Citrus Sinensis ID: 003091

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-------85

MEELKHEQEMRERRNQEREHWRDGRHTESSAPSSRFDELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKEGATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALPTSKSPEHEKESGTTYAAGRSRRAEPERTLTDSQRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAEKQRGYELDDDLKSAHSQSSSGRYSRGWKETNMEAESMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASKWALEDDESDDEQKRSSRGLGLSYSSSGSENAGDGPSKADDVDFTIDASIPVQPDSGMNEEQRQKLRRLEVSLIEYRESLEERGIKSSEEIEKKVAIHRKRLESEYGLADPNEDVSGNKRRDRRDEILDSRKRHRSQSQSESPPPRKSSIRDRERESDLDRDRERHRDRDRAHDFESERGRERREKSGSRERDDHDRDRGRDRDRDRRRRVK

ccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccEEEccccccccHHHHHHHHcccccEEEEEEcccccHHHccccccEEEEEEccHHHHHHHHHHccccEEccEEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccccccccccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccHHHHHHcccHHHHHHccccHHHHHHHHHHccccccccHHHHHHHcccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccHHcccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccHHHHHHHHcc

cHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHcccccccccccccccccccEEEEEcccccccHHHHHHHHccccccEEEEEEccccHHHHccccccEEEEEccHHHHHHHHHHccccEEccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccHEEEEcccccccEEEEEEEEEEccccccccccccccEEcccccEccccccccccccccccccccccHccccccccccccccHHHHHHHHHHHHHccHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHccccccccccccccccccHHccccccccccccccccccccccccccccHHHHccccHHHHHHHHHHccccccccHHHHHHHHcccccccccccccccccccccccccccccccccHHHccccHcccccccccccccHHHHHcccccccccccccccccHHcccccccccccccccccccccccccccHHccccccccccccccccccccccccccccHHccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHcccccHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccc

MEELKHEQEMRERRNQErehwrdgrhtessapssrfdelpddfdpsgklpgsfddgdpqttnlyvgnlspqvdenfllrtfgrfgpiasvkimwprtEEERRRQRNcgfvafmnradgqaakdemQGVVVYEYELKigwgksvalpsqalpapppgqmairskegatvilsgpsgppvttvpsqnselvltpnvpdimvippedrhlrHVIDTLALYVLDGGCAFEQAImergrgnplFNFLFELGSKEHTYYVWRLYsfaqgdtlqrwrtepfimitgsgrwippalptskspehekesgttyaagrsrraepertltdsqRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTEsltlketpiptKVARLMLVSDVlhnssapvknasaYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFlrsgnsgvtpfhsicgdapeidkknnsedtcdlsktnQDTALAMGKGAAIKELMNLPLSELERRcrhnglslvgGREMMVARLLSLEDAEKqrgyeldddlksahsqsssgrysrgwketnMEAEsmglsgwngyeedeklsqavgsvplgtmlttpqpeikaftkkekndpvlpaskwaleddesddeqkrssrglglsysssgsenagdgpskaddvdftidasipvqpdsgmneEQRQKLRRLEVSLIEYRESLEERGIKSSEEIEKKVAIHRKRLeseygladpnedvsgnkrrdrRDEILDsrkrhrsqsqsesppprkssirdreresdldrdrerhrdrdrahdfesergrerreksgsrerddhdrdrgrdrdrdrrrrvk

meelkheqEMRERrnqerehwrdgrhtessapssrfdELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRtfgrfgpiasvkimwprtEEERRRQRNCGFVAFMNradgqaakdemQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKEGATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPAlptskspehekesgttyaagrsrraepertltdsqrdeFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTesltlketpiPTKVARLMLVSDVLHnssapvknasayrTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNglslvggrEMMVARLLSLEDAEKQRGYeldddlksahsqsssgrysrgwketNMEAESMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKaftkkekndpvlpaskwaleddesddeqkrssrglglsysssgsenagdgpskADDVDFTIDAsipvqpdsgmneeqrQKLRRLEVSLIEYREsleergiksseeiEKKVAIHRkrleseygladpnedvsgnkrrdrrdeildsrkrhrsqsqsesppprkssirdreresdldrdrerhrdrdrahdfesergrerreksgsrerddhdrdrgrdrdrdrrrrvk

MEELKHeqemrerrnqereHWRDGRHTESSAPSSRFDELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSValpsqalpapppGQMAIRSKEGATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALPTSKSPEHEKESGTTYAAGRSRRAEPERTLTDSQRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAEKQRGYELDDDLKSAHSQSSSGRYSRGWKETNMEAESMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASKWALEDDESDDEQKrssrglglsysssgsENAGDGPSKADDVDFTIDASIPVQPDSGMNEEQRQKLRRLEVSLIEYRESLEERGIKSSEEIEKKVAIHRKRLESEYGLADPNEDVSGNKRRDRRDEILDSRKRHrsqsqsesppprkssirdreresdldrdrerhrdrdrAHDFesergrerreksgsrerddhdrdrgrdrdrdrrrrVK

*************************************************************NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTE****RQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSV********************************************LVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIP*****************************************************QIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICG*******************************AAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLL*****************************************************************************************************************************************************************************************************************************************************************************************************************

MEELKH******************************************************TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPR******RQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQM*****************************LVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLY****************************************************************RDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITG*ITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLR***************************************************************************************************************************************************************************************************************************************************LEVSLIE*****************************************************************************************************************************************

*************************************ELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKEGATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALP*********************************RDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAEKQRGY*********************WKETNMEAESMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASKWAL*********************************KADDVDFTIDASIPVQPDSGMNEEQRQKLRRLEVSLIEYRESLEERGIKSSEEIEKKVAIHRKRLESEYGLADPNEDVSGNKRRDRRDEIL************************************************************************************

*****HEQEMRERRN*************************************FDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMA***************************ELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALPT***************************LTDSQRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGN******************************TNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAE**R************************************************************************************************************************************************EQRQKLRRLEVSLIEYRESLEERGIKSSEEIEKKVAIHRKRLESEYGL********************************************************************************************************

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MEELKHEQEMRERRNQEREHWRDGRHTESSAPSSRFDELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKEGATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALPTSKSPEHEKESGTTYAAGRSRRAEPERTLTDSQxxxxxxxxxxxxxxxxxxxxxMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAEKQRGYELDDDLKSAHSQSSSGRYSRGWKETNMEAESMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASKWALEDDESDDEQKRSSRGLGLSYSSSGSENAGDGPSKADDVDFTIDASIPVQPDSGMxxxxxxxxxxxxxxxxxxxxxLEERGIKSSEEIEKKVAIHRKRLESEYGLADPNEDVSGNKRRDRRDEILDSRKRHRSQSQSESPPPRKSSIRDRERESDLDRDRERHRDRDRAHDFESERGRERREKSGSRERDDHDRDRGRDRDRDRRRRVK

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		848	2.2.26 [Sep-21-2011]
Q5R7X2		1028	U2 snRNP-associated SURP	yes	no	0.525	0.433	0.402	9e-97
O15042		1029	U2 snRNP-associated SURP	yes	no	0.525	0.433	0.401	1e-96
Q6NV83		1029	U2 snRNP-associated SURP	yes	no	0.525	0.433	0.399	3e-96
P32831		672	Negative growth regulator	yes	no	0.099	0.125	0.344	1e-08
Q9LEB3		428	Polyadenylate-binding pro	N/A	no	0.100	0.198	0.340	8e-08
F4I3B3		445	Polyadenylate-binding pro	no	no	0.097	0.186	0.326	5e-07
Q10200		466	Uncharacterized protein C	yes	no	0.227	0.414	0.235	7e-07
Q9SX80		434	Polyadenylate-binding pro	no	no	0.107	0.209	0.323	1e-06
Q9SX79		432	Polyadenylate-binding pro	no	no	0.107	0.210	0.313	1e-06
Q15415		496	RNA-binding motif protein	no	no	0.155	0.266	0.277	1e-06

>sp\|Q5R7X2\|SR140_PONAB U2 snRNP-associated SURP motif-containing protein OS=Pongo abelii GN=U2SURP PE=2 SV=1	Back alignment and function desciption

 Score =  355 bits (911), Expect = 9e-97,   Method: Compositional matrix adjust.
 Identities = 193/480 (40%), Positives = 274/480 (57%), Gaps = 34/480 (7%)

Query: 2   EELKHEQEMRERRNQER---------EHWRDGRHTESSAPSSRF-DELPDDFDPSGKLPG 51
           EELK  QE R+ R++ +         +   DG+     APS R    + DD+      PG
Sbjct: 209 EELKQIQEERDERHKTKGRLSRFEPPQSDSDGQRRSMDAPSRRNRSSVLDDY-----APG 263

Query: 52  SFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVA 111
           S D GDP TTNLY+GN++PQ++E  L + FGRFGP+ASVKIMWPRT+EER R+RNCGFVA
Sbjct: 264 SHDVGDPSTTNLYLGNINPQMNEEMLCQEFGRFGPLASVKIMWPRTDEERARERNCGFVA 323

Query: 112 FMNRADGQAAKDEMQGVVVYEYELKIGWGKSV-----------ALPSQALPAPPPGQMAI 160
           FMNR D + A   + G ++  +E+K+GWGK+V           ++    LP PPP  +  
Sbjct: 324 FMNRRDAERALKNLNGKMIMSFEMKLGWGKAVPIPPHPIYIPPSMMEHTLP-PPPSGLPF 382

Query: 161 RSKEGATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLD 220
            ++      L  P+  P+   P    +   T +   + V+ P +R+L  +I  +  +V+ 
Sbjct: 383 NAQPRER--LKNPNA-PMLPPPKNKEDFEKTLSQAIVKVVIPTERNLLALIHRMIEFVVR 439

Query: 221 GGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGS 280
            G  FE  IM R   NP+F FLFE  +  H YY W+LYS  QGD+  +WRTE F M    
Sbjct: 440 EGPMFEAMIMNREINNPMFRFLFENQTPAHVYYRWKLYSILQGDSPTKWRTEDFRMFKNG 499

Query: 281 GRWIPPALPTSKSPEHEKESGTTYAAGRSRRAEPERTLTDSQRDEFEDMLRALTLERSQI 340
             W PP L        E++    +    S++      L + QRD+ E++LR LT  ++ I
Sbjct: 500 SFWRPPPLNPYLHGMSEEQETEAFVEEPSKKG----ALKEEQRDKLEEILRGLTPRKNDI 555

Query: 341 KEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYR 400
            +AM F L+NA+AA EIV+ +TESL++ +TP+P K+ARL LVSDVL+NSSA V NAS YR
Sbjct: 556 GDAMVFCLNNAEAAEEIVDCITESLSILKTPLPKKIARLYLVSDVLYNSSAKVANASYYR 615

Query: 401 TKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFL 460
             FE  L  I    N  YR+I G + +E  K+RV+   + W DW ++ + ++  L+  FL
Sbjct: 616 KFFETKLCQIFSDLNATYRTIQGHLQSENFKQRVMTCFRAWEDWAIYPEPFLIKLQNIFL 675

Pongo abelii (taxid: 9601)

>sp\|O15042\|SR140_HUMAN U2 snRNP-associated SURP motif-containing protein OS=Homo sapiens GN=U2SURP PE=1 SV=2	Back alignment and function description

>sp\|Q6NV83\|SR140_MOUSE U2 snRNP-associated SURP motif-containing protein OS=Mus musculus GN=U2surp PE=1 SV=3	Back alignment and function description

>sp\|P32831\|NGR1_YEAST Negative growth regulatory protein NGR1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NGR1 PE=1 SV=2	Back alignment and function description

>sp\|Q9LEB3\|RBP47_NICPL Polyadenylate-binding protein RBP47 OS=Nicotiana plumbaginifolia GN=RBP47 PE=1 SV=1	Back alignment and function description

>sp\|F4I3B3\|RB47A_ARATH Polyadenylate-binding protein RBP47A OS=Arabidopsis thaliana GN=RBP47A PE=2 SV=1	Back alignment and function description

>sp\|Q10200\|YBY1_SCHPO Uncharacterized protein C11C11.01 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPBC11C11.01 PE=1 SV=2	Back alignment and function description

>sp\|Q9SX80\|R47CP_ARATH Polyadenylate-binding protein RBP47C' OS=Arabidopsis thaliana GN=RBP47C' PE=2 SV=1	Back alignment and function description

>sp\|Q9SX79\|RB47C_ARATH Polyadenylate-binding protein RBP47C OS=Arabidopsis thaliana GN=RBP47C PE=2 SV=1	Back alignment and function description

>sp\|Q15415\|RBY1F_HUMAN RNA-binding motif protein, Y chromosome, family 1 member F/J OS=Homo sapiens GN=RBMY1F PE=2 SV=2	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		848
224089390		988	predicted protein [Populus trichocarpa]	0.974	0.836	0.840	0.0
224141985		955	predicted protein [Populus trichocarpa]	0.949	0.842	0.832	0.0
296082150		941	unnamed protein product [Vitis vinifera]	0.929	0.837	0.821	0.0
356526679		972	PREDICTED: U2 snRNP-associated SURP moti	0.959	0.837	0.804	0.0
147857263		1384	hypothetical protein VITISV_025939 [Viti	0.892	0.546	0.833	0.0
356560817		971	PREDICTED: U2 snRNP-associated SURP moti	0.965	0.843	0.809	0.0
255548712		979	RNA binding protein, putative [Ricinus c	0.966	0.837	0.818	0.0
449441850		961	PREDICTED: U2 snRNP-associated SURP moti	0.933	0.824	0.826	0.0
357517325		1139	U2-associated protein SR140 [Medicago tr	0.890	0.662	0.795	0.0
297812707		948	RNA recognition motif-containing protein	0.959	0.858	0.728	0.0

>gi\|224089390\|ref\|XP_002308714.1\| predicted protein [Populus trichocarpa] gi\|222854690\|gb\|EEE92237.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score = 1355 bits (3508), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 709/844 (84%), Positives = 764/844 (90%), Gaps = 18/844 (2%)

Query: 1   MEELKHEQEMRERRNQEREHWRDGRHTESSAPSSRFDELPDDFDPSGKLPGSFDDGDPQT 60
           MEELKHE EMRERRNQEREHWR+GRHTESSAPSSRFDELPDDFDPSGKLPGSFDDGDPQT
Sbjct: 127 MEELKHEHEMRERRNQEREHWREGRHTESSAPSSRFDELPDDFDPSGKLPGSFDDGDPQT 186

Query: 61  TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQA 120
           TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQA
Sbjct: 187 TNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQA 246

Query: 121 AKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKE----------GATVIL 170
           AKDEMQGV+VYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKE          GATVIL
Sbjct: 247 AKDEMQGVIVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKEVCYGFLPKPIGATVIL 306

Query: 171 SGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIM 230
           SGPSGPPVT+VP+QNSELVLTPNVPDIMV PPED HLRHVIDT+ALYVLDGGCAFEQAIM
Sbjct: 307 SGPSGPPVTSVPNQNSELVLTPNVPDIMVAPPEDDHLRHVIDTMALYVLDGGCAFEQAIM 366

Query: 231 ERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALPT 290
           +RGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRW+PP+LPT
Sbjct: 367 QRGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWVPPSLPT 426

Query: 291 SKSPEHEKESGTTYAAGRSRRAEPERTLTDSQRDEFEDMLRALTLERSQIKEAMGFALDN 350
           +KSPEHEKESG+T+AAGRSRR +PERTLTD QRDEFEDMLRALTLERSQIK+AMGFALDN
Sbjct: 427 AKSPEHEKESGSTHAAGRSRRVDPERTLTDPQRDEFEDMLRALTLERSQIKDAMGFALDN 486

Query: 351 ADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDI 410
            DAAGE+VEVLTESLTLKETPIPTKVARLMLVSD+LHNSSAPVKNASAYRTKFEA LPDI
Sbjct: 487 VDAAGEVVEVLTESLTLKETPIPTKVARLMLVSDILHNSSAPVKNASAYRTKFEAALPDI 546

Query: 411 MESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPF 470
           MESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRS NSGV PF
Sbjct: 547 MESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSSNSGVIPF 606

Query: 471 HSICGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLS 530
           HS+CGDAPEI+KKN++EDT D  KTNQD ALAMGKGAA KELM+LPL+ELERRCRHNGLS
Sbjct: 607 HSMCGDAPEIEKKNSTEDTVDGGKTNQDAALAMGKGAATKELMDLPLAELERRCRHNGLS 666

Query: 531 LVGGREMMVARLLSLEDAEKQRGYELDDDLKSAHSQSSSGRYSRGWKETNMEAESMGLSG 590
           LVGGRE MVARLL+LE+AEKQRGYELD DLK A S SSS RYS   +E N++   +GL+G
Sbjct: 667 LVGGRETMVARLLNLEEAEKQRGYELDGDLKIAQSNSSSSRYSSVHREVNVDPGPVGLTG 726

Query: 591 WNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASKWALEDDESDDEQK 650
           WN Y ED+  SQ   SV L + L  PQPE+KAF KKEKNDPVLPASKWA +DDESDDEQK
Sbjct: 727 WNIYGEDDTPSQNKRSVSLVSTLPIPQPELKAFAKKEKNDPVLPASKWARDDDESDDEQK 786

Query: 651 RSSRGLGLSYSSSGSENAGDGPSKADDVDFTIDASIPVQPDSGMNEEQRQKLRRLEVSLI 710
           RS R LGLSYSSSGSENAGDG  K D+++F  DASIP QP+SGMNEEQRQKLRRLEV+LI
Sbjct: 787 RSVRDLGLSYSSSGSENAGDGQGKEDEMEFATDASIPTQPESGMNEEQRQKLRRLEVALI 846

Query: 711 EYRESLEERGIKSSEEIEKKVAIHRKRLESEYGLADPNEDVSGNK-----RRDRRDEILD 765
           EYRESLEE+G+K+SEE E+KVA+HRKRLESEYGL+  NEDV+GNK     RRDRRD+  +
Sbjct: 847 EYRESLEEQGMKNSEEFERKVAVHRKRLESEYGLSSSNEDVTGNKRISSERRDRRDDNHE 906

Query: 766 -SRKRHRSQSQSESPPPRKSSIRDRERESDLDRDRERHRDRDRAHDFESE-RGRERREKS 823
            SRKRHRS+S+SES P RK S+RDRERE D D+DRERHR+RDR ++ ESE R R+ REKS
Sbjct: 907 SSRKRHRSESRSES-PQRKLSLRDREREHDSDKDRERHRERDRGNNLESERRDRDYREKS 965

Query: 824 GSRE 827
           GS+E
Sbjct: 966 GSKE 969

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|224141985\|ref\|XP_002324341.1\| predicted protein [Populus trichocarpa] gi\|222865775\|gb\|EEF02906.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

>gi\|296082150\|emb\|CBI21155.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356526679\|ref\|XP_003531944.1\| PREDICTED: U2 snRNP-associated SURP motif-containing protein-like [Glycine max]	Back alignment and taxonomy information

>gi\|147857263\|emb\|CAN79213.1\| hypothetical protein VITISV_025939 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356560817\|ref\|XP_003548683.1\| PREDICTED: U2 snRNP-associated SURP motif-containing protein-like [Glycine max]	Back alignment and taxonomy information

>gi\|255548712\|ref\|XP_002515412.1\| RNA binding protein, putative [Ricinus communis] gi\|223545356\|gb\|EEF46861.1\| RNA binding protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|449441850\|ref\|XP_004138695.1\| PREDICTED: U2 snRNP-associated SURP motif-containing protein-like [Cucumis sativus] gi\|449493301\|ref\|XP_004159248.1\| PREDICTED: U2 snRNP-associated SURP motif-containing protein-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357517325\|ref\|XP_003628951.1\| U2-associated protein SR140 [Medicago truncatula] gi\|355522973\|gb\|AET03427.1\| U2-associated protein SR140 [Medicago truncatula]	Back alignment and taxonomy information

>gi\|297812707\|ref\|XP_002874237.1\| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata] gi\|297320074\|gb\|EFH50496.1\| RNA recognition motif-containing protein [Arabidopsis lyrata subsp. lyrata]	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		848
TAIR\|locus:2179295		946	RRC1 "reduced red-light respon	0.721	0.646	0.773	6.4e-298
TAIR\|locus:2183775		947	AT5G10800 [Arabidopsis thalian	0.746	0.668	0.723	6.4e-287
UNIPROTKB\|F1MHP1		1035	U2SURP "Uncharacterized protei	0.504	0.413	0.406	7e-92
UNIPROTKB\|E2R1V3		1028	U2SURP "Uncharacterized protei	0.504	0.416	0.407	1.1e-91
UNIPROTKB\|O15042		1029	U2SURP "U2 snRNP-associated SU	0.504	0.415	0.406	1.5e-91
UNIPROTKB\|F1SKE6		1029	U2SURP "Uncharacterized protei	0.504	0.415	0.406	1.5e-91
RGD\|1307882		985	U2surp "U2 snRNP-associated SU	0.504	0.434	0.404	3.8e-91
UNIPROTKB\|E1C0P9		985	U2SURP "Uncharacterized protei	0.504	0.434	0.406	6.2e-91
MGI\|MGI:1915208		1029	U2surp "U2 snRNP-associated SU	0.504	0.415	0.404	6.2e-91
UNIPROTKB\|E7ET15		1028	U2SURP "U2 snRNP-associated SU	0.504	0.416	0.402	1.7e-90

TAIR\|locus:2179295 RRC1 "reduced red-light responses in cry1cry2 background 1" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 2477 (877.0 bits), Expect = 6.4e-298, Sum P(2) = 6.4e-298
 Identities = 487/630 (77%), Positives = 538/630 (85%)

Query:    22 RDGRHTESSAPSSRFDELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRTF 81
             RD R  +SS PSSRFDELPDDFDPSG+ PGSFDDGDPQTTNLYVGNLSP+VDENFLLRTF
Sbjct:   143 RD-RQGDSS-PSSRFDELPDDFDPSGR-PGSFDDGDPQTTNLYVGNLSPKVDENFLLRTF 199

Query:    82 GRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGK 141
             GRFGPIASVKIMWPRT+EE+RRQRNCGFV+FMNRADGQAAKDEMQG++VYEYELKIGWGK
Sbjct:   200 GRFGPIASVKIMWPRTDEEKRRQRNCGFVSFMNRADGQAAKDEMQGIIVYEYELKIGWGK 259

Query:   142 SVXXXXXXXXXXXXGQMAIRSKEGATVILSGPSGPPV-TTVPSQNSELVLTPNVPDIMVI 200
             +V            G MAIRSKEG  ++ SG +GPP+ T+VP+QNSELVLTPNVPDI V+
Sbjct:   260 AVSLPSQALPAPPPGHMAIRSKEGCNLVFSGQTGPPIITSVPNQNSELVLTPNVPDITVV 319

Query:   201 PPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSF 260
              PED HLRHVIDTLALYVLDG CAFEQAIMERGRGNPLF F+FELGSKEHTYYVWRLYSF
Sbjct:   320 TPEDEHLRHVIDTLALYVLDGECAFEQAIMERGRGNPLFKFMFELGSKEHTYYVWRLYSF 379

Query:   261 AQGDTLQRWRTEPFIMITGSGRWIPPALPTSKSPEHEKESGTTYAAGRSRRAEPERTLTD 320
             AQGDTLQRWRTEP+IMITGSGRWIPP LP +++ EHEKES +TYAAGR+RRAE ERTLTD
Sbjct:   380 AQGDTLQRWRTEPYIMITGSGRWIPPPLPVTRTQEHEKESASTYAAGRTRRAEVERTLTD 439

Query:   321 SQRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLM 380
              QRDEFEDMLRALTLERSQIKEAMGFALDNADAAGE+VEVLTESLTLKET IPTKVARLM
Sbjct:   440 PQRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEVVEVLTESLTLKETSIPTKVARLM 499

Query:   381 LVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQV 440
             LVSD+LHNSSA VKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQV
Sbjct:   500 LVSDILHNSSARVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQV 559

Query:   441 WSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSEDTCDLSKTNQDTA 500
             W+DWFLFSDAY+ GLR+TFLRSG SGVT FHSICGDAPEI+ K+ +++  D+ K N D A
Sbjct:   560 WADWFLFSDAYIYGLRSTFLRSGVSGVTSFHSICGDAPEIENKSYADNMSDIGKINPDAA 619

Query:   501 LAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAEKQRGYELDDDL 560
             LA+GKGAA +ELMNLP++ELERRCRHNGLSLVGGR MMV RLLSLED EKQRGYE  D++
Sbjct:   620 LAIGKGAARQELMNLPIAELERRCRHNGLSLVGGRVMMVTRLLSLEDTEKQRGYEAVDEI 679

Query:   561 KSAHSQSSSGRYSRGWKETNMEAESMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEI 620
                H Q+ S      W+E   E E +     N Y E E + + V    L T +  PQPE+
Sbjct:   680 PK-HPQNHST-----WEEVKSEREHIK----NSYAEVE-MKEPVN---LPTTIPIPQPEL 725

Query:   621 KAFTKKEKNDPVLPASKWALEDDESDDEQK 650
             KAF  KEKN+ +LPASKWA +DDE+DDEQK
Sbjct:   726 KAFVGKEKNELILPASKWARDDDEADDEQK 755

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA;ISS

GO:0005634 "nucleus" evidence=ISM

GO:0000278 "mitotic cell cycle" evidence=RCA

GO:0000394 "RNA splicing, via endonucleolytic cleavage and ligation" evidence=RCA

GO:0000956 "nuclear-transcribed mRNA catabolic process" evidence=RCA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=RCA

GO:0006396 "RNA processing" evidence=RCA

GO:0007346 "regulation of mitotic cell cycle" evidence=RCA

GO:0009887 "organ morphogenesis" evidence=RCA

GO:0009888 "tissue development" evidence=RCA

GO:0010228 "vegetative to reproductive phase transition of meristem" evidence=RCA

GO:0010413 "glucuronoxylan metabolic process" evidence=RCA

GO:0010638 "positive regulation of organelle organization" evidence=RCA

GO:0016926 "protein desumoylation" evidence=RCA

GO:0033044 "regulation of chromosome organization" evidence=RCA

GO:0045492 "xylan biosynthetic process" evidence=RCA

GO:0050665 "hydrogen peroxide biosynthetic process" evidence=RCA

TAIR\|locus:2183775 AT5G10800 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

UNIPROTKB\|F1MHP1 U2SURP "Uncharacterized protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|E2R1V3 U2SURP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|O15042 U2SURP "U2 snRNP-associated SURP motif-containing protein" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|F1SKE6 U2SURP "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

RGD\|1307882 U2surp "U2 snRNP-associated SURP domain containing" [Rattus norvegicus (taxid:10116)]	Back alignment and assigned GO terms

UNIPROTKB\|E1C0P9 U2SURP "Uncharacterized protein" [Gallus gallus (taxid:9031)]	Back alignment and assigned GO terms

MGI\|MGI:1915208 U2surp "U2 snRNP-associated SURP domain containing" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|E7ET15 U2SURP "U2 snRNP-associated SURP motif-containing protein" [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

Your Input:
	estExt_fgenesh4_pg.C_LG_VI1900	hypothetical protein (988 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

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		848
cd12223		84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	1e-52
smart00582		124	smart00582, RPR, domain present in proteins, which	2e-18
pfam01805		54	pfam01805, Surp, Surp module	2e-16
smart00648		54	smart00648, SWAP, Suppressor-of-White-APricot spli	3e-16
smart00360		73	smart00360, RRM, RNA recognition motif	1e-15
cd00590		72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-13
cd12346		72	cd12346, RRM3_NGR1_NAM8_like, RNA recognition moti	7e-13
cd12352		72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	8e-12
pfam00076		70	pfam00076, RRM_1, RNA recognition motif	1e-11
cd12619		75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	5e-11
cd12353		75	cd12353, RRM2_TIA1_like, RNA recognition motif 2 i	7e-11
cd12309		79	cd12309, RRM2_Spen, RNA recognition motif 2 in the	1e-10
cd12382		80	cd12382, RRM_RBMX_like, RNA recognition motif in h	2e-10
cd12381		79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	4e-10
cd12380		80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	7e-10
cd12354		73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	2e-09
cd12555		87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	2e-09
cd12447		76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	4e-09
cd12355		80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-08
cd12227		77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	2e-08
cd12335		83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	2e-08
cd12614		74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	2e-08
cd12347		73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-08
pfam08312		46	pfam08312, cwf21, cwf21 domain	5e-08
TIGR01628		562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-08
cd12224		74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	6e-08
TIGR01642		509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	8e-08
PRK12678		672	PRK12678, PRK12678, transcription termination fact	1e-07
cd12336		75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-07
cd12399		78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-07
cd12378		80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	2e-07
cd12520		74	cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA	2e-07
cd12616		81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	2e-07
cd12377		78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	3e-07
TIGR01628		562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-07
PRK12678		672	PRK12678, PRK12678, transcription termination fact	4e-07
cd12375		77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	6e-07
cd12334		74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	7e-07
PRK12678		672	PRK12678, PRK12678, transcription termination fact	1e-06
PRK12678		672	PRK12678, PRK12678, transcription termination fact	1e-06
PRK12678		672	PRK12678, PRK12678, transcription termination fact	2e-06
cd12345		80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-06
cd12556		85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	2e-06
TIGR01642		509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	3e-06
cd12613		80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	3e-06
cd12622		74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	3e-06
cd12361		77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	5e-06
cd12328		73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	7e-06
COG0724		306	COG0724, COG0724, RNA-binding proteins (RRM domain	8e-06
TIGR01628		562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-05
TIGR01642		509	TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, la	1e-05
cd12651		79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	1e-05
pfam14259		69	pfam14259, RRM_6, RNA recognition motif (a	1e-05
pfam08648		158	pfam08648, DUF1777, Protein of unknown function (D	1e-05
cd12262		82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	1e-05
cd12298		78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	3e-05
TIGR01622		457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-05
TIGR01622		457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	3e-05
cd12523		78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	3e-05
cd12351		77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	3e-05
cd12363		78	cd12363, RRM_TRA2, RNA recognition motif in transf	3e-05
cd03562		114	cd03562, CID, CID (CTD-Interacting Domain) domain	3e-05
cd12379		77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	3e-05
cd12592		75	cd12592, RRM_RBM7, RNA recognition motif in verteb	4e-05
cd12448		73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	4e-05
cd12251		72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-05
cd12360		78	cd12360, RRM_cwf2, RNA recognition motif in yeast	5e-05
cd12615		74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	6e-05
cd12449		80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	6e-05
cd12284		73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	7e-05
cd12655		85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	8e-05
cd12362		73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	8e-05
cd12639		79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	9e-05
cd12522		79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	1e-04
cd12637		80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	1e-04
cd12407		76	cd12407, RRM_FOX1_like, RNA recognition motif in v	1e-04
cd12393		78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	1e-04
PRK12678		672	PRK12678, PRK12678, transcription termination fact	2e-04
cd12311		73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	2e-04
cd12239		82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	2e-04
cd12310		72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	2e-04
cd12418		75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-04
TIGR01628		562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
pfam13893		56	pfam13893, RRM_5, RNA recognition motif	3e-04
cd12316		74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	3e-04
cd12365		73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	4e-04
cd12408		77	cd12408, RRM_eIF3G_like, RNA recognition motif in	4e-04
cd12383		83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	5e-04
cd12461		81	cd12461, RRM_SCAF4, RNA recognition motif found in	5e-04
cd12332		71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	6e-04
cd12641		89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	7e-04
cd12612		82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	7e-04
pfam10243		506	pfam10243, MIP-T3, Microtubule-binding protein MIP	7e-04
cd12327		80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	8e-04
cd12236		91	cd12236, RRM_snRNP70, RNA recognition motif in U1	9e-04
PLN03134		144	PLN03134, PLN03134, glycine-rich RNA-binding prote	9e-04
cd12229		81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	9e-04
cd12610		84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	9e-04
cd12640		79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	0.001
cd12618		80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.001
pfam12871		97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	0.001
pfam12871		97	pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 3	0.001
cd12654		86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	0.001
cd12373		73	cd12373, RRM_SRSF3_like, RNA recognition motif in	0.001
cd12243		71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	0.001
cd12617		80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	0.001
cd12370		76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.001
cd12344		81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.002
cd12638		92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	0.002
PRK12678		672	PRK12678, PRK12678, transcription termination fact	0.003
TIGR01622		457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.003
cd12240		78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.003
cd12325		72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	0.003
cd12318		82	cd12318, RRM5_RBM19_like, RNA recognition motif 5	0.003
cd12656		86	cd12656, RRM3_HuD, RNA recognition motif 3 in vert	0.003
cd12341		68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.004
cd12415		82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	0.004

>gnl\|CDD\|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated protein SR140 and similar proteins	Back alignment and domain information

 Score =  177 bits (451), Expect = 1e-52
 Identities = 62/84 (73%), Positives = 70/84 (83%)

Query: 60  TTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQ 119
           TTNLYVGNL+P+V E  L + FGRFGP+ASVKIMWPRTEEERRR RNCGFVAFMNRAD +
Sbjct: 1   TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60

Query: 120 AAKDEMQGVVVYEYELKIGWGKSV 143
            A DE+ G  V  YELK+GWGK+V
Sbjct: 61  RALDELDGKDVMGYELKLGWGKAV 84

This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). Length = 84

>gnl\|CDD\|214731 smart00582, RPR, domain present in proteins, which are involved in regulation of nuclear pre-mRNA	Back alignment and domain information

>gnl\|CDD\|216714 pfam01805, Surp, Surp module	Back alignment and domain information

>gnl\|CDD\|197818 smart00648, SWAP, Suppressor-of-White-APricot splicing regulator	Back alignment and domain information

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

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

>gnl\|CDD\|240792 cd12346, RRM3_NGR1_NAM8_like, RNA recognition motif 3 in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240798 cd12352, RRM1_TIA1_like, RNA recognition motif 1 in granule-associated RNA binding proteins p40-TIA-1 and TIAR	Back alignment and domain information

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

>gnl\|CDD\|241063 cd12619, RRM2_PUB1, RNA recognition motif 2 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240799 cd12353, RRM2_TIA1_like, RNA recognition motif 2 in granule-associated RNA binding proteins p40-TIA-1 and TIAR	Back alignment and domain information

>gnl\|CDD\|240755 cd12309, RRM2_Spen, RNA recognition motif 2 in the Spen (split end) protein family	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\|240827 cd12381, RRM4_I_PABPs, RNA recognition motif 4 in type I polyadenylate-binding 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\|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\|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)	Back alignment and domain information

>gnl\|CDD\|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240673 cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240781 cd12335, RRM2_SF3B4, RNA recognition motif 2 in splicing factor 3B subunit 4 (SF3B4) and similar proteins	Back alignment and domain information

>gnl\|CDD\|241058 cd12614, RRM1_PUB1, RNA recognition motif 1 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) and similar proteins	Back alignment and domain information

>gnl\|CDD\|203903 pfam08312, cwf21, cwf21 domain	Back alignment and domain information

>gnl\|CDD\|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

>gnl\|CDD\|240670 cd12224, RRM_RBM22, RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins	Back alignment and domain information

>gnl\|CDD\|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|240782 cd12336, RRM_RBM7_like, RNA recognition motif in RNA-binding protein 7 (RBM7) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins	Back alignment and domain information

>gnl\|CDD\|240824 cd12378, RRM1_I_PABPs, RNA recognition motif 1 in type I polyadenylate-binding proteins	Back alignment and domain information

>gnl\|CDD\|240964 cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA-binding protein MRN1 and similar proteins	Back alignment and domain information

>gnl\|CDD\|241060 cd12616, RRM1_TIAR, RNA recognition motif 1 in nucleolysin TIAR and similar proteins	Back alignment and domain information

>gnl\|CDD\|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family	Back alignment and domain information

>gnl\|CDD\|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|240821 cd12375, RRM1_Hu_like, RNA recognition motif 1 in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins	Back alignment and domain information

>gnl\|CDD\|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor 3B subunit 4 (SF3B4) and similar proteins	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins	Back alignment and domain information

>gnl\|CDD\|241000 cd12556, RRM2_RBM15B, RNA recognition motif 2 in putative RNA binding motif protein 15B (RBM15B) from vertebrate	Back alignment and domain information

>gnl\|CDD\|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>gnl\|CDD\|241057 cd12613, RRM2_NGR1_NAM8_like, RNA recognition motif 2 in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins	Back alignment and domain information

>gnl\|CDD\|241066 cd12622, RRM3_PUB1, RNA recognition motif 3 in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 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\|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily	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\|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

>gnl\|CDD\|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit, splicing factor	Back alignment and domain information

>gnl\|CDD\|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins	Back alignment and domain information

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

>gnl\|CDD\|219953 pfam08648, DUF1777, Protein of unknown function (DUF1777)	Back alignment and domain information

>gnl\|CDD\|240708 cd12262, RRM2_4_MRN1, RNA recognition motif 2 and 4 in RNA-binding protein MRN1 and similar proteins	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\|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family	Back alignment and domain information

>gnl\|CDD\|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family	Back alignment and domain information

>gnl\|CDD\|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA-binding protein MRN1 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240797 cd12351, RRM4_SHARP, RNA recognition motif 4 in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins	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\|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1	Back alignment and domain information

>gnl\|CDD\|240825 cd12379, RRM2_I_PABPs, RNA recognition motif 2 found in type I polyadenylate-binding proteins	Back alignment and domain information

>gnl\|CDD\|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)	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

>gnl\|CDD\|240806 cd12360, RRM_cwf2, RNA recognition motif in yeast pre-mRNA-splicing factor Cwc2 and similar proteins	Back alignment and domain information

>gnl\|CDD\|241059 cd12615, RRM1_TIA1, RNA recognition motif 1 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240895 cd12449, RRM_CIRBP_RBM3, RNA recognition motif in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) 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\|241099 cd12655, RRM3_HuC, RNA recognition motif 3 in vertebrate Hu-antigen C (HuC)	Back alignment and domain information

>gnl\|CDD\|240808 cd12362, RRM3_CELF1-6, RNA recognition motif 3 in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins	Back alignment and domain information

>gnl\|CDD\|241083 cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2 in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 and similar proteins	Back alignment and domain information

>gnl\|CDD\|241081 cd12637, RRM2_FCA, RNA recognition motif 2 in plant flowering time control protein FCA and similar proteins	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\|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\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|240757 cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240685 cd12239, RRM2_RBM40_like, RNA recognition motif 2 in RNA-binding protein 40 (RBM40) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family	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\|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family	Back alignment and domain information

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

>gnl\|CDD\|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1)	Back alignment and domain information

>gnl\|CDD\|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240829 cd12383, RRM_RBM42, RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240907 cd12461, RRM_SCAF4, RNA recognition motif found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family	Back alignment and domain information

>gnl\|CDD\|241085 cd12641, RRM_TRA2B, RNA recognition motif in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins	Back alignment and domain information

>gnl\|CDD\|241056 cd12612, RRM2_SECp43, RNA recognition motif 2 in tRNA selenocysteine-associated protein 1 (SECp43)	Back alignment and domain information

>gnl\|CDD\|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3	Back alignment and domain information

>gnl\|CDD\|240773 cd12327, RRM2_DAZAP1, RNA recognition motif 2 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240682 cd12236, RRM_snRNP70, RNA recognition motif in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins	Back alignment and domain information

>gnl\|CDD\|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional	Back alignment and domain information

>gnl\|CDD\|240675 cd12229, RRM_G3BP, RNA recognition motif (RRM) in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins	Back alignment and domain information

>gnl\|CDD\|241054 cd12610, RRM1_SECp43, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43)	Back alignment and domain information

>gnl\|CDD\|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein and similar proteins	Back alignment and domain information

>gnl\|CDD\|241062 cd12618, RRM2_TIA1, RNA recognition motif 2 in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term	Back alignment and domain information

>gnl\|CDD\|221821 pfam12871, PRP38_assoc, Pre-mRNA-splicing factor 38-associated hydrophilic C-term	Back alignment and domain information

>gnl\|CDD\|241098 cd12654, RRM3_HuB, RNA recognition motif 3 in vertebrate Hu-antigen B (HuB)	Back alignment and domain information

>gnl\|CDD\|240819 cd12373, RRM_SRSF3_like, RNA recognition motif in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240689 cd12243, RRM1_MSSP, RNA recognition motif 1 in the c-myc gene single-strand binding proteins (MSSP) family	Back alignment and domain information

>gnl\|CDD\|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR and similar proteins	Back alignment and domain information

>gnl\|CDD\|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins	Back alignment and domain information

>gnl\|CDD\|240790 cd12344, RRM1_SECp43_like, RNA recognition motif 1 in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins	Back alignment and domain information

>gnl\|CDD\|241082 cd12638, RRM3_CELF1_2, RNA recognition motif 3 in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins	Back alignment and domain information

>gnl\|CDD\|237171 PRK12678, PRK12678, transcription termination factor Rho; Provisional	Back alignment and domain information

>gnl\|CDD\|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family	Back alignment and domain information

>gnl\|CDD\|240686 cd12240, RRM_NCBP2, RNA recognition motif found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240771 cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition motif 1 in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins	Back alignment and domain information

>gnl\|CDD\|240764 cd12318, RRM5_RBM19_like, RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|241100 cd12656, RRM3_HuD, RNA recognition motif 3 in vertebrate Hu-antigen D (HuD)	Back alignment and domain information

>gnl\|CDD\|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins	Back alignment and domain information

>gnl\|CDD\|240861 cd12415, RRM3_RBM28_like, RNA recognition motif 3 in RNA-binding protein 28 (RBM28) 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		848
KOG0151		877	consensus Predicted splicing regulator, contains R	100.0
smart00582		121	RPR domain present in proteins, which are involved	99.87
KOG4368		757	consensus Predicted RNA binding protein, contains	99.77
KOG2669		325	consensus Regulator of nuclear mRNA [RNA processin	99.75
PLN03134		144	glycine-rich RNA-binding protein 4; Provisional	99.62
cd03562		114	CID CID (CTD-Interacting Domain) domain family; CI	99.58
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.49
PF01805		55	Surp: Surp module; InterPro: IPR000061 SWAP is der	99.49
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.4
smart00648		54	SWAP Suppressor-of-White-APricot splicing regulato	99.4
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	99.39
PF00076		70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.38
KOG0122		270	consensus Translation initiation factor 3, subunit	99.37
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	99.36
KOG0121		153	consensus Nuclear cap-binding protein complex, sub	99.32
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	99.31
KOG0149		247	consensus Predicted RNA-binding protein SEB4 (RRM	99.31
KOG0107		195	consensus Alternative splicing factor SRp20/9G8 (R	99.28
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	99.27
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	99.27
PLN03120		260	nucleic acid binding protein; Provisional	99.26
KOG0111		298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.26
PF04818		64	CTD_bind: RNA polymerase II-binding domain.; Inter	99.25
KOG0125		376	consensus Ataxin 2-binding protein (RRM superfamil	99.25
KOG4207		256	consensus Predicted splicing factor, SR protein su	99.22
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	99.22
KOG0132		894	consensus RNA polymerase II C-terminal domain-bind	99.21
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	99.2
PLN03213		759	repressor of silencing 3; Provisional	99.2
KOG0126		219	consensus Predicted RNA-binding protein (RRM super	99.19
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	99.18
PF14259		70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.18
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.17
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	99.15
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.15
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.14
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	99.14
KOG0113		335	consensus U1 small nuclear ribonucleoprotein (RRM	99.14
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.14
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.11
KOG0114		124	consensus Predicted RNA-binding protein (RRM super	99.07
smart00362		72	RRM_2 RNA recognition motif.	99.07
KOG0105		241	consensus Alternative splicing factor ASF/SF2 (RRM	99.07
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	99.06
PLN03121		243	nucleic acid binding protein; Provisional	99.06
KOG0130		170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	99.05
COG0724		306	RNA-binding proteins (RRM domain) [General functio	99.05
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	99.03
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	99.03
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	99.02
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.01
smart00360		71	RRM RNA recognition motif.	98.99
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.97
KOG0108		435	consensus mRNA cleavage and polyadenylation factor	98.96
PF12243		139	CTK3: CTD kinase subunit gamma CTK3	98.95
cd00590		74	RRM RRM (RNA recognition motif), also known as RBD	98.94
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.93
KOG0415		479	consensus Predicted peptidyl prolyl cis-trans isom	98.93
PF13893		56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.9
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	98.88
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.88
KOG0153		377	consensus Predicted RNA-binding protein (RRM super	98.86
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	98.85
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.82
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.78
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	98.78
KOG0132		894	consensus RNA polymerase II C-terminal domain-bind	98.76
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.75
smart00361		70	RRM_1 RNA recognition motif.	98.74
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.71
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.62
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	98.61
KOG4661		940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.49
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	98.46
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	98.44
KOG1847		878	consensus mRNA splicing factor [RNA processing and	98.44
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	98.44
KOG1457		284	consensus RNA binding protein (contains RRM repeat	98.41
KOG4208		214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.37
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	98.34
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	98.34
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	98.3
KOG1548		382	consensus Transcription elongation factor TAT-SF1	98.3
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	98.23
KOG0533		243	consensus RRM motif-containing protein [RNA proces	98.23
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	98.22
KOG4209		231	consensus Splicing factor RNPS1, SR protein superf	98.11
KOG0226		290	consensus RNA-binding proteins [General function p	98.08
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	98.05
KOG0116		419	consensus RasGAP SH3 binding protein rasputin, con	98.04
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	98.03
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	97.91
KOG4454		267	consensus RNA binding protein (RRM superfamily) [G	97.87
KOG4660		549	consensus Protein Mei2, essential for commitment t	97.78
KOG1190		492	consensus Polypyrimidine tract-binding protein [RN	97.77
KOG1457		284	consensus RNA binding protein (contains RRM repeat	97.72
KOG1995		351	consensus Conserved Zn-finger protein [General fun	97.67
PF11608		90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.61
PF04059		97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.58
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	97.46
COG5175		480	MOT2 Transcriptional repressor [Transcription]	97.35
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	97.28
KOG4676		479	consensus Splicing factor, arginine/serine-rich [R	97.2
KOG0151		877	consensus Predicted splicing regulator, contains R	97.05
KOG4210		285	consensus Nuclear localization sequence binding pr	96.95
KOG0112		975	consensus Large RNA-binding protein (RRM superfami	96.82
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	96.75
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	96.72
PF08777		105	RRM_3: RNA binding motif; InterPro: IPR014886 This	96.66
KOG1855		484	consensus Predicted RNA-binding protein [General f	96.66
KOG4849		498	consensus mRNA cleavage factor I subunit/CPSF subu	96.41
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	96.4
KOG0112		975	consensus Large RNA-binding protein (RRM superfami	96.34
KOG1456		494	consensus Heterogeneous nuclear ribonucleoprotein	96.3
KOG1190		492	consensus Polypyrimidine tract-binding protein [RN	96.18
KOG1456		494	consensus Heterogeneous nuclear ribonucleoprotein	96.13
KOG4211		510	consensus Splicing factor hnRNP-F and related RNA-	95.9
PF14605		53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	95.75
KOG0129		520	consensus Predicted RNA-binding protein (RRM super	95.65
KOG3152		278	consensus TBP-binding protein, activator of basal	95.63
KOG4211		510	consensus Splicing factor hnRNP-F and related RNA-	95.43
PF08312		46	cwf21: cwf21 domain; InterPro: IPR013170 The cwf21	95.41
KOG2314		698	consensus Translation initiation factor 3, subunit	95.23
KOG2416		718	consensus Acinus (induces apoptotic chromatin cond	95.22
KOG0796		319	consensus Spliceosome subunit [RNA processing and	95.11
PF05172		100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	95.1
KOG1548		382	consensus Transcription elongation factor TAT-SF1	95.08
KOG4307		944	consensus RNA binding protein RBM12/SWAN [General	95.05
PF04847		184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	94.78
PF02037		35	SAP: SAP domain; InterPro: IPR003034 The SAP (afte	94.73
KOG0129		520	consensus Predicted RNA-binding protein (RRM super	94.48
KOG2193		584	consensus IGF-II mRNA-binding protein IMP, contain	94.17
KOG2888		453	consensus Putative RNA binding protein [General fu	94.16
KOG2253		668	consensus U1 snRNP complex, subunit SNU71 and rela	93.93
smart00513		35	SAP Putative DNA-binding (bihelical) motif predict	93.83
KOG1365		508	consensus RNA-binding protein Fusilli, contains RR	93.36
KOG2888		453	consensus Putative RNA binding protein [General fu	93.26
PF08952		146	DUF1866: Domain of unknown function (DUF1866) ; In	93.11
KOG4307		944	consensus RNA binding protein RBM12/SWAN [General	93.09
KOG0115		275	consensus RNA-binding protein p54nrb (RRM superfam	93.0
KOG0128		881	consensus RNA-binding protein SART3 (RRM superfami	92.94
PF15023		166	DUF4523: Protein of unknown function (DUF4523)	92.92
PF08675		87	RNA_bind: RNA binding domain; InterPro: IPR014789	92.59
KOG1996		378	consensus mRNA splicing factor [RNA processing and	92.31
KOG2068		327	consensus MOT2 transcription factor [Transcription	91.74
KOG4368		757	consensus Predicted RNA binding protein, contains	90.84
cd00197		115	VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamil	90.11
KOG2202		260	consensus U2 snRNP splicing factor, small subunit,	89.83
KOG1847		878	consensus mRNA splicing factor [RNA processing and	89.74
KOG4574		1007	consensus RNA-binding protein (contains RRM and Pu	89.16
KOG0128		881	consensus RNA-binding protein SART3 (RRM superfami	89.1
KOG4246		1194	consensus Predicted DNA-binding protein, contains	88.64
KOG2071		579	consensus mRNA cleavage and polyadenylation factor	87.69
KOG0835		367	consensus Cyclin L [General function prediction on	87.11
KOG2135		526	consensus Proteins containing the RNA recognition	86.84
KOG4285		350	consensus Mitotic phosphoprotein [Cell cycle contr	86.6
PF03467		176	Smg4_UPF3: Smg-4/UPF3 family; InterPro: IPR005120	83.94
KOG2548		653	consensus SWAP mRNA splicing regulator [RNA proces	82.44
KOG0113		335	consensus U1 small nuclear ribonucleoprotein (RRM	82.3
KOG0105		241	consensus Alternative splicing factor ASF/SF2 (RRM	82.04

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

Probab=100.00  E-value=1e-123  Score=1038.74  Aligned_cols=674  Identities=53%  Similarity=0.814  Sum_probs=605.1

Q ss_pred             ChhhhhhHHHHHHHHHhhhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEecCCCCCCHHHHHHH
Q 003091            1 MEELKHEQEMRERRNQEREHWRDGRHTESSAPSSRFDELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRT   80 (848)
Q Consensus         1 ~Eelk~~qe~re~r~~~r~~~~~g~~~~~~~~~~~~~~~~~~~~~~g~~~gs~~~~d~~~t~LfVgNLp~~vte~~L~~~   80 (848)
                      +||||++||+||+|++.|....  .+++.+++.++++++|..++++|. +|+|+++||.+||||||||++.|+++.|...
T Consensus       118 keELkr~QE~Re~R~~~r~~~~--~~~~d~~~s~r~~~~p~~~~~s~~-~gsfDdgDP~TTNlyv~Nlnpsv~E~~ll~t  194 (877)
T KOG0151|consen  118 KEELKRIQEEREERHKDRHHLE--DPQSDSAVSSRFDPLPSRFDPSGR-PGSFDDGDPQTTNLYVGNLNPSVDENFLLRT  194 (877)
T ss_pred             HHHHHHHHHHHHHHhhhhhccc--ccccCcchhhccCCCccccCCCCC-CCcCCCCCCcccceeeecCCccccHHHHHHH
Confidence            5899999999999999988663  345567788999999999988885 9999999999999999999999999999999


Q ss_pred             hccCCCeeEEEEeCCCcccccCCcccEEEEEeCCHHHHHHHHHHcCCceecCeEEEEEeccCCCCCCCCCCCCCCCcccc
Q 003091           81 FGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAI  160 (848)
Q Consensus        81 F~~fG~I~svkI~~pr~d~~tg~~rg~gFV~F~~~~~A~~Ai~~lnG~~i~G~~L~V~~ak~~~~p~~~~~~p~p~~~~~  160 (848)
                      |+.||+|.+|+|||||++.+..+.+.||||.|+++.+|++|+..|||..+.++.|+++||+++++|+.+.+.||++++..
T Consensus       195 fGrfgPlasvKimwpRtEeEk~r~r~cgfvafmnR~D~era~k~lqg~iv~~~e~K~gWgk~V~ip~~p~~ipp~~h~~~  274 (877)
T KOG0151|consen  195 FGRFGPLASVKIMWPRTEEEKRRERNCGFVAFMNRADAERALKELQGIIVMEYEMKLGWGKAVPIPNIPIYIPPPLHEAT  274 (877)
T ss_pred             hcccCcccceeeecccchhhhccccccceeeehhhhhHHHHHHHhcceeeeeeeeeeccccccccCCccccCCChhhhcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccCCCccccCCCCCCCCcCCCCCCcccccCCCCCCcccCCCCchhhhhHHHHHHHHHhhccHHHHHHHHHhcCCCCccc
Q 003091          161 RSKEGATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFN  240 (848)
Q Consensus       161 ~~~~g~~~~~~gp~~pp~~~~~~~~~~~~~~~~~~~i~v~~P~d~~~~~~Id~~a~~V~~~G~~FE~~l~~~e~~np~f~  240 (848)
                      .++.+.+..+.+..+| ..++|+++++++.+++++.+.|.+|+|.++.++||+||.||++.|+.||+|||+++.+||+|+
T Consensus       275 lp~p~s~Lpfnaqp~p-~~~~pn~N~e~~~~edv~~i~Vvip~d~~L~~vidrM~~fV~~egp~fea~im~re~~nplF~  353 (877)
T KOG0151|consen  275 LPPPPSNLPFNAQPGP-PKSLPNQNAELVNTEDVEDILVVIPTDRHLLMVIDRMAEFVVREGPMFEAMIMERERGNPLFS  353 (877)
T ss_pred             CCCCccCCcccCCCCc-cccCCCccccccCcCCccceeEecCchHHHHHHHHHHHHHHhccCccHHHHHHHhhccChhHH
Confidence            8888888888877676 668899999999899999999999999999999999999999999999999999999999999


Q ss_pred             ccccCCCCCcceeeEEeeeeccCCccccccCCccccccCCCcccCCCCCCCCCCchhhhcccccccccCCCCCCCCCCCH
Q 003091          241 FLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALPTSKSPEHEKESGTTYAAGRSRRAEPERTLTD  320 (848)
Q Consensus       241 FL~d~~s~~h~YYrwkl~s~~~gd~~~~~~~~pf~~~~~~~~w~PP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~  320 (848)
                      |||+.+++.|+||+||||+|+|||+++.|+++||.||.+|++|+||+++......++.+..++++.+.   ...++.|+.
T Consensus       354 flfen~s~~htyyrwklySilQgdT~~ewr~e~frmfknggrwipppin~~~~~mp~ee~~~t~a~~e---~~~k~~Ltd  430 (877)
T KOG0151|consen  354 FLFENGSPAHTYYRWKLYSILQGDTPQEWRTEPFRMFKNGGRWIPPPINNYRKGMPEEEERSTDAEGE---SEDKGALTD  430 (877)
T ss_pred             HHHhcCchHHHHHHHHHHHHHcCCCHHHhhhhhhhhcccCceecCCCCCcccccCchhhhcccccccc---hhhhcccch
Confidence            99999999999999999999999999999999999999999999999988766555555555666543   345678999


Q ss_pred             HHHHHHHHHHHhcccCHHHHHHHHHHHHhccccHHHHHHHHHHHhcccCCCcccchheeeeehhhhccCCCCCCCccchH
Q 003091          321 SQRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYR  400 (848)
Q Consensus       321 ~~~~~l~~lL~~Lt~tr~sI~~~~~w~l~h~~~a~eiv~~l~~~l~~~~~~~~~KL~~LYLinDIL~ns~~~~~~a~~yr  400 (848)
                      .+|++|++||+.|||.|.+|.+||.|||+|+++|.+||+||+++|+..++++++||++|||||||||||.++|+|||.||
T Consensus       431 ~qRdklE~liR~LTpEk~sIg~aM~FalenA~aa~EI~eci~eSlt~~~t~~~kKiarLyLvsDIL~N~sarv~nas~YR  510 (877)
T KOG0151|consen  431 LQRDKLEDLIRGLTPEKSSIGDAMVFALENADAAGEIVECITESLTNKETPLPKKIARLYLVSDILHNSSARVANASAYR  510 (877)
T ss_pred             HHHHHHHHHHHhcCcccchHHHHHHHHHhhhhhHHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHhhhhhhhhHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhHHHHHHHHHHHhhhhcccchHHHHHHHHHHHHhhccCccCcHHHHHHHHHHhccCCCCCCccccccCCCCccc
Q 003091          401 TKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEI  480 (848)
Q Consensus       401 ~~fe~~Lp~if~~l~~~~~~~~~r~~ae~~k~kV~~vL~iWe~~~vf~~~~i~~L~~~f~~~~~~~~~~~~~~~~~~~~~  480 (848)
                      ..||+.|+.||..|+.+|+++.|||+++.|+++|++||++|++|.||+.+||.+|+++|++ .+++++++++ +++.+++
T Consensus       511 ~~FEa~L~~Ifd~l~~~yr~I~gRIkaE~fkqRV~kVirvWedW~ifpe~~l~~l~~~Flg-~~~~~~~~~s-e~~~~di  588 (877)
T KOG0151|consen  511 KSFEATLEDIFDDLNDLYRSIGGRIKAEAFKQRVMKVIRVWEDWAIFPEDFLIGLQNTFLG-LNNIVTEKES-EADAPDI  588 (877)
T ss_pred             HHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHhc-CCCCcccccc-cccchhh
Confidence            9999999999999999999999999999999999999999999999999999999999999 4566788888 8899999


Q ss_pred             cccCCCccc--ccccccchhhHhhhCchhhHHHhhcCChHHHHHHHHHcCccccCChHHHHHHHHhHHHHhhhcccccch
Q 003091          481 DKKNNSEDT--CDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAEKQRGYELDD  558 (848)
Q Consensus       481 e~~~~~~d~--~dg~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~c~~~gl~~~~~~~~~~~rL~~~~~~~~~~~~~~~~  558 (848)
                      ++.-...++  .||.+++  +      .++-.+++..++++|+..| ++++..-++..++++++.++.....|..+|+..
T Consensus       589 e~~~~a~~eedldgvple--~------~~agip~~n~pi~eld~~~-l~~dd~ldgipm~~e~~ss~s~~~~~sk~e~vd  659 (877)
T KOG0151|consen  589 ENAPLAGNEEDLDGVPLE--D------EDAGIPLMNTPIDELDGRP-LNLDDDLDGIPMMVETKSSLSDPETPSKWEAVD  659 (877)
T ss_pred             ccCcccCchhhccCCCch--h------hhcCCccccCchhhhcccc-ccccccccCceeeeeeccccCCCcccccccccC
Confidence            888775444  4565543  2      2345678889999999999 999999999999999999999999999988777


Q ss_pred             hh-hhcccCCCCCCCCCCCccccCCccccCCcCCCCCchhhhhhcccCCcccccccCCCChhhhhhhhhhcCCCCccccc
Q 003091          559 DL-KSAHSQSSSGRYSRGWKETNMEAESMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASK  637 (848)
Q Consensus       559 ~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k  637 (848)
                      .. +.+|+.+++.     |-.+...++++    .++|.++++..                            .||    |
T Consensus       660 ~~~~~~q~vstsk-----we~~~~~~~~~----~~s~~~~e~ed----------------------------~~~----k  698 (877)
T KOG0151|consen  660 ESFKEGQAVSTSK-----WEHVDDEFEPK----KNSYDEVEEED----------------------------NPV----K  698 (877)
T ss_pred             cccccccccchhh-----hhhcccccccc----cccccchhccc----------------------------ccc----c
Confidence            66 7777765433     66666666654    46666665522                            233    8


Q ss_pred             cccccCCchHHHhhccCCCCcccCCCCCCCCCCCCCCCCccccccCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHH
Q 003091          638 WALEDDESDDEQKRSSRGLGLSYSSSGSENAGDGPSKADDVDFTIDASIPVQPDSGMNEEQRQKLRRLEVSLIEYRESLE  717 (848)
Q Consensus       638 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~kl~~~~~~~~~~r~~~e  717 (848)
                      |   +|+.+|+++..       +++ |+++.|  ..+.+.+....+.|+..+++.+++.+.+++++.+++++.+|++.++
T Consensus       699 ~---~de~~~~~~~~-------~ss-~~~~~d--~l~sg~~~lk~~~sv~~qpe~~~d~~l~q~~r~~~~a~~e~~e~~~  765 (877)
T KOG0151|consen  699 Y---DDEDRDKLRDI-------ESS-GSDNQD--ELESGERDLKPGSSVREQPENERDRLLRQDVRVEAIALIEYREADE  765 (877)
T ss_pred             c---chhhhHHHhhh-------hhh-cccccc--ccCCCCccCCCCCccccChhhHHHHHHHHHHHHHHHHhhhhhhhhh
Confidence            9   66667777655       444 888888  4567778888889999999999999999999999999999999999


Q ss_pred             HhccCChHHHHHHHHHHhhhhhhhcCCCC
Q 003091          718 ERGIKSSEEIEKKVAIHRKRLESEYGLAD  746 (848)
Q Consensus       718 e~~~~~~ee~~~~~~~~r~~~~~~~~~~~  746 (848)
                      |++.++.++++++.+..+++++..||.+.
T Consensus       766 e~~~k~s~~~~rk~e~~~~r~e~~~g~S~  794 (877)
T KOG0151|consen  766 EQGMKRSEDKERKVEIERKRKERKRGHSG  794 (877)
T ss_pred             hhhccchhhhhhhcchhHHHHHhhhcccC
Confidence            99999999999999999999999988875

>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA	Back alignment and domain information

>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]	Back alignment and domain information

>KOG2669 consensus Regulator of nuclear mRNA [RNA processing and modification]	Back alignment and domain information

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

>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1	Back alignment and domain information

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

>PF01805 Surp: Surp module; InterPro: IPR000061 SWAP is derived from the Suppressor-of-White-APricot splicing regulator from Drosophila melanogaster	Back alignment and domain information

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

>smart00648 SWAP Suppressor-of-White-APricot splicing regulator	Back alignment and domain information

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

>PF00076 RRM_1: RNA recognition motif	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

>TIGR01659 sex-lethal sex-lethal family splicing factor	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

>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

>KOG0149 consensus Predicted RNA-binding protein SEB4 (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

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

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

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

>PF04818 CTD_bind: RNA polymerase II-binding domain	Back alignment and domain information

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

>KOG4207 consensus Predicted splicing factor, SR protein 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

>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

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

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

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

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

>PF14259 RRM_6: RNA recognition motif (a	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

>KOG0145 consensus RNA-binding protein ELAV/HU (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

>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

>KOG0113 consensus U1 small nuclear ribonucleoprotein (RRM 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

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

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

>smart00362 RRM_2 RNA recognition motif	Back alignment and domain information

>KOG0105 consensus Alternative splicing factor ASF/SF2 (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

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

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

>COG0724 RNA-binding proteins (RRM domain) [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

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

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

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

>smart00360 RRM RNA recognition motif	Back alignment and domain information

>TIGR01649 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family	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

>PF12243 CTK3: CTD kinase subunit gamma CTK3	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

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

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

>PF13893 RRM_5: RNA recognition motif	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

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [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

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

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

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

>KOG0147 consensus Transcriptional coactivator CAPER (RRM superfamily) [Transcription]	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

>smart00361 RRM_1 RNA recognition motif	Back alignment and domain information

>KOG4206 consensus Spliceosomal protein snRNP-U1A/U2B [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

>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

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

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

>KOG1847 consensus mRNA splicing factor [RNA processing and modification]	Back alignment and domain information

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

>KOG1457 consensus RNA binding protein (contains RRM repeats) [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

>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

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

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

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

>KOG0533 consensus RRM motif-containing 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

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

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

>KOG0106 consensus Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [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

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

>KOG4454 consensus RNA binding protein (RRM superfamily) [General function prediction only]	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

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

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

>KOG1995 consensus Conserved Zn-finger protein [General function prediction only]	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

>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

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

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

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

>KOG4676 consensus Splicing factor, arginine/serine-rich [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

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

>KOG0112 consensus Large 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

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

>KOG1855 consensus Predicted RNA-binding protein [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

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

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

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

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

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

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

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

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

>PF08312 cwf21: cwf21 domain; InterPro: IPR013170 The cwf21 domain is found in proteins involved in mRNA splicing	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

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

>KOG0796 consensus Spliceosome subunit [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

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

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]	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

>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []	Back alignment and domain information

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

>KOG2888 consensus Putative RNA binding protein [General function prediction only]	Back alignment and domain information

>KOG2253 consensus U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification]	Back alignment and domain information

>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation	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

>KOG2888 consensus Putative RNA binding protein [General function prediction only]	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

>KOG4307 consensus RNA binding protein RBM12/SWAN [General function prediction only]	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

>PF15023 DUF4523: Protein of unknown function (DUF4523)	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

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

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

>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]	Back alignment and domain information

>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain	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

>KOG1847 consensus mRNA splicing factor [RNA processing and modification]	Back alignment and domain information

>KOG4574 consensus RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only]	Back alignment and domain information

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

>KOG4246 consensus Predicted DNA-binding protein, contains SAP domain [General function prediction only]	Back alignment and domain information

>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]	Back alignment and domain information

>KOG0835 consensus Cyclin L [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

>KOG4285 consensus Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning]	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

>KOG2548 consensus SWAP mRNA splicing regulator [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

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

Homologous Structure Templates