Citrus Sinensis ID: 003204

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-------84

MSSFSITRKKTPFQKHREEEEAKKKRAEDETARLYAEFVESFQGDSGPGSKAFVRGGTIDPNDKLKEAEGEKSKDGVSVPKKGSRYVPSFIPPPLAAKGKDSERKKEEERPREKDRGKSRNIDNFMEELKHEQEMRERRNQEREHWRDGRHTESSAPSSRFDELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKEGATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALPTSKSPEHEKESGTTYAAGRSRRAEPERTLTDSQRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAEKQRGYELDDDLKSAHSQSSSGRYSRGWKETNMEAESMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASKWALEDDESDDEQKRSSRGLGLSYSSSGSENAGDGPSKADDVDFTIDASIPVQPDSGMNEEQRSDHRLLSFAFLLIEK

cccccccccccccHHHHHHHHHHHHHcHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccEEEccccccccHHHHHHHHcccccEEEEEEEcccccccccccccEEEEEEccHHHHHHHHHHccccEEccEEEEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcHHHHHHHHHHHccccccccccccccccccccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccHHHHHHHHHHHHHccccHHHHHHHHHHHcccccccHHHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHcccccHHHHHccccHHHHHHHHHHccccccccHHHHHHHHccHHHHHHHccccccccHHHHcccccccccccccccccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHEEEEEccc

cccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccEEEEEcccccccHHHHHHHHcccccEEEEEEEccccHHHHccccccEEEEEccHHHHHHHHHHccccEEccEEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccHHHHHHHHHHHHHHHHccHHHHHHHHHcccccccHHEEEcccccccEEEEEEEEEEEcccccccccccccEEcccccEcccccccccccccccccccHHHHccccccccccccccHHHHHHHHHHHHHccHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHcccccccccccccccccHHHHcccccccccccccccccccccccccccHHHcccccHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHccccccHccccccccccccccccccccccccHccccccccccccccHHHHcccccccccccccccccHHHHccccccccccccccHHccccccccHHHcccccccccEEccccccccccccccccHHHHcccccccccccccccHHHHHHHHHHHHHHHHHcc

mssfsitrkktpfqkhREEEEAKKKRAEDETARLYAEFVEsfqgdsgpgskafvrggtidpndklkeaegekskdgvsvpkkgsryvpsfippplaakgkdserkkeeerprekdrgksrnIDNFMEELKHEQEMRERRNQErehwrdgrhtessapssrfdelpddfdpsgklpgsfddgdpqttnlyvgnlspqvdenfllrtfgrfgpiasvkimwprtEEERRRQRNcgfvafmnradgqaakdemQGVVVYEYELKigwgksvalpsqalpapppgqmairskegatvilsgpsgppvttvpsqnselvltpnvpdimvippedrhlrHVIDTLALYVLDGGCAFEQAImergrgnplFNFLFELGSKEHTYYVWRLYsfaqgdtlqrwrtepfimitgsgrwippalptskspehekesgttyaagrsrraepertltdsqRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTEsltlketpiptKVARLMLVSDVlhnssapvknasaYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFlrsgnsgvtpfhsicgdapeidkknnsedtcdlsktnQDTALAMGKGAAIKELMNLPLSELERRcrhnglslvgGREMMVARLLSLEDAEKqrgyeldddlksahsqsssgrysrgwketnMEAEsmglsgwngyeedeklsqavgsvplgtmlttpqpeikaftkkekndpvlpaskwaleddesddeqkrssrglglsysssgsenagdgpskaddvdftidasipvqpdsgmneeqrsdhRLLSFAFLLIEK

mssfsitrkktpfqkhreeeeakkkraedETARLYAEFvesfqgdsgpgskAFVRGGTIDpndklkeaegekskdgvsvpkkgsryvpsfippplaakgkdserkkeeerprekdrgksrnidnfmEELKHEQEMRERRnqerehwrdgrhtessapssrfdELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRtfgrfgpiasvkimwprtEEERRRQRNCGFVAFMNradgqaakdemQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKEGATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPAlptskspehekesgttyaagrsrraepertltdsqrdeFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTesltlketpiPTKVARLMLVSDVLHnssapvknasayrTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNglslvggrEMMVARLLSLEDAEKQRGYeldddlksahsqsssgrysrgwketNMEAESMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKaftkkekndpvlpaskwaleddesddeqkrssrglglsysssgsenagdgpskADDVDFTIDASIpvqpdsgmneeqrsdhrLLSFAFLLIEK

MSSFSITRKKTPFQKHreeeeakkkraedetarLYAEFVESFQGDSGPGSKAFVRGGTIDPNDKLKEAEGEKSKDGVSVPKKGSRYVPSFIPPPLAAkgkdserkkeeerprekdrgkSRNIDNFMEELKHeqemrerrnqereHWRDGRHTESSAPSSRFDELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSValpsqalpapppGQMAIRSKEGATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALPTSKSPEHEKESGTTYAAGRSRRAEPERTLTDSQRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAEKQRGYELDDDLKSAHSQSSSGRYSRGWKETNMEAESMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASKWALEDDESDDEQKrssrglglsysssgsENAGDGPSKADDVDFTIDASIPVQPDSGMNEEQRSDHRLLSFAFLLIEK

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

******************************TARLYAEFVE**************************************************************************************************************************************************NLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPR*****RRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQA**************************************LVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAI*******PLFNFLFELGSKEHTYYVWRLYSF*************************************************************QRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTL***PIPTKVARLMLVSDVLHNSSA****ASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATF***********************************TNQDTAL*************LPLSELERRCR***LSL*GGREMMVARLLSL**************************************************************************************VLP******************************************************************DHRLLSFAFLLIEK

*****************************ETARLYAEFVESFQGDSGPGSKAFVRGGTIDPNDKLKE**************KGSRYVPSFIPPPLA*********************KSRNIDNFMEELKH*******************************ELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKEGATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALP*********************************RDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAEKQRGY*********************WKETNMEAESMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASKWAL*********************************KADDVDFTIDASIPVQPDSGMNEEQRSDHRLLSFAFLLIEK

************************KR*EDETARLYAEFVESFQGDSGPGSKAFVRGGTID**********************************************************SRNIDNFMEELKHEQEMRERRNQE**************************************GDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAI*************SGPPVT******SELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALPT***************************LTDSQRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSG*******************************TNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAEKQR*****************************************************************************DPVLPA**W********************************************************NEEQRSDHRLLSFAFLLIEK

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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MSSFSITRKKTPFQKHxxxxxxxxxxxxxxxxxxxxxFVESFQGDSGPGSKAFVRGGTIDPNDKLKEAEGEKSKDGVSVPKKGSRYVPSFIPPPLAAKGKDSERKKEEERPREKDRGKSRNxxxxxxxxxxxxxxxxxxxxxREHWRDGRHTESSAPSSRFDELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKEGATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALPTSKSPEHEKESGTTYAAGRSRRAEPERTLTDSQxxxxxxxxxxxxxxxxxxxxxMGFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAEKQRGYELDDDLKSAHSQSSSGRYSRGWKETNMEAESMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASKWALEDDESDDEQKRSSRGLGLSYSSSGSENAGDGPSKADDVDFTIDASIPVQPDSGMNEEQRSDHRLLSFAFLLIEK

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		839	2.2.26 [Sep-21-2011]
Q5R7X2		1028	U2 snRNP-associated SURP	yes	no	0.640	0.522	0.378	1e-103
O15042		1029	U2 snRNP-associated SURP	yes	no	0.640	0.521	0.377	1e-103
Q6NV83		1029	U2 snRNP-associated SURP	yes	no	0.641	0.522	0.375	1e-102
P32831		672	Negative growth regulator	yes	no	0.100	0.125	0.344	2e-08
Q9LEB3		428	Polyadenylate-binding pro	N/A	no	0.101	0.198	0.340	6e-08
F4I3B3		445	Polyadenylate-binding pro	no	no	0.098	0.186	0.326	4e-07
Q10200		466	Uncharacterized protein C	yes	no	0.230	0.414	0.235	9e-07
Q9SX79		432	Polyadenylate-binding pro	no	no	0.108	0.210	0.313	1e-06
Q9SX80		434	Polyadenylate-binding pro	no	no	0.108	0.209	0.323	1e-06
Q15415		496	RNA-binding motif protein	no	no	0.157	0.266	0.277	2e-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 =  375 bits (963), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 219/579 (37%), Positives = 321/579 (55%), Gaps = 42/579 (7%)

Query: 32  ARLYAEFVESFQGDSGPGSKAFVRGGTIDPNDKLKEAEGEKSKDGVSVPKKGSRYVPSFI 91
           A +Y EF+ +F+G  G   K FVRGG ++   +  E + ++ K    + K  SR+     
Sbjct: 114 AEIYEEFLAAFEGSDGNKVKTFVRGGVVNAAKEEHETDEKRGK----IYKPSSRFADQKN 169

Query: 92  PPPLAAKGKD-SERKKEEERP---REKDRGKSRNIDNFMEELKHEQEMRERRNQER---- 143
           PP  ++  +  S    E ++P   + +   K  N++ F EELK  QE R+ R++ +    
Sbjct: 170 PPNQSSNERPPSLLVIETKKPPLKKGEKEKKKSNLELFKEELKQIQEERDERHKTKGRLS 229

Query: 144 -----EHWRDGRHTESSAPSSRF-DELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQV 197
                +   DG+     APS R    + DD+      PGS D GDP TTNLY+GN++PQ+
Sbjct: 230 RFEPPQSDSDGQRRSMDAPSRRNRSSVLDDY-----APGSHDVGDPSTTNLYLGNINPQM 284

Query: 198 DENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQAAKDEMQGVVVYE 257
           +E  L + FGRFGP+ASVKIMWPRT+EER R+RNCGFVAFMNR D + A   + G ++  
Sbjct: 285 NEEMLCQEFGRFGPLASVKIMWPRTDEERARERNCGFVAFMNRRDAERALKNLNGKMIMS 344

Query: 258 YELKIGWGKSV-----------ALPSQALPAPPPGQMAIRSKEGATVILSGPSGPPVTTV 306
           +E+K+GWGK+V           ++    LP PPP  +   ++      L  P+  P+   
Sbjct: 345 FEMKLGWGKAVPIPPHPIYIPPSMMEHTLP-PPPSGLPFNAQPRER--LKNPNA-PMLPP 400

Query: 307 PSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNF 366
           P    +   T +   + V+ P +R+L  +I  +  +V+  G  FE  IM R   NP+F F
Sbjct: 401 PKNKEDFEKTLSQAIVKVVIPTERNLLALIHRMIEFVVREGPMFEAMIMNREINNPMFRF 460

Query: 367 LFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALPTSKSPEHEKESG 426
           LFE  +  H YY W+LYS  QGD+  +WRTE F M      W PP L        E++  
Sbjct: 461 LFENQTPAHVYYRWKLYSILQGDSPTKWRTEDFRMFKNGSFWRPPPLNPYLHGMSEEQET 520

Query: 427 TTYAAGRSRRAEPERTLTDSQRDEFEDMLRALTLERSQIKEAMGFALDNADAAGEIVEVL 486
             +    S++      L + QRD+ E++LR LT  ++ I +AM F L+NA+AA EIV+ +
Sbjct: 521 EAFVEEPSKKG----ALKEEQRDKLEEILRGLTPRKNDIGDAMVFCLNNAEAAEEIVDCI 576

Query: 487 TESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSI 546
           TESL++ +TP+P K+ARL LVSDVL+NSSA V NAS YR  FE  L  I    N  YR+I
Sbjct: 577 TESLSILKTPLPKKIARLYLVSDVLYNSSAKVANASYYRKFFETKLCQIFSDLNATYRTI 636

Query: 547 TGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFL 585
            G + +E  K+RV+   + W DW ++ + ++  L+  FL
Sbjct: 637 QGHLQSENFKQRVMTCFRAWEDWAIYPEPFLIKLQNIFL 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\|Q9SX79\|RB47C_ARATH Polyadenylate-binding protein RBP47C OS=Arabidopsis thaliana GN=RBP47C PE=2 SV=1	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\|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		839
224089390		988	predicted protein [Populus trichocarpa]	0.995	0.845	0.858	0.0
224141985		955	predicted protein [Populus trichocarpa]	0.976	0.857	0.851	0.0
356526679		972	PREDICTED: U2 snRNP-associated SURP moti	0.990	0.854	0.839	0.0
296082150		941	unnamed protein product [Vitis vinifera]	0.967	0.862	0.850	0.0
356560817		971	PREDICTED: U2 snRNP-associated SURP moti	0.992	0.857	0.851	0.0
147857263		1384	hypothetical protein VITISV_025939 [Viti	0.965	0.585	0.820	0.0
357517325		1139	U2-associated protein SR140 [Medicago tr	0.994	0.732	0.775	0.0
255548712		979	RNA binding protein, putative [Ricinus c	0.989	0.847	0.854	0.0
449441850		961	PREDICTED: U2 snRNP-associated SURP moti	0.991	0.865	0.837	0.0
297812707		948	RNA recognition motif-containing protein	0.959	0.849	0.757	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 = 1408 bits (3645), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 726/846 (85%), Positives = 775/846 (91%), Gaps = 11/846 (1%)

Query: 1   MSSFSITRKKTPFQKHREEEEAKKKRAEDETARLYAEFVESFQGDSGPGSKAFVRGGTID 60
           MSSFSITRKKTPFQKHREEEEAKKKRAEDETARLYAEFVESFQGD+ PGSK FVRGGTI+
Sbjct: 1   MSSFSITRKKTPFQKHREEEEAKKKRAEDETARLYAEFVESFQGDNAPGSKTFVRGGTIN 60

Query: 61  PNDKLK-EAEGEKSKDGVSVPKKGSRYVPSFIPPPLAAKGKDSERKKEEERPREKDRGKS 119
           PN+KLK +AEGEKSKDGVSVPKKGSRYVPSFIPPP+A KGK+ ERK+EEERP+EK++GK+
Sbjct: 61  PNEKLKSDAEGEKSKDGVSVPKKGSRYVPSFIPPPMAPKGKEPERKREEERPKEKEKGKT 120

Query: 120 RNIDNFMEELKHEQEMRERRNQEREHWRDGRHTESSAPSSRFDELPDDFDPSGKLPGSFD 179
           RNID+FMEELKHE EMRERRNQEREHWR+GRHTESSAPSSRFDELPDDFDPSGKLPGSFD
Sbjct: 121 RNIDHFMEELKHEHEMRERRNQEREHWREGRHTESSAPSSRFDELPDDFDPSGKLPGSFD 180

Query: 180 DGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMN 239
           DGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMN
Sbjct: 181 DGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMN 240

Query: 240 RADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKE---------- 289
           RADGQAAKDEMQGV+VYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKE          
Sbjct: 241 RADGQAAKDEMQGVIVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKEVCYGFLPKPI 300

Query: 290 GATVILSGPSGPPVTTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCA 349
           GATVILSGPSGPPVT+VP+QNSELVLTPNVPDIMV PPED HLRHVIDT+ALYVLDGGCA
Sbjct: 301 GATVILSGPSGPPVTSVPNQNSELVLTPNVPDIMVAPPEDDHLRHVIDTMALYVLDGGCA 360

Query: 350 FEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWI 409
           FEQAIM+RGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRW+
Sbjct: 361 FEQAIMQRGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWV 420

Query: 410 PPALPTSKSPEHEKESGTTYAAGRSRRAEPERTLTDSQRDEFEDMLRALTLERSQIKEAM 469
           PP+LPT+KSPEHEKESG+T+AAGRSRR +PERTLTD QRDEFEDMLRALTLERSQIK+AM
Sbjct: 421 PPSLPTAKSPEHEKESGSTHAAGRSRRVDPERTLTDPQRDEFEDMLRALTLERSQIKDAM 480

Query: 470 GFALDNADAAGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFE 529
           GFALDN DAAGE+VEVLTESLTLKETPIPTKVARLMLVSD+LHNSSAPVKNASAYRTKFE
Sbjct: 481 GFALDNVDAAGEVVEVLTESLTLKETPIPTKVARLMLVSDILHNSSAPVKNASAYRTKFE 540

Query: 530 ATLPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGN 589
           A LPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRS N
Sbjct: 541 AALPDIMESFNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSSN 600

Query: 590 SGVTPFHSICGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRC 649
           SGV PFHS+CGDAPEI+KKN++EDT D  KTNQD ALAMGKGAA KELM+LPL+ELERRC
Sbjct: 601 SGVIPFHSMCGDAPEIEKKNSTEDTVDGGKTNQDAALAMGKGAATKELMDLPLAELERRC 660

Query: 650 RHNGLSLVGGREMMVARLLSLEDAEKQRGYELDDDLKSAHSQSSSGRYSRGWKETNMEAE 709
           RHNGLSLVGGRE MVARLL+LE+AEKQRGYELD DLK A S SSS RYS   +E N++  
Sbjct: 661 RHNGLSLVGGRETMVARLLNLEEAEKQRGYELDGDLKIAQSNSSSSRYSSVHREVNVDPG 720

Query: 710 SMGLSGWNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASKWALEDDE 769
            +GL+GWN Y ED+  SQ   SV L + L  PQPE+KAF KKEKNDPVLPASKWA +DDE
Sbjct: 721 PVGLTGWNIYGEDDTPSQNKRSVSLVSTLPIPQPELKAFAKKEKNDPVLPASKWARDDDE 780

Query: 770 SDDEQKRSSRGLGLSYSSSGSENAGDGPSKADDVDFTIDASIPVQPDSGMNEEQRSDHRL 829
           SDDEQKRS R LGLSYSSSGSENAGDG  K D+++F  DASIP QP+SGMNEEQR   R 
Sbjct: 781 SDDEQKRSVRDLGLSYSSSGSENAGDGQGKEDEMEFATDASIPTQPESGMNEEQRQKLRR 840

Query: 830 LSFAFL 835
           L  A +
Sbjct: 841 LEVALI 846

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

>gi\|296082150\|emb\|CBI21155.3\| unnamed protein product [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\|147857263\|emb\|CAN79213.1\| hypothetical protein VITISV_025939 [Vitis vinifera]	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\|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\|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		839
TAIR\|locus:2179295		946	RRC1 "reduced red-light respon	0.897	0.795	0.723	3.8e-311
TAIR\|locus:2183775		947	AT5G10800 [Arabidopsis thalian	0.835	0.740	0.701	2.5e-283
UNIPROTKB\|E2R1V3		1028	U2SURP "Uncharacterized protei	0.641	0.523	0.362	1.9e-89
UNIPROTKB\|F1MHP1		1035	U2SURP "Uncharacterized protei	0.641	0.519	0.361	2.4e-89
UNIPROTKB\|O15042		1029	U2SURP "U2 snRNP-associated SU	0.641	0.522	0.361	2.4e-89
UNIPROTKB\|F1SKE6		1029	U2SURP "Uncharacterized protei	0.641	0.522	0.361	2.4e-89
MGI\|MGI:1915208		1029	U2surp "U2 snRNP-associated SU	0.641	0.522	0.36	1e-88
RGD\|1307882		985	U2surp "U2 snRNP-associated SU	0.641	0.546	0.36	1e-88
UNIPROTKB\|E1C0P9		985	U2SURP "Uncharacterized protei	0.641	0.546	0.361	1e-88
UNIPROTKB\|E7ET15		1028	U2SURP "U2 snRNP-associated SU	0.641	0.523	0.358	2.7e-88

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

 Score = 2792 (987.9 bits), Expect = 3.8e-311, Sum P(2) = 3.8e-311
 Identities = 562/777 (72%), Positives = 621/777 (79%)

Query:     1 MSSFSITRKKTPFQKHXXXXXXXXXXXXXXXXXLYAEFVESFQGDSGPGSKAFVRGGTID 60
             MSSFSITRKKTPFQKH                 LY EFVESFQGD+   +K FVRGGTI+
Sbjct:     1 MSSFSITRKKTPFQKHREEEEARKKKAEDETARLYQEFVESFQGDNAT-TKTFVRGGTIN 59

Query:    61 PNDKLK-EAEGEKSKDGVSVPKKGSRYVPSFIPPPLAAXXXXXXXXXXXXXXXXXXXXXS 119
             P DK K ++EGEKSKDG SV KKGSRYVPSF+PPPLA+                     +
Sbjct:    60 PGDKPKVDSEGEKSKDGGSVSKKGSRYVPSFLPPPLASKGKEPEKKREEERPREREKGKT 119

Query:   120 RNIDNFMEELKHXXXXXXXXXXXXXHWRDGRHTESSAPSSRFDELPDDFDPSGKLPGSFD 179
             RNIDNFMEELK                RD R  +SS PSSRFDELPDDFDPSG+ PGSFD
Sbjct:   120 RNIDNFMEELKREQEMRERRNQD----RD-RQGDSS-PSSRFDELPDDFDPSGR-PGSFD 172

Query:   180 DGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMN 239
             DGDPQTTNLYVGNLSP+VDENFLLRTFGRFGPIASVKIMWPRT+EE+RRQRNCGFV+FMN
Sbjct:   173 DGDPQTTNLYVGNLSPKVDENFLLRTFGRFGPIASVKIMWPRTDEEKRRQRNCGFVSFMN 232

Query:   240 RADGQAAKDEMQGVVVYEYELKIGWGKSVXXXXXXXXXXXXGQMAIRSKEGATVILSGPS 299
             RADGQAAKDEMQG++VYEYELKIGWGK+V            G MAIRSKEG  ++ SG +
Sbjct:   233 RADGQAAKDEMQGIIVYEYELKIGWGKAVSLPSQALPAPPPGHMAIRSKEGCNLVFSGQT 292

Query:   300 GPPV-TTVPSQNSELVLTPNVPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERG 358
             GPP+ T+VP+QNSELVLTPNVPDI V+ PED HLRHVIDTLALYVLDG CAFEQAIMERG
Sbjct:   293 GPPIITSVPNQNSELVLTPNVPDITVVTPEDEHLRHVIDTLALYVLDGECAFEQAIMERG 352

Query:   359 RGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPFIMITGSGRWIPPALPTSKS 418
             RGNPLF F+FELGSKEHTYYVWRLYSFAQGDTLQRWRTEP+IMITGSGRWIPP LP +++
Sbjct:   353 RGNPLFKFMFELGSKEHTYYVWRLYSFAQGDTLQRWRTEPYIMITGSGRWIPPPLPVTRT 412

Query:   419 PEHEKESGTTYAAGRSRRAEPERTLTDSQRDEFEDMLRALTLERSQIKEAMGFALDNADA 478
              EHEKES +TYAAGR+RRAE ERTLTD QRDEFEDMLRALTLERSQIKEAMGFALDNADA
Sbjct:   413 QEHEKESASTYAAGRTRRAEVERTLTDPQRDEFEDMLRALTLERSQIKEAMGFALDNADA 472

Query:   479 AGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMES 538
             AGE+VEVLTESLTLKET IPTKVARLMLVSD+LHNSSA VKNASAYRTKFEATLPDIMES
Sbjct:   473 AGEVVEVLTESLTLKETSIPTKVARLMLVSDILHNSSARVKNASAYRTKFEATLPDIMES 532

Query:   539 FNDLYRSITGRITAEALKERVLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSI 598
             FNDLYRSITGRITAEALKERVLKVLQVW+DWFLFSDAY+ GLR+TFLRSG SGVT FHSI
Sbjct:   533 FNDLYRSITGRITAEALKERVLKVLQVWADWFLFSDAYIYGLRSTFLRSGVSGVTSFHSI 592

Query:   599 CGDAPEIDKKNNSEDTCDLSKTNQDTALAMGKGAAIKELMNLPLSELERRCRHNGLSLVG 658
             CGDAPEI+ K+ +++  D+ K N D ALA+GKGAA +ELMNLP++ELERRCRHNGLSLVG
Sbjct:   593 CGDAPEIENKSYADNMSDIGKINPDAALAIGKGAARQELMNLPIAELERRCRHNGLSLVG 652

Query:   659 GREMMVARLLSLEDAEKQRGYELDDDLKSAHSQSSSGRYSRGWKETNMEAESMGLSGWNG 718
             GR MMV RLLSLED EKQRGYE  D++   H Q+ S      W+E   E E +     N 
Sbjct:   653 GRVMMVTRLLSLEDTEKQRGYEAVDEIPK-HPQNHST-----WEEVKSEREHIK----NS 702

Query:   719 YEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASKWALEDDESDDEQK 775
             Y E E + + V    L T +  PQPE+KAF  KEKN+ +LPASKWA +DDE+DDEQK
Sbjct:   703 YAEVE-MKEPVN---LPTTIPIPQPELKAFVGKEKNELILPASKWARDDDEADDEQK 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\|E2R1V3 U2SURP "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

UNIPROTKB\|F1MHP1 U2SURP "Uncharacterized protein" [Bos taurus (taxid:9913)]	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

MGI\|MGI:1915208 U2surp "U2 snRNP-associated SURP domain containing" [Mus musculus (taxid:10090)]	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

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

Fail to connect to STRING server

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		839
cd12223		84	cd12223, RRM_SR140, RNA recognition motif (RRM) in	4e-53
smart00582		124	smart00582, RPR, domain present in proteins, which	1e-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	2e-12
cd12352		72	cd12352, RRM1_TIA1_like, RNA recognition motif 1 i	2e-11
pfam00076		70	pfam00076, RRM_1, RNA recognition motif	2e-11
cd12619		75	cd12619, RRM2_PUB1, RNA recognition motif 2 in yea	3e-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	8e-11
cd12382		80	cd12382, RRM_RBMX_like, RNA recognition motif in h	1e-10
cd12381		79	cd12381, RRM4_I_PABPs, RNA recognition motif 4 in	6e-10
cd12555		87	cd12555, RRM2_RBM15, RNA recognition motif 2 in ve	9e-10
cd12380		80	cd12380, RRM3_I_PABPs, RNA recognition motif 3 fou	1e-09
cd12447		76	cd12447, RRM1_gar2, RNA recognition motif 1 in yea	2e-09
cd12354		73	cd12354, RRM3_TIA1_like, RNA recognition motif 2 i	3e-09
cd12227		77	cd12227, RRM_SCAF4_SCAF8, RNA recognition motif in	1e-08
cd12614		74	cd12614, RRM1_PUB1, RNA recognition motif 1 in yea	2e-08
cd12355		80	cd12355, RRM_RBM18, RNA recognition motif in eukar	2e-08
cd12224		74	cd12224, RRM_RBM22, RNA recognition motif (RRM) fo	3e-08
cd12347		73	cd12347, RRM_PPIE, RNA recognition motif in cyclop	4e-08
cd12335		83	cd12335, RRM2_SF3B4, RNA recognition motif 2 in sp	5e-08
TIGR01628		562	TIGR01628, PABP-1234, polyadenylate binding protei	6e-08
cd12378		80	cd12378, RRM1_I_PABPs, RNA recognition motif 1 in	9e-08
cd12399		78	cd12399, RRM_HP0827_like, RNA recognition motif in	1e-07
cd12336		75	cd12336, RRM_RBM7_like, RNA recognition motif in R	1e-07
COG0724		306	COG0724, COG0724, RNA-binding proteins (RRM domain	2e-07
cd12616		81	cd12616, RRM1_TIAR, RNA recognition motif 1 in nuc	3e-07
cd12520		74	cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA	3e-07
TIGR01628		562	TIGR01628, PABP-1234, polyadenylate binding protei	4e-07
cd12375		77	cd12375, RRM1_Hu_like, RNA recognition motif 1 in	4e-07
cd12334		74	cd12334, RRM1_SF3B4, RNA recognition motif 1 in sp	7e-07
cd12377		78	cd12377, RRM3_Hu, RNA recognition motif 3 in the H	9e-07
cd12556		85	cd12556, RRM2_RBM15B, RNA recognition motif 2 in p	1e-06
cd12345		80	cd12345, RRM2_SECp43_like, RNA recognition motif 2	2e-06
cd12613		80	cd12613, RRM2_NGR1_NAM8_like, RNA recognition moti	2e-06
cd12622		74	cd12622, RRM3_PUB1, RNA recognition motif 3 in yea	3e-06
cd12328		73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	6e-06
cd12361		77	cd12361, RRM1_2_CELF1-6_like, RNA recognition moti	6e-06
cd12651		79	cd12651, RRM2_SXL, RNA recognition motif 2 in Dros	9e-06
TIGR01628		562	TIGR01628, PABP-1234, polyadenylate binding protei	1e-05
cd12262		82	cd12262, RRM2_4_MRN1, RNA recognition motif 2 and	1e-05
pfam14259		69	pfam14259, RRM_6, RNA recognition motif (a	1e-05
cd12363		78	cd12363, RRM_TRA2, RNA recognition motif in transf	1e-05
cd12523		78	cd12523, RRM2_MRN1, RNA recognition motif 2 of RNA	2e-05
cd12298		78	cd12298, RRM3_Prp24, RNA recognition motif 3 in fu	2e-05
cd12351		77	cd12351, RRM4_SHARP, RNA recognition motif 4 in SM	3e-05
cd12448		73	cd12448, RRM2_gar2, RNA recognition motif 2 in yea	3e-05
cd12311		73	cd12311, RRM_SRSF2_SRSF8, RNA recognition motif in	3e-05
cd03562		114	cd03562, CID, CID (CTD-Interacting Domain) domain	3e-05
cd12251		72	cd12251, RRM3_hnRNPR_like, RNA recognition motif 3	4e-05
cd12360		78	cd12360, RRM_cwf2, RNA recognition motif in yeast	4e-05
cd12449		80	cd12449, RRM_CIRBP_RBM3, RNA recognition motif in	4e-05
cd12407		76	cd12407, RRM_FOX1_like, RNA recognition motif in v	6e-05
cd12592		75	cd12592, RRM_RBM7, RNA recognition motif in verteb	6e-05
cd12379		77	cd12379, RRM2_I_PABPs, RNA recognition motif 2 fou	7e-05
cd12284		73	cd12284, RRM2_RBM23_RBM39, RNA recognition motif 2	7e-05
cd12637		80	cd12637, RRM2_FCA, RNA recognition motif 2 in plan	8e-05
cd12522		79	cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA	8e-05
cd12615		74	cd12615, RRM1_TIA1, RNA recognition motif 1 in nuc	8e-05
cd12310		72	cd12310, RRM3_Spen, RNA recognition motif 3 in the	1e-04
cd12655		85	cd12655, RRM3_HuC, RNA recognition motif 3 in vert	1e-04
cd12362		73	cd12362, RRM3_CELF1-6, RNA recognition motif 3 in	2e-04
cd12393		78	cd12393, RRM_ZCRB1, RNA recognition motif in Zinc	2e-04
cd12418		75	cd12418, RRM_Aly_REF_like, RNA recognition motif i	2e-04
cd12408		77	cd12408, RRM_eIF3G_like, RNA recognition motif in	2e-04
cd12639		79	cd12639, RRM3_CELF3_4_5_6, RNA recognition motif 2	2e-04
cd12641		89	cd12641, RRM_TRA2B, RNA recognition motif in Trans	2e-04
TIGR01628		562	TIGR01628, PABP-1234, polyadenylate binding protei	3e-04
cd12365		73	cd12365, RRM_RNPS1, RNA recognition motif in RNA-b	3e-04
cd12332		71	cd12332, RRM1_p54nrb_like, RNA recognition motif 1	3e-04
cd12236		91	cd12236, RRM_snRNP70, RNA recognition motif in U1	3e-04
cd12239		82	cd12239, RRM2_RBM40_like, RNA recognition motif 2	3e-04
cd12316		74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	4e-04
cd12383		83	cd12383, RRM_RBM42, RNA recognition motif in RNA-b	4e-04
cd12461		81	cd12461, RRM_SCAF4, RNA recognition motif found in	4e-04
cd12373		73	cd12373, RRM_SRSF3_like, RNA recognition motif in	5e-04
pfam13893		56	pfam13893, RRM_5, RNA recognition motif	5e-04
cd12612		82	cd12612, RRM2_SECp43, RNA recognition motif 2 in t	7e-04
cd12229		81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	0.001
PLN03134		144	PLN03134, PLN03134, glycine-rich RNA-binding prote	0.001
cd12327		80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	0.001
TIGR01622		457	TIGR01622, SF-CC1, splicing factor, CC1-like famil	0.001
cd12618		80	cd12618, RRM2_TIA1, RNA recognition motif 2 in nuc	0.001
cd12617		80	cd12617, RRM2_TIAR, RNA recognition motif 2 in nuc	0.001
cd12610		84	cd12610, RRM1_SECp43, RNA recognition motif 1 in t	0.001
cd12370		76	cd12370, RRM1_PUF60, RNA recognition motif 1 in (U	0.002
cd12654		86	cd12654, RRM3_HuB, RNA recognition motif 3 in vert	0.002
cd12243		71	cd12243, RRM1_MSSP, RNA recognition motif 1 in the	0.002
cd12240		78	cd12240, RRM_NCBP2, RNA recognition motif found in	0.002
cd12640		79	cd12640, RRM3_Bruno_like, RNA recognition motif 3	0.002
cd12344		81	cd12344, RRM1_SECp43_like, RNA recognition motif 1	0.002
cd12325		72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	0.003
cd12341		68	cd12341, RRM_hnRNPC_like, RNA recognition motif in	0.003
cd12565		76	cd12565, RRM1_MRD1, RNA recognition motif 1 in yea	0.003
cd12415		82	cd12415, RRM3_RBM28_like, RNA recognition motif 3	0.004
cd12638		92	cd12638, RRM3_CELF1_2, RNA recognition motif 3 in	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 =  178 bits (454), Expect = 4e-53
 Identities = 62/84 (73%), Positives = 70/84 (83%)

Query: 185 TTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFMNRADGQ 244
           TTNLYVGNL+P+V E  L + FGRFGP+ASVKIMWPRTEEERRR RNCGFVAFMNRAD +
Sbjct: 1   TTNLYVGNLNPKVTEEVLCQEFGRFGPLASVKIMWPRTEEERRRNRNCGFVAFMNRADAE 60

Query: 245 AAKDEMQGVVVYEYELKIGWGKSV 268
            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\|240999 cd12555, RRM2_RBM15, RNA recognition motif 2 in vertebrate RNA binding motif protein 15 (RBM15)	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\|240893 cd12447, RRM1_gar2, RNA recognition motif 1 in yeast protein gar2 and similar proteins	Back alignment and domain information

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

>gnl\|CDD\|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\|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\|240801 cd12355, RRM_RBM18, RNA recognition motif in eukaryotic RNA-binding protein 18 and similar proteins	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\|240793 cd12347, RRM_PPIE, RNA recognition motif in cyclophilin-33 (Cyp33) 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\|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family	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\|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins	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\|223796 COG0724, COG0724, RNA-binding proteins (RRM domain) [General function prediction only]	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\|240964 cd12520, RRM1_MRN1, RNA recognition motif 1 of RNA-binding protein MRN1 and similar proteins	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\|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\|240823 cd12377, RRM3_Hu, RNA recognition motif 3 in the Hu proteins family	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\|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\|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\|240774 cd12328, RRM2_hnRNPA_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein A subfamily	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\|241095 cd12651, RRM2_SXL, RNA recognition motif 2 in Drosophila sex-lethal (SXL) and similar proteins	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\|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\|222631 pfam14259, RRM_6, RNA recognition motif (a	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\|240967 cd12523, RRM2_MRN1, RNA recognition motif 2 of 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\|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\|240894 cd12448, RRM2_gar2, RNA recognition motif 2 in yeast protein gar2 and similar proteins	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\|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\|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\|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\|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\|241036 cd12592, RRM_RBM7, RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)	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\|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\|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\|240966 cd12522, RRM4_MRN1, RNA recognition motif 4 of RNA-binding protein MRN1 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\|240756 cd12310, RRM3_Spen, RNA recognition motif 3 in the Spen (split end) protein family	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\|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\|240864 cd12418, RRM_Aly_REF_like, RNA recognition motif in the Aly/REF family	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\|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\|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\|130689 TIGR01628, PABP-1234, polyadenylate binding protein, human types 1, 2, 3, 4 family	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\|240778 cd12332, RRM1_p54nrb_like, RNA recognition motif 1 in the p54nrb/PSF/PSP1 family	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\|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\|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\|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\|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\|206064 pfam13893, RRM_5, RNA recognition motif	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\|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\|178680 PLN03134, PLN03134, glycine-rich RNA-binding protein 4; Provisional	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\|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family	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\|241061 cd12617, RRM2_TIAR, RNA recognition motif 2 in nucleolysin TIAR 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\|240816 cd12370, RRM1_PUF60, RNA recognition motif 1 in (U)-binding-splicing factor PUF60 and similar proteins	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\|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\|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\|241084 cd12640, RRM3_Bruno_like, RNA recognition motif 3 in Drosophila melanogaster Bruno protein 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\|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\|240787 cd12341, RRM_hnRNPC_like, RNA recognition motif in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins	Back alignment and domain information

>gnl\|CDD\|241009 cd12565, RRM1_MRD1, RNA recognition motif 1 in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar 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

>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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		839
KOG0151		877	consensus Predicted splicing regulator, contains R	100.0
smart00582		121	RPR domain present in proteins, which are involved	99.88
KOG2669		325	consensus Regulator of nuclear mRNA [RNA processin	99.74
cd03562		114	CID CID (CTD-Interacting Domain) domain family; CI	99.57
PLN03134		144	glycine-rich RNA-binding protein 4; Provisional	99.56
PF01805		55	Surp: Surp module; InterPro: IPR000061 SWAP is der	99.5
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	99.47
KOG4368		757	consensus Predicted RNA binding protein, contains	99.44
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.43
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.42
smart00648		54	SWAP Suppressor-of-White-APricot splicing regulato	99.42
PF00076		70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.4
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	99.38
KOG0122		270	consensus Translation initiation factor 3, subunit	99.32
KOG0149		247	consensus Predicted RNA-binding protein SEB4 (RRM	99.3
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	99.27
KOG0121		153	consensus Nuclear cap-binding protein complex, sub	99.26
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	99.26
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	99.25
PLN03120		260	nucleic acid binding protein; Provisional	99.25
KOG0113		335	consensus U1 small nuclear ribonucleoprotein (RRM	99.23
PF04818		64	CTD_bind: RNA polymerase II-binding domain.; Inter	99.23
PLN03213		759	repressor of silencing 3; Provisional	99.22
KOG0107		195	consensus Alternative splicing factor SRp20/9G8 (R	99.21
KOG4207		256	consensus Predicted splicing factor, SR protein su	99.21
PF14259		70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.2
KOG0125		376	consensus Ataxin 2-binding protein (RRM superfamil	99.19
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	99.16
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	99.16
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	99.15
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.11
KOG0111		298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.11
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	99.1
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.09
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.09
COG0724		306	RNA-binding proteins (RRM domain) [General functio	99.08
smart00362		72	RRM_2 RNA recognition motif.	99.08
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	99.08
PLN03121		243	nucleic acid binding protein; Provisional	99.06
KOG0126		219	consensus Predicted RNA-binding protein (RRM super	99.05
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	99.04
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.03
smart00360		71	RRM RNA recognition motif.	99.01
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	98.99
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	98.97
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.97
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	98.97
cd00590		74	RRM RRM (RNA recognition motif), also known as RBD	98.96
KOG0108		435	consensus mRNA cleavage and polyadenylation factor	98.96
PF12243		139	CTK3: CTD kinase subunit gamma CTK3	98.96
KOG0114		124	consensus Predicted RNA-binding protein (RRM super	98.95
KOG0105		241	consensus Alternative splicing factor ASF/SF2 (RRM	98.93
KOG0415		479	consensus Predicted peptidyl prolyl cis-trans isom	98.92
KOG0130		170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.91
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	98.9
PF13893		56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	98.88
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.86
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.85
KOG0153		377	consensus Predicted RNA-binding protein (RRM super	98.84
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	98.83
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	98.83
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.8
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.8
KOG0132		894	consensus RNA polymerase II C-terminal domain-bind	98.78
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.77
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.72
smart00361		70	RRM_1 RNA recognition motif.	98.72
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	98.69
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	98.63
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.55
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.52
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	98.45
KOG4661		940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.39
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	98.36
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	98.36
KOG1548		382	consensus Transcription elongation factor TAT-SF1	98.3
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	98.3
KOG4208		214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.29
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	98.27
KOG0533		243	consensus RRM motif-containing protein [RNA proces	98.24
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	98.23
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	98.23
KOG1457		284	consensus RNA binding protein (contains RRM repeat	98.22
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	98.15
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	98.06
KOG4209		231	consensus Splicing factor RNPS1, SR protein superf	98.06
KOG1190		492	consensus Polypyrimidine tract-binding protein [RN	98.01
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	97.96
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	97.96
KOG0226		290	consensus RNA-binding proteins [General function p	97.91
KOG1847		878	consensus mRNA splicing factor [RNA processing and	97.89
KOG0116		419	consensus RasGAP SH3 binding protein rasputin, con	97.77
KOG4454		267	consensus RNA binding protein (RRM superfamily) [G	97.76
KOG4660		549	consensus Protein Mei2, essential for commitment t	97.74
COG5175		480	MOT2 Transcriptional repressor [Transcription]	97.41
KOG1457		284	consensus RNA binding protein (contains RRM repeat	97.35
PF04059		97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	97.33
PF11608		90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	97.3
KOG0132		894	consensus RNA polymerase II C-terminal domain-bind	97.16
KOG1995		351	consensus Conserved Zn-finger protein [General fun	97.0
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	96.89
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	96.86
KOG4210		285	consensus Nuclear localization sequence binding pr	96.73
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	96.66
KOG1855		484	consensus Predicted RNA-binding protein [General f	96.35
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	96.35
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	96.26
KOG4211		510	consensus Splicing factor hnRNP-F and related RNA-	96.06
KOG1190		492	consensus Polypyrimidine tract-binding protein [RN	95.86
KOG0112		975	consensus Large RNA-binding protein (RRM superfami	95.83
PF08777		105	RRM_3: RNA binding motif; InterPro: IPR014886 This	95.83
KOG3152		278	consensus TBP-binding protein, activator of basal	95.81
KOG0112		975	consensus Large RNA-binding protein (RRM superfami	95.78
KOG0129		520	consensus Predicted RNA-binding protein (RRM super	95.57
KOG1456		494	consensus Heterogeneous nuclear ribonucleoprotein	95.52
PF14605		53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	95.47
KOG1456		494	consensus Heterogeneous nuclear ribonucleoprotein	95.41
PF02037		35	SAP: SAP domain; InterPro: IPR003034 The SAP (afte	95.05
PF05172		100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	94.88
KOG4676		479	consensus Splicing factor, arginine/serine-rich [R	94.82
KOG4849		498	consensus mRNA cleavage factor I subunit/CPSF subu	94.68
KOG1548		382	consensus Transcription elongation factor TAT-SF1	94.58
KOG0129		520	consensus Predicted RNA-binding protein (RRM super	94.29
smart00513		35	SAP Putative DNA-binding (bihelical) motif predict	94.29
KOG4307		944	consensus RNA binding protein RBM12/SWAN [General	94.19
PF04847		184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	93.65
PF08952		146	DUF1866: Domain of unknown function (DUF1866) ; In	93.45
KOG2193		584	consensus IGF-II mRNA-binding protein IMP, contain	93.34
KOG4211		510	consensus Splicing factor hnRNP-F and related RNA-	93.28
KOG0128		881	consensus RNA-binding protein SART3 (RRM superfami	92.17
PF15023		166	DUF4523: Protein of unknown function (DUF4523)	91.83
KOG2314		698	consensus Translation initiation factor 3, subunit	90.82
KOG2202		260	consensus U2 snRNP splicing factor, small subunit,	90.46
KOG2416		718	consensus Acinus (induces apoptotic chromatin cond	90.04
KOG1996		378	consensus mRNA splicing factor [RNA processing and	89.72
cd00197		115	VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamil	89.47
KOG2068		327	consensus MOT2 transcription factor [Transcription	89.31
KOG0128		881	consensus RNA-binding protein SART3 (RRM superfami	88.41
KOG1365		508	consensus RNA-binding protein Fusilli, contains RR	87.25
KOG0115		275	consensus RNA-binding protein p54nrb (RRM superfam	85.77
KOG0105		241	consensus Alternative splicing factor ASF/SF2 (RRM	85.74
KOG2135		526	consensus Proteins containing the RNA recognition	85.44
PF08675		87	RNA_bind: RNA binding domain; InterPro: IPR014789	84.66
KOG2071		579	consensus mRNA cleavage and polyadenylation factor	82.42
KOG4574		1007	consensus RNA-binding protein (contains RRM and Pu	82.26
KOG4285		350	consensus Mitotic phosphoprotein [Cell cycle contr	82.25

>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=2.9e-140  Score=1175.69  Aligned_cols=754  Identities=50%  Similarity=0.776  Sum_probs=673.8

Q ss_pred             CCCcCccccCCchhhchHHHHHhccccHHHHHHHHHHHHHhhcCCCCCCCCceeeccccCCCCc-ccc-ccCCCCCCCcc
Q 003204            1 MSSFSITRKKTPFQKHREEEEAKKKRAEDETARLYAEFVESFQGDSGPGSKAFVRGGTIDPNDK-LKE-AEGEKSKDGVS   78 (839)
Q Consensus         1 ~~~~~~~~kks~f~k~ke~~E~Kkk~ee~eaA~vy~eFv~sF~~~~~~~~~~fvr~g~~~~~~~-~~~-~~~~~~~~~~~   78 (839)
                      |.+|++..++.++.++||.+++|||+.+.+||++|.+||++|...+..+.|+||+|||++|+.. ... ..++       
T Consensus         3 ~~~f~i~~~s~p~~~~re~e~~kkK~~~~~~a~~~~ef~~~f~~~~~~~~k~fv~~gtina~~~r~~~d~~~~-------   75 (877)
T KOG0151|consen    3 LDAFSIGSVSKPKLSKRENEEEKKKEDAGAAARYYQEFVENFPKGDNVGSKTFVEAGTINAAKARRKLDEKGG-------   75 (877)
T ss_pred             ccccccccccccchhhhhhHhhhcccchhhHHHHHHHHHHhccCCCCccceeeeeccccccccccccchhhcc-------
Confidence            5789999999999999999999999999999999999999998666667899999999999773 222 2221       


Q ss_pred             ccCCCCCCCCCCCCCccccCCCChhhhhhccCccccccCchhhHHHHHHHHHHHHHHHHHHHHhhhhhccCCCCCCCCCC
Q 003204           79 VPKKGSRYVPSFIPPPLAAKGKDSERKKEEERPREKDRGKSRNIDNFMEELKHEQEMRERRNQEREHWRDGRHTESSAPS  158 (839)
Q Consensus        79 ~~~~g~~y~~~~~p~~~~~k~~~~~~k~~~~k~k~~~k~K~r~ld~F~eElk~~Qeere~r~~~r~~~~~G~~~~~~t~~  158 (839)
                        +.++.++|++.+++......++.+.   ..+|.+.++|++||+.|+|||+++||+||+|++.+.+.  -...+.++++
T Consensus        76 --k~k~~~~p~~~~~~~~~~~~~~kk~---~~kk~~~k~K~snle~FkeELkr~QE~Re~R~~~r~~~--~~~~~d~~~s  148 (877)
T KOG0151|consen   76 --KKKSTEVPSFVEPPTRLLVKDPKKG---PLKKKQEKKKKSNLELFKEELKRIQEEREERHKDRHHL--EDPQSDSAVS  148 (877)
T ss_pred             --cccCCCCCCcCCCcchhcccCCCCC---cchhhhcccchhhHHHHHHHHHHHHHHHHHHhhhhhcc--cccccCcchh
Confidence              3367789998888776655444333   34455677889999999999999999999999998865  2233456788


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCccEEEEcCCCCCCCHHHHHHHhccCCCeeEEEEeCCCCccccCCcccEEEEEeC
Q 003204          159 SRFDELPDDFDPSGKLPGSFDDGDPQTTNLYVGNLSPQVDENFLLRTFGRFGPIASVKIMWPRTEEERRRQRNCGFVAFM  238 (839)
Q Consensus       159 sr~~~~p~~~~~~~~~~gs~d~~dp~~ttLfVgNLp~~vtEe~L~~lF~~fG~I~sVkI~~pr~d~~tg~~rg~gFV~F~  238 (839)
                      ++++.+|..+++.+. +|++|++||.+||||||||+|.|+|+.|...|++||+|.+|+|||||++.+..+.+.||||.||
T Consensus       149 ~r~~~~p~~~~~s~~-~gsfDdgDP~TTNlyv~Nlnpsv~E~~ll~tfGrfgPlasvKimwpRtEeEk~r~r~cgfvafm  227 (877)
T KOG0151|consen  149 SRFDPLPSRFDPSGR-PGSFDDGDPQTTNLYVGNLNPSVDENFLLRTFGRFGPLASVKIMWPRTEEEKRRERNCGFVAFM  227 (877)
T ss_pred             hccCCCccccCCCCC-CCcCCCCCCcccceeeecCCccccHHHHHHHhcccCcccceeeecccchhhhccccccceeeeh
Confidence            999999998888775 8999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHhCCCEECCeEEEEEeecCCCCCCCCCCCCCCCcccccccCCCccccCCCCCCCCcCCCCCCcccccCCC
Q 003204          239 NRADGQAAKDEMQGVVVYEYELKIGWGKSVALPSQALPAPPPGQMAIRSKEGATVILSGPSGPPVTTVPSQNSELVLTPN  318 (839)
Q Consensus       239 ~~~dAe~Al~~lnG~~i~Gr~IkV~~ak~~~~p~~a~~~pp~g~~~~~~~~g~~~~~~gp~~pp~~~~p~~~se~~~~~~  318 (839)
                      ++.+|++|+..|+|..++++.|+++|||++++|++++|.||++++.....+++...+.+..+| ..+.|+++.+++.+++
T Consensus       228 nR~D~era~k~lqg~iv~~~e~K~gWgk~V~ip~~p~~ipp~~h~~~lp~p~s~Lpfnaqp~p-~~~~pn~N~e~~~~ed  306 (877)
T KOG0151|consen  228 NRADAERALKELQGIIVMEYEMKLGWGKAVPIPNIPIYIPPPLHEATLPPPPSNLPFNAQPGP-PKSLPNQNAELVNTED  306 (877)
T ss_pred             hhhhHHHHHHHhcceeeeeeeeeeccccccccCCccccCCChhhhccCCCCccCCcccCCCCc-cccCCCccccccCcCC
Confidence            999999999999999999999999999999999999999999999888888888888877666 6688999999999999


Q ss_pred             CCceeccCCCchhhhhHHHHHHHHHhcCChHHHHHHHHhcCCCCcccccccCCCCCcceeeEEEeeeccCCccccccCCc
Q 003204          319 VPDIMVIPPEDRHLRHVIDTLALYVLDGGCAFEQAIMERGRGNPLFNFLFELGSKEHTYYVWRLYSFAQGDTLQRWRTEP  398 (839)
Q Consensus       319 ~~~v~v~~P~D~~~~~~Idk~a~~V~~~G~~FE~~l~~re~~Np~F~FL~d~~s~~h~YYrwrl~s~~~gd~~~~w~~~p  398 (839)
                      +..+.|++|+|.+++.+||+||+||+++|++||+|||+++.+||+|+|||+.+++.|+||+||||||+|||++..|+++|
T Consensus       307 v~~i~Vvip~d~~L~~vidrM~~fV~~egp~fea~im~re~~nplF~flfen~s~~htyyrwklySilQgdT~~ewr~e~  386 (877)
T KOG0151|consen  307 VEDILVVIPTDRHLLMVIDRMAEFVVREGPMFEAMIMERERGNPLFSFLFENGSPAHTYYRWKLYSILQGDTPQEWRTEP  386 (877)
T ss_pred             ccceeEecCchHHHHHHHHHHHHHHhccCccHHHHHHHhhccChhHHHHHhcCchHHHHHHHHHHHHHcCCCHHHhhhhh
Confidence            98899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccccCCccccCCCCCCCCCcchhhhcccccccCcCcCcCcCCCCCHHHHHHHHHHHHhhccchHHHHHHHHHHhhcccc
Q 003204          399 FIMITGSGRWIPPALPTSKSPEHEKESGTTYAAGRSRRAEPERTLTDSQRDEFEDMLRALTLERSQIKEAMGFALDNADA  478 (839)
Q Consensus       399 f~m~~~g~~w~PP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~~r~~l~~lL~~Lt~tr~sI~~~m~w~l~ha~~  478 (839)
                      |+||+||++|+||+++.....++.++..++++.+.   .+.++.|+..+|++|++||+.|||.|.+|+++|.|||+|+++
T Consensus       387 frmfknggrwipppin~~~~~mp~ee~~~t~a~~e---~~~k~~Ltd~qRdklE~liR~LTpEk~sIg~aM~FalenA~a  463 (877)
T KOG0151|consen  387 FRMFKNGGRWIPPPINNYRKGMPEEEERSTDAEGE---SEDKGALTDLQRDKLEDLIRGLTPEKSSIGDAMVFALENADA  463 (877)
T ss_pred             hhhcccCceecCCCCCcccccCchhhhcccccccc---hhhhcccchHHHHHHHHHHHhcCcccchHHHHHHHHHhhhhh
Confidence            99999999999999998765554444445565443   346789999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhccCCCcccceeeeeeeehhcccCCCCCCChhhhHHHHHHhhHHHHHHHHHHhhhhccccchHHHHHH
Q 003204          479 AGEIVEVLTESLTLKETPIPTKVARLMLVSDVLHNSSAPVKNASAYRTKFEATLPDIMESFNDLYRSITGRITAEALKER  558 (839)
Q Consensus       479 a~eIv~~i~~~l~~~~t~~~~KLa~LYLinDILhNs~~~v~na~~yR~~fe~~Lp~IF~~l~~~y~~~~~ri~ae~~k~k  558 (839)
                      |.|||+||+++|++.+|++++||+||||||||||||+++|.|||.||..||..|+.||..|+.+|+++.|||++|.|+++
T Consensus       464 a~EI~eci~eSlt~~~t~~~kKiarLyLvsDIL~N~sarv~nas~YR~~FEa~L~~Ifd~l~~~yr~I~gRIkaE~fkqR  543 (877)
T KOG0151|consen  464 AGEIVECITESLTNKETPLPKKIARLYLVSDILHNSSARVANASAYRKSFEATLEDIFDDLNDLYRSIGGRIKAEAFKQR  543 (877)
T ss_pred             HHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhccCccCcHHHHHHHHHHhccCCCCCCcccccccCCCccccccCCCcc--ccCcccCchhHHHhhcchhhHHH
Q 003204          559 VLKVLQVWSDWFLFSDAYVNGLRATFLRSGNSGVTPFHSICGDAPEIDKKNNSED--TCDLSKTNQDTALAMGKGAAIKE  636 (839)
Q Consensus       559 V~~vL~iWe~~~vfp~~~l~~L~~~fl~~~~s~~~~~~~~~~~~~~~e~~~~~~d--~~dg~~~~~~~~~~~~~~~~~~~  636 (839)
                      |++||++|++|.|||.+||.+|+++||| .+++.+++++ |++.+++++.....+  ++||++++  +.      .+--+
T Consensus       544 V~kVirvWedW~ifpe~~l~~l~~~Flg-~~~~~~~~~s-e~~~~die~~~~a~~eedldgvple--~~------~agip  613 (877)
T KOG0151|consen  544 VMKVIRVWEDWAIFPEDFLIGLQNTFLG-LNNIVTEKES-EADAPDIENAPLAGNEEDLDGVPLE--DE------DAGIP  613 (877)
T ss_pred             HHHHHHHHHHHHhCcHHHHHHHHHHHhc-CCCCcccccc-cccchhhccCcccCchhhccCCCch--hh------hcCCc
Confidence            9999999999999999999999999999 4556678888 999999998886543  56777665  11      11236


Q ss_pred             HhcCChHHHHHHHHHcCcccccChHHHHHHHHhHHHHHHhhcccccchh-hhcccCCCCCCCCCCcccccccccccCCcC
Q 003204          637 LMNLPLSELERRCRHNGLSLVGGREMMVARLLSLEDAEKQRGYELDDDL-KSAHSQSSSGRYSRGWKETNMEAESMGLSG  715 (839)
Q Consensus       637 ~~~~~~~~l~~~c~~~Gl~~~~~~~~~i~rL~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  715 (839)
                      ++..++++|+++| ++++..-+++.+|++++.++..+..|..+|+.+.. +++|+.+     .+-|...+...+++    
T Consensus       614 ~~n~pi~eld~~~-l~~dd~ldgipm~~e~~ss~s~~~~~sk~e~vd~~~~~~q~vs-----tskwe~~~~~~~~~----  683 (877)
T KOG0151|consen  614 LMNTPIDELDGRP-LNLDDDLDGIPMMVETKSSLSDPETPSKWEAVDESFKEGQAVS-----TSKWEHVDDEFEPK----  683 (877)
T ss_pred             cccCchhhhcccc-ccccccccCceeeeeeccccCCCcccccccccCcccccccccc-----hhhhhhcccccccc----
Confidence            7888899999999 99999999999999999999999999999999998 8888873     23488888888877    


Q ss_pred             CCcchhhhhhhhcCCCcCCCCCccCCcchhhhhhccccCCCcccCCccccccCCchHHhhccCCCCCcccCCCCCCCCCC
Q 003204          716 WNGYEEDEKLSQAVGSVPLGTMLTTPQPEIKAFTKKEKNDPVLPASKWALEDDESDDEQKRSSRGLGLSYSSSGSENAGD  795 (839)
Q Consensus       716 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~s~w~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~  795 (839)
                      .++|.++++--                            .||    ||   |||.+++++..       ||| |+++.| 
T Consensus       684 ~~s~~~~e~ed----------------------------~~~----k~---~de~~~~~~~~-------~ss-~~~~~d-  719 (877)
T KOG0151|consen  684 KNSYDEVEEED----------------------------NPV----KY---DDEDRDKLRDI-------ESS-GSDNQD-  719 (877)
T ss_pred             cccccchhccc----------------------------ccc----cc---chhhhHHHhhh-------hhh-cccccc-
Confidence            78888877611                            333    99   88999999988       888 999998 


Q ss_pred             CCCCCCCccccCCCCCcCCCCCCCChHHhhcccceeeeeeecc
Q 003204          796 GPSKADDVDFTIDASIPVQPDSGMNEEQRSDHRLLSFAFLLIE  838 (839)
Q Consensus       796 ~~~~~~~~~~~~~~~~~~~~~~~~~~e~r~~~r~~~~~~~~~~  838 (839)
                       ..+.+..+...+++|+.|++..++.++||++|.++||+++|.
T Consensus       720 -~l~sg~~~lk~~~sv~~qpe~~~d~~l~q~~r~~~~a~~e~~  761 (877)
T KOG0151|consen  720 -ELESGERDLKPGSSVREQPENERDRLLRQDVRVEAIALIEYR  761 (877)
T ss_pred             -ccCCCCccCCCCCccccChhhHHHHHHHHHHHHHHHHhhhhh
Confidence             579999999999999999999999999999999999999986

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

>KOG2669 consensus Regulator of nuclear mRNA [RNA processing and modification]	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

>PLN03134 glycine-rich RNA-binding protein 4; Provisional	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

>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

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

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

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

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

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

>TIGR01659 sex-lethal sex-lethal family splicing factor	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

>KOG0149 consensus Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only]	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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG0111 consensus Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]	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

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

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

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

>smart00362 RRM_2 RNA recognition motif	Back alignment and domain information

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

>PLN03121 nucleic acid binding protein; 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

>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

>KOG0117 consensus Heterogeneous nuclear ribonucleoprotein R (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

>KOG0131 consensus Splicing factor 3b, subunit 4 [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

>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

>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

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

>KOG0105 consensus Alternative splicing factor ASF/SF2 (RRM superfamily) [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

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (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

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

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

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

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

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

>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

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

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

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

>KOG0144 consensus RNA-binding protein CUGBP1/BRUNO (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

>smart00361 RRM_1 RNA recognition motif	Back alignment and domain information

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

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

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

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

>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

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

>KOG0110 consensus RNA-binding protein (RRM superfamily) [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

>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

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

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

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

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

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

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

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

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

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

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

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

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

>KOG1457 consensus RNA binding protein (contains RRM repeats) [General function prediction only]	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

>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

>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

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

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

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

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

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

>KOG1855 consensus Predicted RNA-binding protein [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

>KOG0120 consensus Splicing factor U2AF, large subunit (RRM superfamily) [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

>KOG1190 consensus Polypyrimidine tract-binding protein [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

>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

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

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

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

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

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

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

>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

>KOG4676 consensus Splicing factor, arginine/serine-rich [RNA processing and modification]	Back alignment and domain information

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

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

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

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

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

>KOG4211 consensus Splicing factor hnRNP-F and related RNA-binding proteins [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

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

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

>KOG1996 consensus mRNA splicing factor [RNA processing and modification]	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

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

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

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

>KOG0115 consensus RNA-binding protein p54nrb (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

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

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

>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [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

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

Homologous Structure Templates