4e-04
cd12633		80	cd12633, RRM1_FCA, RNA recognition motif 1 in plan	4e-04
cd12307		74	cd12307, RRM_NIFK_like, RNA recognition motif in n	4e-04
cd12382		80	cd12382, RRM_RBMX_like, RNA recognition motif in h	5e-04
cd12284		73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	5e-04
cd12418		75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	7e-04
cd12363		78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.001
cd12354		73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	0.002
cd12407		76	cd12407, RRM_FOX1_like, RNA recognition motif in v	0.002
cd12448		73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	0.002
cd12251		72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	0.003

>gnl\|CDD\|240884 cd12438, RRM_CNOT4, RNA recognition motif in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins	Back alignment and domain information

 Score =  176 bits (448), Expect = 6e-52
 Identities = 54/100 (54%), Positives = 76/100 (76%), Gaps = 2/100 (2%)

Query: 27  RVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYI 86
           RVIQRNLVY++GLP  LADE++L++ EYFGQYGK+ K+ I+R  + +       S   Y+
Sbjct: 1   RVIQRNLVYVVGLPPRLADEEVLKKPEYFGQYGKIKKIVINRNTSYNGSQ--GPSASAYV 58

Query: 87  TYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYCHAWIR 126
           TYSR++DA+RCIQ+V  + LDGR L+A FGTTKYC ++++
Sbjct: 59  TYSRKEDALRCIQAVDGFYLDGRLLKASFGTTKYCSSFLK 98

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. Length = 98

>gnl\|CDD\|227502 COG5175, MOT2, Transcriptional repressor [Transcription]	Back alignment and domain information

>gnl\|CDD\|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily	Back alignment and domain information

>gnl\|CDD\|215696 pfam00076, RRM_1, RNA recognition motif	Back alignment and domain information

>gnl\|CDD\|214636 smart00360, RRM, RNA recognition motif	Back alignment and domain information

>gnl\|CDD\|214637 smart00361, RRM_1, RNA recognition motif	Back alignment and domain information

>gnl\|CDD\|206064 pfam13893, RRM_5, RNA recognition motif	Back alignment and domain information

>gnl\|CDD\|222631 pfam14259, RRM_6, RNA recognition motif (a	Back alignment and domain information

>gnl\|CDD\|240839 cd12393, RRM_ZCRB1, RNA recognition motif in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240678 cd12232, RRM3_U2AF65, RNA recognition motif 3 found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240826 cd12380, RRM3_I_PABPs, RNA recognition motif 3 found in type I polyadenylate-binding proteins	Back alignment and domain information

>gnl\|CDD\|240820 cd12374, RRM_UHM_SPF45_PUF60, RNA recognition motif in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240859 cd12413, RRM1_RBM28_like, RNA recognition motif 1 in RNA-binding protein 28 (RBM28) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240807 cd12361, RRM1_2_CELF1-6_like, RNA recognition motif 1 and 2 in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA	Back alignment and domain information

>gnl\|CDD\|240860 cd12414, RRM2_RBM28_like, RNA recognition motif 2 in RNA-binding protein 28 (RBM28) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240863 cd12417, RRM_SAFB_like, RNA recognition motif in the scaffold attachment factor (SAFB) family	Back alignment and domain information

>gnl\|CDD\|240744 cd12298, RRM3_Prp24, RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240833 cd12387, RRM3_hnRNPM_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240900 cd12454, RRM2_RIM4_like, RNA recognition motif 2 in yeast meiotic activator RIM4 and similar proteins	Back alignment and domain information

>gnl\|CDD\|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]	Back alignment and domain information

>gnl\|CDD\|241077 cd12633, RRM1_FCA, RNA recognition motif 1 in plant flowering time control protein FCA and similar proteins	Back alignment and domain information

>gnl\|CDD\|240753 cd12307, RRM_NIFK_like, RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240828 cd12382, RRM_RBMX_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240730 cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2 in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family	Back alignment and domain information

>gnl\|CDD\|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins	Back alignment and domain information

>gnl\|CDD\|240800 cd12354, RRM3_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1	Back alignment and domain information

>gnl\|CDD\|240853 cd12407, RRM_FOX1_like, RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins	Back alignment and domain information

>gnl\|CDD\|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240697 cd12251, RRM3_hnRNPR_like, RNA recognition motif 3 in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		917
COG5175		480	MOT2 Transcriptional repressor [Transcription]	100.0
KOG2068		327	consensus MOT2 transcription factor [Transcription	100.0
PLN03134		144	glycine-rich RNA-binding protein 4; Provisional	99.52
PF00076		70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.51
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.51
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.47
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	99.38
PF14259		70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.34
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	99.31
smart00362		72	RRM_2 RNA recognition motif.	99.29
KOG0114		124	consensus Predicted RNA-binding protein (RRM super	99.29
PLN03120		260	nucleic acid binding protein; Provisional	99.27
KOG0125		376	consensus Ataxin 2-binding protein (RRM superfamil	99.27
KOG0107		195	consensus Alternative splicing factor SRp20/9G8 (R	99.26
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	99.26
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	99.25
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	99.25
COG0724		306	RNA-binding proteins (RRM domain) [General functio	99.23
cd00590		74	RRM RRM (RNA recognition motif), also known as RBD	99.23
KOG0111		298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.23
KOG0149		247	consensus Predicted RNA-binding protein SEB4 (RRM	99.22
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	99.21
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.21
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	99.2
smart00360		71	RRM RNA recognition motif.	99.19
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	99.18
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	99.18
KOG0121		153	consensus Nuclear cap-binding protein complex, sub	99.17
PF13893		56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.15
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	99.13
PLN03213		759	repressor of silencing 3; Provisional	99.12
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.12
KOG0122		270	consensus Translation initiation factor 3, subunit	99.12
KOG4207		256	consensus Predicted splicing factor, SR protein su	99.11
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.09
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	99.07
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.05
KOG0126		219	consensus Predicted RNA-binding protein (RRM super	99.04
smart00361		70	RRM_1 RNA recognition motif.	99.02
PLN03121		243	nucleic acid binding protein; Provisional	99.01
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.0
KOG0105		241	consensus Alternative splicing factor ASF/SF2 (RRM	98.94
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.94
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	98.92
KOG0108		435	consensus mRNA cleavage and polyadenylation factor	98.87
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.84
KOG0113		335	consensus U1 small nuclear ribonucleoprotein (RRM	98.82
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.8
KOG0132		894	consensus RNA polymerase II C-terminal domain-bind	98.76
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.76
KOG0130		170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.72
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.69
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.69
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	98.66
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.54
KOG4661		940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.52
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	98.52
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.46
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	98.42
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	98.39
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	98.38
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	98.36
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.36
KOG0153		377	consensus Predicted RNA-binding protein (RRM super	98.32
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	98.32
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	98.3
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	98.29
KOG1548		382	consensus Transcription elongation factor TAT-SF1	98.26
KOG0533		243	consensus RRM motif-containing protein [RNA proces	98.25
KOG0151		877	consensus Predicted splicing regulator, contains R	98.21
KOG4208		214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.19
KOG0415		479	consensus Predicted peptidyl prolyl cis-trans isom	98.18
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	98.15
KOG1548		382	consensus Transcription elongation factor TAT-SF1	98.09
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	97.98
KOG4660		549	consensus Protein Mei2, essential for commitment t	97.93
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	97.92
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	97.75
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	97.75
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	97.73
KOG2202		260	consensus U2 snRNP splicing factor, small subunit,	97.68
KOG1995		351	consensus Conserved Zn-finger protein [General fun	97.66
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	97.65
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	97.63
KOG0116		419	consensus RasGAP SH3 binding protein rasputin, con	97.61
KOG4454		267	consensus RNA binding protein (RRM superfamily) [G	97.54
KOG4209		231	consensus Splicing factor RNPS1, SR protein superf	97.48
KOG1190		492	consensus Polypyrimidine tract-binding protein [RN	97.47
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	97.36
KOG1996		378	consensus mRNA splicing factor [RNA processing and	97.27
PF11608		90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.24
KOG1457		284	consensus RNA binding protein (contains RRM repeat	97.21
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	97.14
PF05172		100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	97.1
PF14605		53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	96.84
PF08777		105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.82
KOG4211		510	consensus Splicing factor hnRNP-F and related RNA-	96.66
PF04059		97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	96.58
KOG2314		698	consensus Translation initiation factor 3, subunit	96.53
KOG1365		508	consensus RNA-binding protein Fusilli, contains RR	96.15
KOG4210		285	consensus Nuclear localization sequence binding pr	96.12
KOG1456		494	consensus Heterogeneous nuclear ribonucleoprotein	96.01
KOG0226		290	consensus RNA-binding proteins [General function p	95.8
KOG3152		278	consensus TBP-binding protein, activator of basal	95.79
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	95.76
KOG1190		492	consensus Polypyrimidine tract-binding protein [RN	95.65
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	95.54
KOG0129		520	consensus Predicted RNA-binding protein (RRM super	95.39
KOG1456		494	consensus Heterogeneous nuclear ribonucleoprotein	94.95
KOG4285		350	consensus Mitotic phosphoprotein [Cell cycle contr	94.23
KOG4211		510	consensus Splicing factor hnRNP-F and related RNA-	94.18
KOG4307		944	consensus RNA binding protein RBM12/SWAN [General	94.01
KOG1457		284	consensus RNA binding protein (contains RRM repeat	93.85
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	93.2
KOG2416		718	consensus Acinus (induces apoptotic chromatin cond	93.15
PF08952		146	DUF1866: Domain of unknown function (DUF1866) ; In	93.11
KOG0129		520	consensus Predicted RNA-binding protein (RRM super	92.96
KOG0112		975	consensus Large RNA-binding protein (RRM superfami	92.6
PF10309		62	DUF2414: Protein of unknown function (DUF2414); In	90.13
PF04847		184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	89.72
KOG0115		275	consensus RNA-binding protein p54nrb (RRM superfam	89.56
KOG0128		881	consensus RNA-binding protein SART3 (RRM superfami	88.96
KOG1365		508	consensus RNA-binding protein Fusilli, contains RR	88.86
PF08675		87	RNA_bind: RNA binding domain; InterPro: IPR014789	88.83
KOG1855		484	consensus Predicted RNA-binding protein [General f	88.47
KOG4307		944	consensus RNA binding protein RBM12/SWAN [General	88.32
KOG2135		526	consensus Proteins containing the RNA recognition	86.89
KOG4849		498	consensus mRNA cleavage factor I subunit/CPSF subu	85.39
KOG2193		584	consensus IGF-II mRNA-binding protein IMP, contain	82.3
PF11767		66	SET_assoc: Histone lysine methyltransferase SET as	81.76
KOG0112		975	consensus Large RNA-binding protein (RRM superfami	81.76
PF03467		176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	81.76

>COG5175 MOT2 Transcriptional repressor [Transcription]	Back alignment and domain information

Probab=100.00  E-value=1.1e-46  Score=399.00  Aligned_cols=155  Identities=46%  Similarity=0.894  Sum_probs=141.7

Q ss_pred             hHHHHHhhhcCCCCccCccCCCCccccccCeEEEeCCCCCCChhH---HHHHHHhhccCcceEEEEEeecCCCCcccCCC
Q 002482            3 SERRQKSQKAKPKPSEGRMHLTNVRVIQRNLVYIIGLPINLADED---LLQRKEYFGQYGKVLKVSISRTATGDIQHSAN   79 (917)
Q Consensus         3 ~ekk~K~qk~K~k~~e~Rk~LanVRVIQKNLVYV~GLP~sIAeED---LLKr~EyFGQYGKIiKIvInrd~~g~~q~~~~   79 (917)
                      .|+|+++..+|+.+-.+||||+++||||||||||+||++.+++|+   +||++|||||||+|+||+|++......  ...
T Consensus        86 ~erk~rekerke~e~~nrkhlsniRVvQKNLvYVigi~pkva~Ee~~~vLk~~eyFGQyGkI~KIvvNkkt~s~n--st~  163 (480)
T COG5175          86 EERKMREKERKEAEGQNRKHLSNIRVVQKNLVYVIGIPPKVADEEVAPVLKRHEYFGQYGKIKKIVVNKKTSSLN--STA  163 (480)
T ss_pred             hhhhccHHHHhhhhcccccccccceeeecceeEEecCCCCCCcccccccccchhhhhhccceeEEEecccccccc--ccc
Confidence            578888888999999999999999999999999999999999999   899999999999999999997653221  122


Q ss_pred             CCcEEEEEeCCHHHHHHHHHHhCCCccCCeeEEEeEccCCCccccccCCCCCCCCccccccCCCCCCCCcHHHHHHhhhh
Q 002482           80 NSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYCHAWIRNMPCSVPDCLYLHDFGSQEDSFTKDEIVSAFTR  159 (917)
Q Consensus        80 prGsAFVTFs~~EDA~rAIqaLNG~~LDGR~LRASfGTTKYCssFLRn~~C~NpdCmYLHE~g~~~DsFTKeEm~~~~tr  159 (917)
                      ...++||||.++|||++||.++||..+|||.|||+|||||||++||||++|+||+||||||+|+++|+|||+||....+.
T Consensus       164 ~h~gvYITy~~kedAarcIa~vDgs~~DGr~lkatYGTTKYCtsYLRn~~CpNp~CMyLHEpg~e~Ds~tK~el~n~qh~  243 (480)
T COG5175         164 SHAGVYITYSTKEDAARCIAEVDGSLLDGRVLKATYGTTKYCTSYLRNAVCPNPDCMYLHEPGPEKDSLTKDELCNSQHK  243 (480)
T ss_pred             ccceEEEEecchHHHHHHHHHhccccccCceEeeecCchHHHHHHHcCCCCCCCCeeeecCCCcccccccHHHHhhhhhh
Confidence            34678999999999999999999999999999999999999999999999999999999999999999999999976544

>KOG2068 consensus MOT2 transcription factor [Transcription]	Back alignment and domain information

>PLN03134 glycine-rich RNA-binding protein 4; Provisional	Back alignment and domain information

>PF00076 RRM_1: RNA recognition motif	Back alignment and domain information

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor	Back alignment and domain information

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor	Back alignment and domain information

>TIGR01659 sex-lethal sex-lethal family splicing factor	Back alignment and domain information

>PF14259 RRM_6: RNA recognition motif (a	Back alignment and domain information

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>smart00362 RRM_2 RNA recognition motif	Back alignment and domain information

>KOG0114 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>PLN03120 nucleic acid binding protein; Provisional	Back alignment and domain information

>KOG0125 consensus Ataxin 2-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0107 consensus Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family	Back alignment and domain information

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

>TIGR01659 sex-lethal sex-lethal family splicing factor	Back alignment and domain information

>COG0724 RNA-binding proteins (RRM domain) [General function prediction only]	Back alignment and domain information

>cd00590 RRM RRM (RNA recognition motif), 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	Back alignment and domain information

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]	Back alignment and domain information

>TIGR01645 half-pint poly-U binding splicing factor, half-pint family	Back alignment and domain information

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

>smart00360 RRM RNA recognition motif	Back alignment and domain information

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]	Back alignment and domain information

>TIGR01622 SF-CC1 splicing factor, CC1-like family	Back alignment and domain information

>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>PF13893 RRM_5: RNA recognition motif	Back alignment and domain information

>TIGR01622 SF-CC1 splicing factor, CC1-like family	Back alignment and domain information

>PLN03213 repressor of silencing 3; Provisional	Back alignment and domain information

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family	Back alignment and domain information

>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]	Back alignment and domain information

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family	Back alignment and domain information

>KOG0148 consensus Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0126 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>smart00361 RRM_1 RNA recognition motif	Back alignment and domain information

>PLN03121 nucleic acid binding protein; Provisional	Back alignment and domain information

>TIGR01648 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family	Back alignment and domain information

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family	Back alignment and domain information

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0108 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification]	Back alignment and domain information

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]	Back alignment and domain information

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]	Back alignment and domain information

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only]	Back alignment and domain information

>TIGR01642 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>KOG0127 consensus Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG4661 consensus Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription]	Back alignment and domain information

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]	Back alignment and domain information

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]	Back alignment and domain information

>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0123 consensus Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification; Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]	Back alignment and domain information

>KOG0533 consensus RRM motif-containing protein [RNA processing and modification]	Back alignment and domain information

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]	Back alignment and domain information

>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]	Back alignment and domain information

>KOG0415 consensus Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]	Back alignment and domain information

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]	Back alignment and domain information

>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG4660 consensus Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>KOG4205 consensus RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification]	Back alignment and domain information

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0110 consensus RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]	Back alignment and domain information

>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]	Back alignment and domain information

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]	Back alignment and domain information

>KOG0146 consensus RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]	Back alignment and domain information

>KOG0116 consensus RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms]	Back alignment and domain information

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>KOG4209 consensus Splicing factor RNPS1, SR protein superfamily [RNA processing and modification]	Back alignment and domain information

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]	Back alignment and domain information

>KOG4212 consensus RNA-binding protein hnRNP-M [RNA processing and modification]	Back alignment and domain information

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]	Back alignment and domain information

>PF11608 Limkain-b1: Limkain b1; InterPro: IPR024582 This entry represents a conserved domain found in limkain b1, which is a novel human autoantigen, localised to a subset of ABCD3 and PXF marked peroxisomes	Back alignment and domain information

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]	Back alignment and domain information

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>PF05172 Nup35_RRM: Nup53/35/40-type RNA recognition motif; InterPro: IPR007846 The MPPN (Mitotic PhosphoProtein N end) family is uncharacterised however it probably plays a role in the cell cycle because the family includes mitotic phosphoproteins O13026 from SWISSPROT []	Back alignment and domain information

>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif	Back alignment and domain information

>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation	Back alignment and domain information

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]	Back alignment and domain information

>PF04059 RRM_2: RNA recognition motif 2; InterPro: IPR007201 This RNA recognition motif 2 is found in Meiosis protein mei2	Back alignment and domain information

>KOG2314 consensus Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]	Back alignment and domain information

>KOG4210 consensus Nuclear localization sequence binding protein [Transcription]	Back alignment and domain information

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]	Back alignment and domain information

>KOG0226 consensus RNA-binding proteins [General function prediction only]	Back alignment and domain information

>KOG3152 consensus TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription]	Back alignment and domain information

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG1190 consensus Polypyrimidine tract-binding protein [RNA processing and modification]	Back alignment and domain information

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification]	Back alignment and domain information

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]	Back alignment and domain information

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification]	Back alignment and domain information

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]	Back alignment and domain information

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]	Back alignment and domain information

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification]	Back alignment and domain information

>KOG2416 consensus Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics]	Back alignment and domain information

>PF08952 DUF1866: Domain of unknown function (DUF1866) ; InterPro: IPR015047 This domain, found in synaptojanin, has no known function	Back alignment and domain information

>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function	Back alignment and domain information

>PF04847 Calcipressin: Calcipressin; InterPro: IPR006931 Calcipressin 1 negatively regulates calcineurin (IPR015757 from INTERPRO) by direct binding and is essential for the survival of T helper type 1 cells	Back alignment and domain information

>KOG0115 consensus RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG0128 consensus RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification]	Back alignment and domain information

>KOG1365 consensus RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification; General function prediction only]	Back alignment and domain information

>PF08675 RNA_bind: RNA binding domain; InterPro: IPR014789 This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN)	Back alignment and domain information

>KOG1855 consensus Predicted RNA-binding protein [General function prediction only]	Back alignment and domain information

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]	Back alignment and domain information

>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]	Back alignment and domain information

>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]	Back alignment and domain information

>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]	Back alignment and domain information

>PF11767 SET_assoc: Histone lysine methyltransferase SET associated; InterPro: IPR024636 The SET domain is a protein-protein interaction domain found in protein lysine methyltransferase enzymes	Back alignment and domain information

>KOG0112 consensus Large RNA-binding protein (RRM superfamily) [General function prediction only]	Back alignment and domain information

>PF03467 Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120 Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism by which eukaryotic cells detect and degrade transcripts containing premature termination codons	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		917
2cpi_A		111	Solution Structure Of The Rna Recognition Motif Of		7e-20

>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4 Length = 111

Back alignment and structure

Iteration: 1

Score = 96.3 bits (238), Expect = 7e-20, Method: Composition-based stats. Identities = 46/96 (47%), Positives = 68/96 (70%), Gaps = 2/96 (2%) Query: 26 VRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVY 85 VRV+Q+NLV+++GL LAD ++L+R EYFG++GK+ KV I+ + + S S Y Sbjct: 10 VRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTS--YAGSQGPSASAY 67 Query: 86 ITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYC 121 +TY R +DA+R IQ V++ ++DGR L+A GTTKYC Sbjct: 68 VTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYC 103

PyMOL of 2cpi

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		917
2cpi_A		111	CCR4-NOT transcription complex subunit 4; RNA reco	2e-38
2a3j_A		127	U1 small nuclear ribonucleoprotein A; computationa	2e-09
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-09
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	3e-05
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	7e-04
2jvo_A		108	Nucleolar protein 3; nucleus, phosphorylation, rib	1e-08
2f3j_A		177	RNA and export factor binding protein 2; RRM domai	1e-08
3s8s_A		110	Histone-lysine N-methyltransferase SETD1A; chromat	1e-08
2e44_A		96	Insulin-like growth factor 2 mRNA binding protein	1e-08
3lqv_A		115	PRE-mRNA branch site protein P14; cysless mutant,	2e-08
1nu4_A		97	U1A RNA binding domain; RNA recognition motif, U1	3e-08
2kt5_A		124	RNA and export factor-binding protein 2; chaperone	5e-08
2la4_A		101	Nuclear and cytoplasmic polyadenylated RNA-bindin	6e-08
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	7e-08
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	5e-04
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	6e-04
1s79_A		103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	7e-08
3ulh_A		107	THO complex subunit 4; nuclear protein, RNA bindin	9e-08
2dgu_A		103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	1e-07
2ytc_A		85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	1e-07
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-07
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	2e-07
2do0_A		114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	4e-07
2i2y_A		150	Fusion protein consists of immunoglobin G- binding	6e-07
1why_A		97	Hypothetical protein riken cDNA 1810017N16; RNA re	6e-07
1x5p_A		97	Negative elongation factor E; structure genomics,	9e-07
2ywk_A		95	Putative RNA-binding protein 11; RRM-domain, struc	1e-06
2nlw_A		105	Eukaryotic translation initiation factor 3 subunit	1e-06
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	1e-06
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	1e-05
2err_A		109	Ataxin-2-binding protein 1; protein-RNA complex, R	1e-06
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	1e-06
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	1e-06
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	6e-04
1fje_B		175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	1e-06
1fje_B		175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-05
2bz2_A		121	Negative elongation factor E; NELF E, RNA recognit	1e-06
4a8x_A		88	RNA-binding protein with serine-rich domain 1; tra	1e-06
3ue2_A		118	Poly(U)-binding-splicing factor PUF60; RNA recogni	2e-06
1wf1_A		110	RNA-binding protein RALY; structural genomics, RRM	2e-06
2cpx_A		115	Hypothetical protein FLJ11016; RRM domain, structu	2e-06
1x4g_A		109	Nucleolysin TIAR; structural genomics, RRM domain,	2e-06
2kvi_A		96	Nuclear polyadenylated RNA-binding protein 3; RNA-	2e-06
2fy1_A		116	RNA-binding motif protein, Y chromosome, family 1	2e-06
2dgv_A		92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	2e-06
2cpj_A		99	Non-POU domain-containing octamer-binding protein;	2e-06
3v4m_A		105	Splicing factor U2AF 65 kDa subunit; canonical RNA	2e-06
1x5o_A		114	RNA binding motif, single-stranded interacting pro	2e-06
1rk8_A		165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	2e-06
2cpd_A		99	Apobec-1 stimulating protein; RNA recognition moti	3e-06
1x4e_A		85	RNA binding motif, single-stranded interacting pro	3e-06
2hvz_A		101	Splicing factor, arginine/serine-rich 7; RRM, RNA	3e-06
2dgp_A		106	Bruno-like 4, RNA binding protein; RRM domain, str	4e-06
2do4_A		100	Squamous cell carcinoma antigen recognized by T- c	4e-06
2e5h_A		94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-06
2cpf_A		98	RNA binding motif protein 19; RNA recognition moti	4e-06
2xs2_A		102	Deleted in azoospermia-like; RNA binding protein-R	6e-06
2yh0_A		198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	6e-06
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	6e-06
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	3e-04
2dgt_A		92	RNA-binding protein 30; RRM domain, structural gen	7e-06
1h2v_Z		156	20 kDa nuclear CAP binding protein; CAP-binding-co	7e-06
2cqc_A		95	Arginine/serine-rich splicing factor 10; RNA recog	8e-06
2dnh_A		105	Bruno-like 5, RNA binding protein; RRM domain, RBD	8e-06
3egn_A		143	RNA-binding protein 40; RNA recognition motif (RRM	8e-06
1x4c_A		108	Splicing factor, arginine/serine-rich 1; structura	9e-06
1x4a_A		109	Splicing factor, arginine/serine-rich 1 (splicing	9e-06
2krb_A		81	Eukaryotic translation initiation factor 3 subunit	9e-06
2dnq_A		90	RNA-binding protein 4B; RRM domain,RBD, structural	1e-05
2kxn_B		129	Transformer-2 protein homolog beta; SR protein, RR	1e-05
2cq0_A		103	Eukaryotic translation initiation factor 3 subunit	1e-05
2pe8_A		105	Splicing factor 45; RRM, protein binding; 2.00A {H	2e-05
3pgw_A		282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	2e-05
1wex_A		104	Hypothetical protein (riken cDNA 2810036L13); stru	2e-05
2dnp_A		90	RNA-binding protein 14; RRM domain, RBD, structura	2e-05
2cqi_A		103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	2e-05
2xnq_A		97	Nuclear polyadenylated RNA-binding protein 3; tran	3e-05
1oo0_B		110	CG8781-PA, drosophila Y14; RNA recognition motif,	3e-05
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	3e-05
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-04
1whw_A		99	Hypothetical protein riken cDNA 1200009A02; RNA re	3e-05
3beg_B		115	Splicing factor, arginine/serine-rich 1; kinase, S	4e-05
2x1f_A		96	MRNA 3'-END-processing protein RNA15; transcriptio	4e-05
3s6e_A		114	RNA-binding protein 39; ferredoxin-like, structura	4e-05
3r27_A		100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	5e-05
1jmt_A		104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	5e-05
2kn4_A		158	Immunoglobulin G-binding protein G, splicing FACT	5e-05
2dit_A		112	HIV TAT specific factor 1 variant; structural geno	5e-05
2ek1_A		95	RNA-binding protein 12; RNA recognition motif, dim	6e-05
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	6e-05
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	3e-04
2voo_A		193	Lupus LA protein; RNA-binding protein, RNA recogni	6e-05
1wg1_A		88	KIAA1579 protein, homolog EXC-7; RBD, structural g	6e-05
3md3_A		166	Nuclear and cytoplasmic polyadenylated RNA-bindin	7e-05
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	7e-05
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	7e-05
3d2w_A		89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	8e-05
2cq3_A		103	RNA-binding protein 9; RRM domain, structural geno	8e-05
3mdf_A		85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	8e-05
1x4h_A		111	RNA-binding protein 28; structural genomics, RRM d	1e-04
3ns6_A		100	Eukaryotic translation initiation factor 3 subuni;	1e-04
1wf0_A		88	TDP-43, TAR DNA-binding protein-43; structural gen	1e-04
2dnm_A		103	SRP46 splicing factor; RRM domain, RBD, structural	1e-04
2dis_A		109	Unnamed protein product; structural genomics, RRM	1e-04
1whx_A		111	Hypothetical protein riken cDNA 1200009A02; RNA re	2e-04
1p27_B		106	RNA-binding protein 8A; nuclear protein, mRNA spli	2e-04
2dnl_A		114	Cytoplasmic polyadenylation element binding protei	2e-04
1fjc_A		96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	2e-04
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	2e-04
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	4e-04
2ku7_A		140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	2e-04
1sjq_A		105	Polypyrimidine tract-binding protein 1; babbab mot	2e-04
2e5g_A		94	U6 snRNA-specific terminal uridylyltransferase 1;	2e-04
2dnz_A		95	Probable RNA-binding protein 23; RNA recognition m	2e-04
2lea_A		135	Serine/arginine-rich splicing factor 2; SR protein	3e-04
2fc9_A		101	NCL protein; structure genomics, RRM_1 domain, str	3e-04
2cqp_A		98	RNA-binding protein 12; RNA recognition motif, RRM	3e-04
2cph_A		107	RNA binding motif protein 19; RNA recognition moti	3e-04
1x5u_A		105	Splicing factor 3B subunit 4 (spliceosome associat	3e-04
1x5s_A		102	Cold-inducible RNA-binding protein; structure geno	3e-04
1iqt_A		75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-04
2jvr_A		111	Nucleolar protein 3; RNA recognition motif, nucleu	4e-04
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04
2e5j_A		97	Methenyltetrahydrofolate synthetase domain contain	5e-04
3ex7_B		126	RNA-binding protein 8A; protein-RNA complex, mRNA	6e-04
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	6e-04
2jrs_A		108	RNA-binding protein 39; RNA binding motif of RBM39	6e-04
2cqg_A		103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	7e-04
2cpz_A		115	CUG triplet repeat RNA-binding protein 1; RRM doma	8e-04
2khc_A		118	Testis-specific RNP-type RNA binding protein; RRM,	8e-04
2cqb_A		102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	9e-04

>2cpi_A CCR4-NOT transcription complex subunit 4; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111	Back alignment and structure

 Score =  137 bits (347), Expect = 2e-38
 Identities = 46/103 (44%), Positives = 69/103 (66%), Gaps = 2/103 (1%)

Query: 19  GRMHLTNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSA 78
                 +VRV+Q+NLV+++GL   LAD ++L+R EYFG++GK+ KV I+ + +     S 
Sbjct: 3   SGSSGASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSY--AGSQ 60

Query: 79  NNSCCVYITYSREDDAIRCIQSVHSYILDGRPLRACFGTTKYC 121
             S   Y+TY R +DA+R IQ V++ ++DGR L+A  GTTKYC
Sbjct: 61  GPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLGTTKYC 103

PyMOL of 2cpi

>2a3j_A U1 small nuclear ribonucleoprotein A; computationally designed protein, RRM, U1A, RNA binding protein; NMR {Homo sapiens} Length = 127	Back alignment and structure

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284	Back alignment and structure

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284	Back alignment and structure

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3h2u_B 3h2v_E Length = 284	Back alignment and structure

>2jvo_A Nucleolar protein 3; nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding, rRNA processing; NMR {Saccharomyces cerevisiae} PDB: 2osq_A Length = 108	Back alignment and structure

>2f3j_A RNA and export factor binding protein 2; RRM domain, RBD domain., transport protein; NMR {Mus musculus} Length = 177	Back alignment and structure

>3s8s_A Histone-lysine N-methyltransferase SETD1A; chromatin modification, transcription regulation, structural genomics, structural genomics consortium; 1.30A {Homo sapiens} Length = 110	Back alignment and structure

>2e44_A Insulin-like growth factor 2 mRNA binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 96	Back alignment and structure

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} PDB: 2f9d_A 2f9j_A 2fho_B Length = 115	Back alignment and structure

>1nu4_A U1A RNA binding domain; RNA recognition motif, U1 small nuclear ribonucleoprotein, R binding domain, RNA binding protein; HET: MLA; 1.80A {Homo sapiens} SCOP: d.58.7.1 PDB: 1drz_A* 1urn_A 3hhn_B* 3egz_A* 1zzn_A* 1u6b_A* 3cun_A* 3cul_A* 3g8s_A* 3g8t_A* 3g96_A* 3g9c_A* 3irw_P* 3mum_P* 3mur_P* 3mut_P* 3muv_P* 3mxh_P* 3p49_B 3r1h_A* ... Length = 97	Back alignment and structure

>2kt5_A RNA and export factor-binding protein 2; chaperone, mRNA processing, mRNA splicing, transport, nucleus, RNA-binding, spliceosome, transport; NMR {Mus musculus} Length = 124	Back alignment and structure

>2la4_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNA recognition, stress granules, nucleus, RNA-binding, transcription; NMR {Saccharomyces cerevisiae} Length = 101	Back alignment and structure

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292	Back alignment and structure

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292	Back alignment and structure

>2ghp_A U4/U6 snRNA-associated splicing factor PRP24; RNA chaperone, RNA binding domain, RNA recognition motif, SP factor, snRNP, spliceosome; 2.70A {Saccharomyces cerevisiae} SCOP: d.58.7.1 d.58.7.1 d.58.7.1 PDB: 2go9_A 2kh9_A Length = 292	Back alignment and structure

>1s79_A Lupus LA protein; RRM, alpha/beta, RNA binding protein, translation; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103	Back alignment and structure

>3ulh_A THO complex subunit 4; nuclear protein, RNA binding, structural genomi center for structural genomics, JCSG, protein structure INI PSI-biology; 2.54A {Homo sapiens} PDB: 1no8_A Length = 107	Back alignment and structure

>2dgu_A Heterogeneous nuclear ribonucleoprotein Q; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dk2_A Length = 103	Back alignment and structure

>2ytc_A PRE-mRNA-splicing factor RBM22; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 85	Back alignment and structure

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175	Back alignment and structure

>3nmr_A Cugbp ELAV-like family member 1; RRM, PRE-mRNA splicing, RNA binding protein-RNA complex; 1.85A {Homo sapiens} PDB: 3nna_A 3nnc_A 2dhs_A 3nnh_A Length = 175	Back alignment and structure

>2do0_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RNA recognition motif, RRM, RNA binding domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114	Back alignment and structure

>2i2y_A Fusion protein consists of immunoglobin G- binding protein G and splicing factor,...; protein-RNA complex RRM alpha-beta sandwich BETA1-alpha1- BETA2-BETA3-alpha2-BETA4; NMR {Streptococcus SP} PDB: 2i38_A Length = 150	Back alignment and structure

>1why_A Hypothetical protein riken cDNA 1810017N16; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 97	Back alignment and structure

>1x5p_A Negative elongation factor E; structure genomics, RRM domain, PARP14, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 97	Back alignment and structure

>2ywk_A Putative RNA-binding protein 11; RRM-domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; 1.54A {Homo sapiens} Length = 95	Back alignment and structure

>2nlw_A Eukaryotic translation initiation factor 3 subunit 9; eukaryotic initiation factor 3 complex, RNA recognition motif; NMR {Homo sapiens} Length = 105	Back alignment and structure

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216	Back alignment and structure

>2qfj_A FBP-interacting repressor; protein-DNA complex; HET: DNA; 2.10A {Homo sapiens} PDB: 3uwt_A 2kxf_A 2kxh_A Length = 216	Back alignment and structure

>2err_A Ataxin-2-binding protein 1; protein-RNA complex, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109	Back alignment and structure

>3sde_A Paraspeckle component 1; RRM, anti parallel right handed coiled-coil, NOPS, DBHS, RNA protein, RNA binding; 1.90A {Homo sapiens} PDB: 3sde_B Length = 261	Back alignment and structure

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167	Back alignment and structure

>1fxl_A Paraneoplastic encephalomyelitis antigen HUD; protein-RNA complex, AU-rich element, transcription/RNA complex; 1.80A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1g2e_A 1fnx_H 1d8z_A 1d9a_A 3hi9_A Length = 167	Back alignment and structure

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175	Back alignment and structure

>1fje_B Nucleolin RBD12, protein C23; RNP, RRM, RNA binding domain, RNA-protein complex, nucleolus, structural protein/RNA complex; NMR {Mesocricetus auratus} SCOP: d.58.7.1 d.58.7.1 PDB: 1rkj_A 2krr_A Length = 175	Back alignment and structure

>4a8x_A RNA-binding protein with serine-rich domain 1; transcription, splicing, RNA processing, nonsense mediated D NMD, HDAC, histone deacetylation; 1.90A {Homo sapiens} Length = 88	Back alignment and structure

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} PDB: 3us5_A 2dny_A Length = 118	Back alignment and structure

>1wf1_A RNA-binding protein RALY; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wf2_A Length = 110	Back alignment and structure

>2cpx_A Hypothetical protein FLJ11016; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 115	Back alignment and structure

>1x4g_A Nucleolysin TIAR; structural genomics, RRM domain, TIA-1 related protein, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109	Back alignment and structure

>2kvi_A Nuclear polyadenylated RNA-binding protein 3; RNA-binding motif, RRM, transcription termination, NUC phosphoprotein; NMR {Saccharomyces cerevisiae} Length = 96	Back alignment and structure

>2fy1_A RNA-binding motif protein, Y chromosome, family 1 member A1; RNA binding protein, structure, protein-RNA complex, RNA stem-loop, structural protein/RNA complex; NMR {Homo sapiens} Length = 116	Back alignment and structure

>2dgv_A HnRNP M, heterogeneous nuclear ribonucleoprotein M; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} PDB: 2dh9_A Length = 92	Back alignment and structure

>2cpj_A Non-POU domain-containing octamer-binding protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99	Back alignment and structure

>3v4m_A Splicing factor U2AF 65 kDa subunit; canonical RNA binding protein, RNA splicing, structural GENO joint center for structural genomics, JCSG; HET: MSE; 1.80A {Mus musculus} PDB: 1o0p_A 1opi_A Length = 105	Back alignment and structure

>1x5o_A RNA binding motif, single-stranded interacting protein 1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114	Back alignment and structure

>1rk8_A CG8781-PA, CG8781-PA protein; mRNA processing, RRM, RBD, NMD, oskar mRNA localization, translation; 1.90A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 1hl6_A 2x1g_A Length = 165	Back alignment and structure

>2cpd_A Apobec-1 stimulating protein; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 99	Back alignment and structure

>1x4e_A RNA binding motif, single-stranded interacting protein 2; structural genomics, RRM domain, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 85	Back alignment and structure

>2hvz_A Splicing factor, arginine/serine-rich 7; RRM, RNA binding protein; NMR {Homo sapiens} Length = 101	Back alignment and structure

>2dgp_A Bruno-like 4, RNA binding protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dgq_A Length = 106	Back alignment and structure

>2do4_A Squamous cell carcinoma antigen recognized by T- cells 3; RRM domaim, RDB, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 100	Back alignment and structure

>2e5h_A Zinc finger CCHC-type and RNA-binding motif- containing protein 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94	Back alignment and structure

>2cpf_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98	Back alignment and structure

>2xs2_A Deleted in azoospermia-like; RNA binding protein-RNA complex; 1.35A {Mus musculus} PDB: 2xs7_A 2xs5_A 2xsf_A Length = 102	Back alignment and structure

>2yh0_A Splicing factor U2AF 65 kDa subunit; PRE-mRNA splicing, transcription, RNA binding protein, mRNA processing; NMR {Homo sapiens} PDB: 2yh1_A Length = 198	Back alignment and structure

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(PGPUPUPGPUPUPUPUPUPUPUPU)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168	Back alignment and structure

>1b7f_A Protein (SXL-lethal protein), RNA (5'-R(PGPUPUPGPUPUPUPUPUPUPUPU)-3; splicing regulation, RNP domain, RNA complex; 2.60A {Drosophila melanogaster} SCOP: d.58.7.1 d.58.7.1 PDB: 3sxl_A* 1sxl_A 2sxl_A Length = 168	Back alignment and structure

>2dgt_A RNA-binding protein 30; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 92	Back alignment and structure

>1h2v_Z 20 kDa nuclear CAP binding protein; CAP-binding-complex, RNP domain, MIF4G domain, RNA maturation, RNA export, nuclear protein, RNA-binding; 2.0A {Homo sapiens} SCOP: d.58.7.1 PDB: 1h2u_X* 1h2t_Z 1n52_B* 1n54_B 3fex_B 3fey_B 1h6k_X Length = 156	Back alignment and structure

>2cqc_A Arginine/serine-rich splicing factor 10; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 95	Back alignment and structure

>2dnh_A Bruno-like 5, RNA binding protein; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} PDB: 2dnk_A 2dno_A Length = 105	Back alignment and structure

>3egn_A RNA-binding protein 40; RNA recognition motif (RRM), RNP motif, U11/U12-65K protein, DI-snRNP, U1A protein, U2B protein; 2.50A {Homo sapiens} Length = 143	Back alignment and structure

>1x4c_A Splicing factor, arginine/serine-rich 1; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 108	Back alignment and structure

>1x4a_A Splicing factor, arginine/serine-rich 1 (splicing factor 2, alternate splicing factor)...; structure genomics, SURP domain, splicing factor SF2; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109	Back alignment and structure

>2krb_A Eukaryotic translation initiation factor 3 subunit B; EIF3, eukaryotic initiation factor, EIF3B, EIF3J; NMR {Homo sapiens} Length = 81	Back alignment and structure

>2dnq_A RNA-binding protein 4B; RRM domain,RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90	Back alignment and structure

>2kxn_B Transformer-2 protein homolog beta; SR protein, RRM, splicing factor, RNA protein complex, SMN, binding protein-RNA complex; NMR {Homo sapiens} PDB: 2rra_A 2rrb_A Length = 129	Back alignment and structure

>2cq0_A Eukaryotic translation initiation factor 3 subunit 4; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103	Back alignment and structure

>2pe8_A Splicing factor 45; RRM, protein binding; 2.00A {Homo sapiens} PDB: 2peh_A Length = 105	Back alignment and structure

>3pgw_A U1-A; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 1fht_A 2u1a_A 2aym_A 2b0g_A Length = 282	Back alignment and structure

>1wex_A Hypothetical protein (riken cDNA 2810036L13); structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.7.1 Length = 104	Back alignment and structure

>2dnp_A RNA-binding protein 14; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 90	Back alignment and structure

>2cqi_A Nucleolysin TIAR; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, ST genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103	Back alignment and structure

>2xnq_A Nuclear polyadenylated RNA-binding protein 3; transcription termination, RNA processi recognition, RRM; HET: CAF; 1.30A {Saccharomyces cerevisiae} PDB: 2xnr_A 2l41_A Length = 97	Back alignment and structure

>1oo0_B CG8781-PA, drosophila Y14; RNA recognition motif, splicing, protein complex, EXON junct complex, signaling protein; 1.85A {Drosophila melanogaster} SCOP: d.58.7.1 PDB: 2hyi_B* 2j0s_D* 2xb2_D* Length = 110	Back alignment and structure

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172	Back alignment and structure

>2g4b_A Splicing factor U2AF 65 kDa subunit; protein-RNA complex, RNA splicing factor, RNA recognition motif, RNA binding protein/RNA complex; 2.50A {Homo sapiens} PDB: 2u2f_A Length = 172	Back alignment and structure

>1whw_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 99	Back alignment and structure

>3beg_B Splicing factor, arginine/serine-rich 1; kinase, SR protein kinase, SR protein, PRE-mRNA splicing, at binding, chromosome partition; HET: SEP ANP; 2.90A {Homo sapiens} SCOP: d.58.7.1 PDB: 2o3d_A 1wg4_A Length = 115	Back alignment and structure

>2x1f_A MRNA 3'-END-processing protein RNA15; transcription-RNA complex, mRNA processing; 1.60A {Saccharomyces cerevisiae} PDB: 2x1b_A 2x1a_A 2km8_B Length = 96	Back alignment and structure

>3s6e_A RNA-binding protein 39; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative, PSI-biology; HET: MSE CIT; 0.95A {Mus musculus} PDB: 2lq5_A Length = 114	Back alignment and structure

>3r27_A HnRNP L, heterogeneous nuclear ribonucleoprotein L; RBD fold, protein binding, nucleus; 2.04A {Homo sapiens} Length = 100	Back alignment and structure

>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline, PPII helix, peptide recognition, RNA binding protein; 2.20A {Homo sapiens} SCOP: d.58.7.3 Length = 104	Back alignment and structure

>2kn4_A Immunoglobulin G-binding protein G, splicing FACT arginine/serine-rich 2, S35, splicing factor SC35,; RRM domain, cell WALL; NMR {Streptococcus SP} Length = 158	Back alignment and structure

>2dit_A HIV TAT specific factor 1 variant; structural genomics, RRM_1 domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 112	Back alignment and structure

>2ek1_A RNA-binding protein 12; RNA recognition motif, dimer, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.00A {Homo sapiens} PDB: 2ek6_A Length = 95	Back alignment and structure

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205	Back alignment and structure

>3tyt_A Heterogeneous nuclear ribonucleoprotein L; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 1.60A {Mus musculus} PDB: 3s01_A 3to8_A Length = 205	Back alignment and structure

>2voo_A Lupus LA protein; RNA-binding protein, RNA recognition motif, systemic lupus erythematosus, phosphoprotein, RNA maturation; 1.8A {Homo sapiens} SCOP: a.4.5.46 d.58.7.1 PDB: 2von_A 2vod_A 2vop_A 1zh5_A 1yty_A 1s7a_A Length = 193	Back alignment and structure

>1wg1_A KIAA1579 protein, homolog EXC-7; RBD, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wi6_A Length = 88	Back alignment and structure

>3md3_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RNP, RBD, poly(U) binding, tandem, acetylation, cytopla nucleus; 2.70A {Saccharomyces cerevisiae} Length = 166	Back alignment and structure

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198	Back alignment and structure

>1qm9_A Polypyrimidine tract-binding protein; ribonucleoprotein, RNP, RNA, spicing, translation; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 Length = 198	Back alignment and structure

>3d2w_A TAR DNA-binding protein 43; DP-43 proteinopathy, TDP-43 inclusions, RNA recognition MOTI U, ALS, RRM; HET: DNA; 1.65A {Mus musculus} Length = 89	Back alignment and structure

>2cq3_A RNA-binding protein 9; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103	Back alignment and structure

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ALT splicing, mRNA processing, mRNA splicing; 1.85A {Homo sapiens} PDB: 2kyx_A 3lpy_A* Length = 85	Back alignment and structure

>1x4h_A RNA-binding protein 28; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111	Back alignment and structure

>3ns6_A Eukaryotic translation initiation factor 3 subuni; 1.25A {Saccharomyces cerevisiae} PDB: 3ns5_A Length = 100	Back alignment and structure

>1wf0_A TDP-43, TAR DNA-binding protein-43; structural genomics, RRM domain, riken structural genomics/proteomics initiative RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 88	Back alignment and structure

>2dnm_A SRP46 splicing factor; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 103	Back alignment and structure

>2dis_A Unnamed protein product; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 109	Back alignment and structure

>1whx_A Hypothetical protein riken cDNA 1200009A02; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 Length = 111	Back alignment and structure

>1p27_B RNA-binding protein 8A; nuclear protein, mRNA splicing; 2.00A {Homo sapiens} SCOP: d.58.7.1 Length = 106	Back alignment and structure

>2dnl_A Cytoplasmic polyadenylation element binding protein 3; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 114	Back alignment and structure

>1fjc_A Nucleolin RBD2, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1 Length = 96	Back alignment and structure

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229	Back alignment and structure

>2adc_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 2evz_A Length = 229	Back alignment and structure

>2ku7_A MLL1 PHD3-CYP33 RRM chimeric protein; transcriptional regulation, RRM domain, transcr; NMR {Homo sapiens} Length = 140	Back alignment and structure

>1sjq_A Polypyrimidine tract-binding protein 1; babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105	Back alignment and structure

>2e5g_A U6 snRNA-specific terminal uridylyltransferase 1; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 94	Back alignment and structure

>2dnz_A Probable RNA-binding protein 23; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95	Back alignment and structure

>2lea_A Serine/arginine-rich splicing factor 2; SR protein, RNA binding protein; NMR {Homo sapiens} PDB: 2leb_A 2lec_A Length = 135	Back alignment and structure

>2fc9_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 101	Back alignment and structure

>2cqp_A RNA-binding protein 12; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 98	Back alignment and structure

>2cph_A RNA binding motif protein 19; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: d.58.7.1 Length = 107	Back alignment and structure

>1x5u_A Splicing factor 3B subunit 4 (spliceosome associated protein 49) (SAP 49) (SF3B50)...; structure genomics,RRM domain,splicing factor 3B; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 105	Back alignment and structure

>1x5s_A Cold-inducible RNA-binding protein; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102	Back alignment and structure

>1iqt_A AUF1, heterogeneous nuclear ribonucleoprotein D0; RNA-binding protein, hnRNP, telomere, DNA-binding protein, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 1wtb_A 1x0f_A Length = 75	Back alignment and structure

>2jvr_A Nucleolar protein 3; RNA recognition motif, nucleus, phosphorylation, ribonucleoprotein, ribosome biogenesis, RNA-binding; NMR {Saccharomyces cerevisiae} PDB: 2osr_A Length = 111	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>2e5j_A Methenyltetrahydrofolate synthetase domain containing; RRM domain, RBD, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 97	Back alignment and structure

>3ex7_B RNA-binding protein 8A; protein-RNA complex, mRNA processing, mRNA splicing, mRNA transport, nonsense-mediated mRNA decay, nucleus; HET: ADP; 2.30A {Homo sapiens} PDB: 2j0q_D* Length = 126	Back alignment and structure

>2cjk_A Nuclear polyadenylated RNA-binding protein 4; HRP1, RNA-binding, RNA processing, mRNA processing, nonsense-mediated mRNA decay, cleavage; NMR {Saccharomyces cerevisiae} PDB: 2km8_C Length = 167	Back alignment and structure

>2jrs_A RNA-binding protein 39; RNA binding motif of RBM39_human (caper), RRM2 domain, solution structure, structural genomics, PSI-2; NMR {Homo sapiens} Length = 108	Back alignment and structure

>2cqg_A TDP-43, TAR DNA-binding protein-43; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 103	Back alignment and structure

>2cpz_A CUG triplet repeat RNA-binding protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2rq4_A 2rqc_A Length = 115	Back alignment and structure

>2khc_A Testis-specific RNP-type RNA binding protein; RRM, RNA recognition motif, bruno; NMR {Drosophila melanogaster} Length = 118	Back alignment and structure

>2cqb_A Peptidyl-prolyl CIS-trans isomerase E; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 102	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

No hit with probability above 80.00

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	E-value
Query		917
d2cpia1		89	d.58.7.1 (A:101-189) E3 ubiquitin protein ligase C	3e-17
d1no8a_		78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	1e-10
d1cvja1		80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	3e-10
d1o0pa_		104	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	2e-09
d2cpha1		94	d.58.7.1 (A:454-547) Probable RNA-binding protein	2e-09
d2cpea1		101	d.58.7.1 (A:353-453) RNA-binding protein EWS {Huma	5e-09
d1x5ta1		83	d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Hu	6e-09
d1b7fa2		85	d.58.7.1 (A:205-289) Sex-lethal protein {Drosophil	1e-08
d2cpja1		86	d.58.7.1 (A:65-150) Non-POU domain-containing octa	2e-08
d1h2vz_		93	d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding pro	2e-08
d2cpfa1		85	d.58.7.1 (A:362-446) Probable RNA-binding protein	3e-08
d1rk8a_		88	d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Dr	4e-08
d1b7fa1		82	d.58.7.1 (A:123-204) Sex-lethal protein {Drosophil	7e-08
d1cvja2		89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	2e-07
d2cqca1		83	d.58.7.1 (A:109-191) Arginine/serine-rich splicing	2e-07
d2cqba1		89	d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomer	2e-07
d1wf2a_		98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	2e-07
d1x5ua1		93	d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Hu	3e-07
d1x4ga1		96	d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo s	3e-07
d1nu4a_		91	d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo	3e-07
d2f9da1		114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	5e-07
d2cqia1		90	d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sa	5e-07
d1uawa_		77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	6e-07
d2ghpa1		81	d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splici	9e-07
d1x0fa1		75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	1e-06
d2cq0a1		90	d.58.7.1 (A:231-320) Eukaryotic translation initia	2e-06
d2u2fa_		85	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-06
d2cq3a1		93	d.58.7.1 (A:110-202) RNA-binding protein 9 {Human	6e-06
d1whwa_		99	d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm	8e-06
d1fjca_		96	d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocrice	8e-06
d2dita1		99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	9e-06
d1hd0a_		75	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	1e-05
d1x4ea1		72	d.58.7.1 (A:8-79) RNA-binding motif, single-strand	1e-05
d1fxla1		82	d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Hom	1e-05
d2ghpa3		86	d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splici	1e-05
d1x4aa1		95	d.58.7.1 (A:9-103) Splicing factor, arginine/serin	2e-05
d1fxla2		85	d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Ho	3e-05
d1u2fa_		90	d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit	3e-05
d2disa1		96	d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {	4e-05
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_		104	d.58.7.3 (A:) 5e-05
d2cpza1		102	d.58.7.1 (A:383-484) CUG triplet repeat RNA-bindin	6e-05
d2cqga1		90	d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TD	7e-05
d1x4ba1		103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	1e-04
d2bz2a1		79	d.58.7.1 (A:35-113) Negative elongation factor E,	2e-04
d1wf0a_		88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-04
d1p1ta_		104	d.58.7.1 (A:) Cleavage stimulation factor, 64 kda	5e-04
d2cpxa1		102	d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41	6e-04
d2cpda1		86	d.58.7.1 (A:223-308) APOBEC1 stimulating protein {	7e-04
d1l3ka2		79	d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1	0.001
d2cqpa1		86	d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mous	0.001
d1u6fa1		139	d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypa	0.001
d2cqha1		80	d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 is	0.002
d1x5sa1		90	d.58.7.1 (A:8-97) Cold-inducible RNA-binding prote	0.002
d1zh5a2		85	d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo	0.003
d1x5oa1		101	d.58.7.1 (A:8-108) RNA-binding motif, single-stran	0.003

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]} Length = 89	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 75.2 bits (184), Expect = 3e-17
 Identities = 40/89 (44%), Positives = 63/89 (70%), Gaps = 2/89 (2%)

Query: 25  NVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCV 84
           +VRV+Q+NLV+++GL   LAD ++L+R EYFG++GK+ KV I+ + +     S   S   
Sbjct: 2   SVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYA--GSQGPSASA 59

Query: 85  YITYSREDDAIRCIQSVHSYILDGRPLRA 113
           Y+TY R +DA+R IQ V++ ++DGR L+A
Sbjct: 60  YVTYIRSEDALRAIQCVNNVVVDGRTLKA 88

PyMOL of d2cpia1

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]} Length = 78	Back information, alignment and structure

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 80	Back information, alignment and structure

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104	Back information, alignment and structure

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 94	Back information, alignment and structure

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]} Length = 101	Back information, alignment and structure

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 83	Back information, alignment and structure

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 85	Back information, alignment and structure

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]} Length = 86	Back information, alignment and structure

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 93	Back information, alignment and structure

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 85	Back information, alignment and structure

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 88	Back information, alignment and structure

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]} Length = 82	Back information, alignment and structure

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 89	Back information, alignment and structure

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]} Length = 83	Back information, alignment and structure

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89	Back information, alignment and structure

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]} Length = 98	Back information, alignment and structure

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 93	Back information, alignment and structure

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 96	Back information, alignment and structure

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]} Length = 91	Back information, alignment and structure

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]} Length = 114	Back information, alignment and structure

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]} Length = 90	Back information, alignment and structure

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]} Length = 77	Back information, alignment and structure

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 81	Back information, alignment and structure

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]} Length = 75	Back information, alignment and structure

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]} Length = 90	Back information, alignment and structure

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 85	Back information, alignment and structure

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]} Length = 93	Back information, alignment and structure

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]} Length = 99	Back information, alignment and structure

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]} Length = 96	Back information, alignment and structure

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 99	Back information, alignment and structure

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]} Length = 75	Back information, alignment and structure

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 72	Back information, alignment and structure

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 82	Back information, alignment and structure

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 86	Back information, alignment and structure

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 95	Back information, alignment and structure

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]} Length = 85	Back information, alignment and structure

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 90	Back information, alignment and structure

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]} Length = 96	Back information, alignment and structure

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]} Length = 104	Back information, alignment and structure

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]} Length = 102	Back information, alignment and structure

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 90	Back information, alignment and structure

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]} Length = 103	Back information, alignment and structure

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]} Length = 79	Back information, alignment and structure

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]} Length = 88	Back information, alignment and structure

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]} Length = 104	Back information, alignment and structure

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]} Length = 102	Back information, alignment and structure

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]} Length = 86	Back information, alignment and structure

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 79	Back information, alignment and structure

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]} Length = 86	Back information, alignment and structure

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]} Length = 139	Back information, alignment and structure

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]} Length = 80	Back information, alignment and structure

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]} Length = 90	Back information, alignment and structure

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]} Length = 85	Back information, alignment and structure

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]} Length = 101	Back information, alignment and structure

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Alignment Graph	Length	Definition	Probability
Query		917
d2cpia1		89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.88
d1rk8a_		88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.68
d1u6fa1		139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.68
d2cqba1		89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.66
d2cq0a1		90	Eukaryotic translation initiation factor 3 subunit	99.66
d2cq3a1		93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.65
d1whwa_		99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d1x5ua1		93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.64
d1fxla1		82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.64
d2ghpa3		86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.63
d1h2vz_		93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.63
d1b7fa1		82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.63
d2cpza1		102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.62
d2cqia1		90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.62
d2f9da1		114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.61
d2cpha1		94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.61
d1no8a_		78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.61
d2u2fa_		85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.61
d1b7fa2		85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.61
d1p1ta_		104	Cleavage stimulation factor, 64 kda subunit {Human	99.61
d1cvja1		80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.61
d2cpja1		86	Non-POU domain-containing octamer-binding protein,	99.61
d1fxla2		85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.6
d1x5sa1		90	Cold-inducible RNA-binding protein {Human (Homo sa	99.6
d1cvja2		89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.6
d1x4ha1		98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.6
d1x4ga1		96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.6
d2cpfa1		85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.59
d1x4ba1		103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.59
d1x5ta1		83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.59
d1whxa_		111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.58
d2adca1		109	Polypyrimidine tract-binding protein {Human (Homo	99.58
d2cqda1		103	RNA-binding region containing protein 1 {Human (Ho	99.58
d2cqca1		83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.58
d2cpea1		101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.58
d1nu4a_		91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.56
d1x4aa1		95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.56
d1x5oa1		101	RNA-binding motif, single-stranded-interacting pro	99.56
d2cqga1		90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.56
d2ghpa1		81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.55
d2cq4a1		101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.55
d2cpxa1		102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.55
d2bz2a1		79	Negative elongation factor E, NELF-E {Human (Homo	99.54
d1wf2a_		98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.54
d1l3ka1		84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.53
d1uawa_		77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.52
d2adca2		88	Polypyrimidine tract-binding protein {Human (Homo	99.52
d2adba1		108	Polypyrimidine tract-binding protein {Human (Homo	99.51
d3begb1		87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.51
d1wi6a1		75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.5
d1hd0a_		75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.5
d1fjca_		96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.5
d2cqha1		80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.49
d2cpda1		86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.49
d1x4ea1		72	RNA-binding motif, single-stranded-interacting pro	99.48
d1zh5a2		85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.48
d1fjeb1		91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.48
d1wg1a_		88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.48
d2msta_		75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.47
d1wf0a_		88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.47
d2ghpa2		75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.47
d1weza_		102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.47
d1l3ka2		79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.47
d2disa1		96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.47
d2b0ga1		83	Splicesomal U1A protein {Drosophila melanogaster [	99.47
d1wi8a_		104	Eukaryotic translation initiation factor 4B {Human	99.46
d1whya_		97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.46
d1u1qa_		183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.46
d1wexa_		104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.45
d1wg4a_		98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.45
d2cqpa1		86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.44
d1x0fa1		75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.44
d1wg5a_		104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.44
d1x4fa1		99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.43
d2cpya1		103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.41
d2cq1a1		88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.4
d1weya_		104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.4
d2dita1		99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.38
d1x4da1		89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.33
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_		104	U2	99.32
d1wela1		112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.3
d1owxa_		113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.25
d1u2fa_		90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.18
d1o0pa_		104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.17
d1u1qa_		183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.14
d2cq2a1		101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.14
d1wwha1		81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.12
d1ufwa_		95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	96.03
d2dgxa1		73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	95.65
d1uw4a_		91	RNA processing protein UPF3x, RRM domain {Human (H	95.46
d1whva_		100	Poly(A)-specific ribonuclease PARN {Mouse (Mus mus	90.65

>d2cpia1 d.58.7.1 (A:101-189) E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: E3 ubiquitin protein ligase CNOT4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.88  E-value=9.4e-23  Score=157.56  Aligned_cols=89  Identities=45%  Similarity=0.802  Sum_probs=80.1

Q ss_pred             CCCCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHCC
Q ss_conf             88642226769995799998736787778842268643799994258987556789970899994989999999998289
Q 002482           24 TNVRVIQRNLVYIIGLPINLADEDLLQRKEYFGQYGKVLKVSISRTATGDIQHSANNSCCVYITYSREDDAIRCIQSVHS  103 (917)
Q Consensus        24 anVRVIQKNLVYVvGLP~sIAeEELLRk~EyFGQYGKIiKIvInrd~~g~~q~~~~psgsAYVTFss~EDA~kAI~ALNG  103 (917)
                      ++|||+|+|+|||+|||+.+++|||++.+|+|++||+|.+|.|.+++.+..  ...++|+|||+|.++++|.+||+.|||
T Consensus         1 ~~~Rviq~n~vyV~nLp~~~t~~~l~~~~e~F~~~G~I~~v~i~~~~~~~~--~~~~~g~aFV~f~~~~~A~~Ai~~lng   78 (89)
T d2cpia1           1 ASVRVVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAG--SQGPSASAYVTYIRSEDALRAIQCVNN   78 (89)
T ss_dssp             SCCCCCCSSCEEEEEECTTTCCHHHHHSTTTTTTTSCEEEEEEECCSSCCS--SSCCCEEEEEEESSHHHHHHHHHHHTT
T ss_pred             CCEEEEECCEEEEECCCCCCCHHHHHHHHHHHCCCCCCEEEEEEECCCCCC--CCCCCEEEEEECCCCHHHHHHHHHHCC
T ss_conf             965598268899979897638789998898763558825877720267687--777653799851541229999998589


Q ss_pred             CCCCCEEEEEE
Q ss_conf             86699069996
Q 002482          104 YILDGRPLRAC  114 (917)
Q Consensus       104 s~LdGRvLRAS  114 (917)
                      ..++||.|||+
T Consensus        79 ~~~~gr~lkvS   89 (89)
T d2cpia1          79 VVVDGRTLKAS   89 (89)
T ss_dssp             EEETTEEEEEE
T ss_pred             CEECCEEEEEC
T ss_conf             99999788879

PyMOL of d2cpia1

>d1rk8a_ d.58.7.1 (A:) RNA-binding protein 8 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}	Back information, alignment and structure

>d1u6fa1 d.58.7.1 (A:1-139) RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId: 5693]}	Back information, alignment and structure

>d2cqba1 d.58.7.1 (A:1-89) Peptidyl-prolyl cis-trans isomerase E, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq0a1 d.58.7.1 (A:231-320) Eukaryotic translation initiation factor 3 subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq3a1 d.58.7.1 (A:110-202) RNA-binding protein 9 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whwa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x5ua1 d.58.7.1 (A:7-99) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fxla1 d.58.7.1 (A:37-118) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ghpa3 d.58.7.1 (A:206-291) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1h2vz_ d.58.7.1 (Z:) CBP20, 20KDa nuclear cap-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1b7fa1 d.58.7.1 (A:123-204) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d2cpza1 d.58.7.1 (A:383-484) CUG triplet repeat RNA-binding protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqia1 d.58.7.1 (A:1-90) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2f9da1 d.58.7.1 (A:12-125) Pre-mRNA branch site protein p14 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpha1 d.58.7.1 (A:454-547) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1no8a_ d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1b7fa2 d.58.7.1 (A:205-289) Sex-lethal protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d1p1ta_ d.58.7.1 (A:) Cleavage stimulation factor, 64 kda subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1cvja1 d.58.7.1 (A:11-90) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpja1 d.58.7.1 (A:65-150) Non-POU domain-containing octamer-binding protein, NonO {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1fxla2 d.58.7.1 (A:119-203) Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x5sa1 d.58.7.1 (A:8-97) Cold-inducible RNA-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1cvja2 d.58.7.1 (A:91-179) Poly(A)-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4ha1 d.58.7.1 (A:8-105) RNA-binding protein 28 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x4ga1 d.58.7.1 (A:8-103) Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpfa1 d.58.7.1 (A:362-446) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x4ba1 d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucleoproteins A2/B1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x5ta1 d.58.7.1 (A:8-90) Splicing factor 3B subunit 4 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whxa_ d.58.7.1 (A:) Probable RNA-binding protein 19, Rbm19 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2adca1 d.58.7.1 (A:335-443) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqda1 d.58.7.1 (A:1-103) RNA-binding region containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqca1 d.58.7.1 (A:109-191) Arginine/serine-rich splicing factor 10 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpea1 d.58.7.1 (A:353-453) RNA-binding protein EWS {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1nu4a_ d.58.7.1 (A:) Splicesomal U1A protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4aa1 d.58.7.1 (A:9-103) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x5oa1 d.58.7.1 (A:8-108) RNA-binding motif, single-stranded-interacting protein 1, RBMS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqga1 d.58.7.1 (A:96-185) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ghpa1 d.58.7.1 (A:116-196) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpxa1 d.58.7.1 (A:291-392) RNA-binding protein 41, RBM41 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2bz2a1 d.58.7.1 (A:35-113) Negative elongation factor E, NELF-E {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wf2a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoproteins C1/C2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1uawa_ d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2adca2 d.58.7.1 (A:444-531) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2adba1 d.58.7.1 (A:177-284) Polypyrimidine tract-binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d3begb1 d.58.7.1 (B:121-207) Splicing factor, arginine/serine-rich 1, SFRS1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wi6a1 d.58.7.1 (A:69-143) Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1hd0a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein d0 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fjca_ d.58.7.1 (A:) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}	Back information, alignment and structure

>d2cqha1 d.58.7.1 (A:2-81) IGF-II mRNA-binding protein 2 isoform A {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cpda1 d.58.7.1 (A:223-308) APOBEC1 stimulating protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4ea1 d.58.7.1 (A:8-79) RNA-binding motif, single-stranded-interacting protein 2, RBMS2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1zh5a2 d.58.7.1 (A:105-189) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1fjeb1 d.58.7.1 (B:1-91) Nucleolin {Golden hamster (Mesocricetus auratus) [TaxId: 10036]}	Back information, alignment and structure

>d1wg1a_ d.58.7.1 (A:) Probable RNA-binding protein KIAA1579 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2msta_ d.58.7.1 (A:) Neural RNA-binding protein Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wf0a_ d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2ghpa2 d.58.7.1 (A:41-115) U4/U6 snRNA-associated-splicing factor PRP24 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1weza_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1l3ka2 d.58.7.1 (A:103-181) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2disa1 d.58.7.1 (A:8-103) Hypothetical protein FLJ20273 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2b0ga1 d.58.7.1 (A:1-83) Splicesomal U1A protein {Drosophila melanogaster [TaxId: 7227]}	Back information, alignment and structure

>d1wi8a_ d.58.7.1 (A:) Eukaryotic translation initiation factor 4B {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whya_ d.58.7.1 (A:) Putative RNA-binding protein 15B, Rbm15b {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wexa_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein L-like {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wg4a_ d.58.7.1 (A:) Splicing factor, arginine/serine-rich 9 (SFRS9) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cqpa1 d.58.7.1 (A:917-1002) RNA-binding protein 12 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x0fa1 d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wg5a_ d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprotein H' {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4fa1 d.58.7.1 (A:8-106) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cpya1 d.58.7.1 (A:536-638) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq1a1 d.58.7.1 (A:51-138) Polypyrimidine tract-binding protein 2, PTBP2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1weya_ d.58.7.1 (A:) Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2dita1 d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1x4da1 d.58.7.1 (A:8-96) Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1jmta_ d.58.7.3 (A:) U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wela1 d.58.7.1 (A:412-523) RNA-binding protein 12 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1owxa_ d.58.7.1 (A:) Lupus LA protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1u2fa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1o0pa_ d.58.7.1 (A:) Splicing factor U2AF 65 KDa subunit {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1u1qa_ d.58.7.1 (A:) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cq2a1 d.58.7.1 (A:25-125) Alkylation repair AlkB homolog 8, ALKBH8 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ufwa_ d.58.7.1 (A:) Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2dgxa1 d.58.7.1 (A:563-635) Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1uw4a_ d.58.7.4 (A:) RNA processing protein UPF3x, RRM domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1whva_ d.58.7.1 (A:) Poly(A)-specific ribonuclease PARN {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure