Citrus Sinensis ID: 041390

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-------64

MDSYEATKLVFSRIKAIDPENASKIMGYLLIQDNGDKEMIRLAFGPETLLHNLIFKAKTHLSNASASASASATNPSSLSPSSAPWLPPASLSYANVVNGSSCSSTNAAASASESLYYSNISNNNSYASSDIADDFHQFQDHLSFLDESSELASSTDADHHNHHHLLKRSLSLPVHPNVCFGSDDDPNSGLGWKHCLYFAKGFCKNGTACKFHHIHSPEAATAAAIVGSPSKLSEFELSQELLLRSKASVQQRKLAAASQFMGSFPYNKCMNFLNDTQRSAALMMGDELHNKFGTCSRPERNDFFGSMNPSARQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVTFVYPETVKLILAKGNPHFVCDSRVLVKPYKEKGKVQEKKQQQHQQQMERGEYSSACSSPSGPFDFHFGGRMLYNNQEMLRRKLEEQADLQQAIEMQGRRLMNLQLHLKNNHLNHQFHHGLSNGSPIPSPTLSHSPNNRTRIFPFEGSDEEVPPEESGVSPVTDSQITDHLFHREENRTSNHNKNNNSDGNDKEEKPNSDENDLCDSLEHILPDNLFASPKKSAGGHITVFSSASAEVDEKNTSSVTSTNNNTKLPSTSLNMSSLNSCLLQMSRFSSGQGTIGM

ccHHHHHHHHHHHHHHcccccHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccEEEEcccccccccHHHHHHHHcccccEEEEEEcccccccEEEEEEccHHHHHHHHHccccEEEcccEEEEEEcccccccHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

ccHHHHHHHHHHHHHHccHHHHHHHHHHHHHcccccHHHHHHHcccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccccEEEcccccccccHHccccccccccHHHHHHHHHHHHccHHcHcccccHccccccccccccccccccccHcccEEEccHHHHHcccccccccccccccccccccEEEEEEcccccccHHHHHHHHHHccccEEEEcccccccEEEEEEEEcHHHHHHHHHcccccEEcccEEEEEcccccccccccccHHHHHHccccccccccccccccccccccHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHccccHHccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc

MDSYEATKLVFSRIkaidpenasKIMGYLLIQDNGDKEMIRlafgpetllHNLIFKAKthlsnasasasasatnpsslspssapwlppaslsyanvvngsscsstnaaASASESLYYsnisnnnsyassdiaddfhqfQDHLsfldesselasstdadhhnhhhllkrslslpvhpnvcfgsdddpnsglgwkhCLYFAKGfckngtackfhhihspeaATAAAivgspsklsEFELSQELLLRSKASVQQRKLAAASQfmgsfpynkcmnfLNDTQRSAALMMGDElhnkfgtcsrperndffgsmnpsarqiyltfpadstfreedvsnyfsiygpvhdvripyqqkrmfgfvTFVYPETVKLILAkgnphfvcdsrvlvkpykekgkVQEKKQQQHQQQMergeyssacsspsgpfdfhfggrmlyNNQEMLRRKLEEQADLQQAIEMQGRRLMNLQLHLKNnhlnhqfhhglsngspipsptlshspnnrtrifpfegsdeevppeesgvspvtdsqitdhlfhreenrtsnhnknnnsdgndkeekpnsdendlcdslehilpdnlfaspkksagghitvfssasaevdekntssvtstnnntklpstslnmSSLNSCLLQMSrfssgqgtigm

MDSYEATKLVFsrikaidpenaskIMGYLLIQDNGDKEMIRLAFGPETLLHNLIFKAKTHLSNASASASASATNPSSLSPSSAPWLPPASLSYANVVNGSSCSSTNAAASASESLYYSNISNNNSYASSDIADDFHQFQDHLSFLDESSELASSTDADHHNHHHLLKRSLSLPVHPNVCFGSDDDPNSGLGWKHCLYFAKGFCKNGTACKFHHIHSPEAATAAAIVGSPSKLSEFELSQELLLRSKASVQQRKLAAASQFMGSFPYNKCMNFLNDTQRSAALMMGDELHNKFGTCSRPERNDFFGSMNPSARQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVTFVYPETVKLILAKGNPHFVCDSRVLVKPYKEKGKVQEKKQQQHQQQMERGEYSSACSSPSGPFDFHFGGRMLYNNQEMLRRKLEEQADLQQAIEMQGRRLMNLQLHLKNNHLNHQFHHGLSNGSPIPSPTLSHSPNNRTRIFPFEGSDEEVPPEESGVSPVTDSQITDHLfhreenrtsnhnknnnsdgndkeekpNSDENDLCDSLEHILPDNLFASPKKSAGGHITVFSsasaevdekntssvtstnnntklpstSLNMSSLNSCLLQMSrfssgqgtigm

MDSYEATKLVFSRIKAIDPENASKIMGYLLIQDNGDKEMIRLAFGPETLLHNLIFKAKTHlsnasasasasatnpsslspssapwlppaslsYANVVNGsscsstnaaasaseslyysnisnnnsyassdiaddFHQFQDHLSFLDESSELASSTDADHHNHHHLLKRSLSLPVHPNVCFGSDDDPNSGLGWKHCLYFAKGFCKNGTACKFHHIHSPEAATAAAIVGSPSKlsefelsqelllrsKASVQQRKLAAASQFMGSFPYNKCMNFLNDTQRSAALMMGDELHNKFGTCSRPERNDFFGSMNPSARQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVTFVYPETVKLILAKGNPHFVCDSRVLVKPYkekgkvqekkqqqhqqqmeRGEYSSACSSPSGPFDFHFGGRMLYNNQEMLRRKLEEQADLQQAIEMQGRRlmnlqlhlknnhlnhqfhhGLSNGSPIPSPTLSHSPNNRTRIFPFegsdeevppeesgvspvTDSQITDHLFHReenrtsnhnknnnsdgndkeeKPNSDENDLCDSLEHILPDNLFASPKKSAGGHITVFSSASAEVDEKntssvtstnnntKlpstslnmsslnscllqmsRFSSGQGTIGM

*******KLVFSRIKAIDPENASKIMGYLLIQDNGDKEMIRLAFGPETLLHNLIFKAKT**********************************************************************************************************LKRSLSLPVHPNVCFGSDDDPNSGLGWKHCLYFAKGFCKNGTACKFHHIHSPEAATAAAIV****************************AAASQFMGSFPYNKCMNFLNDTQRSAALMMGDELHNKFGTC*******FFG****SARQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVTFVYPETVKLILAKGNPHFVCDSRVLVKP***********************************DFHFGGRMLYN*************************LMNLQLHLKNNHL***************************************************************************************************************************************************************************

****EATKLVFSRIKAIDPENASKIMGYLLIQDNGDKEMIRLAFGPETLLHNLIFKAKTHL************************************************************************************************************************************HCLYFAKGFCKNGTACKFHHI***************************************************************************************************IYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVTFVYPETVKLILAKGNPHFVCDSRVLVKPY*************************************************************************************************************************************************************************************************************************************LNMSSLNSCLLQMSRFSS****IGM

MDSYEATKLVFSRIKAIDPENASKIMGYLLIQDNGDKEMIRLAFGPETLLHNLIFKAKTH***********************PWLPPASLSYANVVNGSSCSSTNAAASASESLYYSNISNNNSYASSDIADDFHQFQDHLSFLDESSELASSTDADHHNHHHLLKRSLSLPVHPNVCFGSDDDPNSGLGWKHCLYFAKGFCKNGTACKFHHIHSPEAATAAAIVGSPSKLSEFELSQELLLRSKA********AASQFMGSFPYNKCMNFLNDTQRSAALMMGDELHNKFGTCSRPERNDFFGSMNPSARQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVTFVYPETVKLILAKGNPHFVCDSRVLVKPY*****************************PSGPFDFHFGGRMLYNNQEMLRRKLEEQADLQQAIEMQGRRLMNLQLHLKNNHLNHQFHHGLSNGSPIPSPTLSHSPNNRTRIFPFEG*****************SQITDHLFHREENRTS**********************DLCDSLEHILPDNLFASPKKSAGGHITVFSSA****************NNTKLPSTSLNMSSLNSCLLQMSRF*********

MDSYEATKLVFSRIKAIDPENASKIMGYLLIQDNGDKEMIRLAFGPETLLHNLIFKAKTHLSNA**********************************************************NNSYASSDIADDFHQFQDHLSFLDESSELASSTDADHHNHHHLLKRSLSLPVHPNVCFGSDDDPNSGLGWKHCLYFAKGFCKNGTACKFHHIHSPEAATAAAIVGSPSKLSEFELSQELLLRSKASVQQRKLAAASQFMGSFPYNKCMNFLNDTQRSAALMMGDELHNKFGTCSRPERNDFFGSMNPSARQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVTFVYPETVKLILAKGNPHFVCDSRVLVKPYKEKGKVQEKKQQQHQQ*MERGEYSSACSSPSGPFDFHFGGRMLYNNQEMLRRKLEEQADLQQAIEMQGRRLMNLQLHLKNNHLN*QF*HGLSNGSPIPS********************************************************************************************************************************TSLNMSSLNSCLLQ*S***********

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		639	2.2.26 [Sep-21-2011]
Q0D3J9		682	Zinc finger CCCH domain-c	yes	no	0.920	0.862	0.413	1e-111
Q10M00		688	Zinc finger CCCH domain-c	no	no	0.928	0.861	0.403	1e-104
Q10LZ9		677	Zinc finger CCCH domain-c	no	no	0.929	0.877	0.404	1e-102
Q9SV09		540	Zinc finger CCCH domain-c	yes	no	0.809	0.957	0.428	2e-98
Q94CJ8		650	Zinc finger CCCH domain-c	no	no	0.757	0.744	0.409	7e-85
Q9SJ41		536	Zinc finger CCCH domain-c	no	no	0.546	0.651	0.341	1e-43
Q6ZK57		653	Zinc finger CCCH domain-c	no	no	0.391	0.382	0.361	9e-36
Q84ZT0		513	Putative zinc finger CCCH	no	no	0.298	0.372	0.359	4e-27
Q54PB2		895	Multiple RNA-binding doma	yes	no	0.122	0.087	0.383	0.0002

>sp\|Q0D3J9\|C3H53_ORYSJ Zinc finger CCCH domain-containing protein 53 OS=Oryza sativa subsp. japonica GN=Os07g0682400 PE=2 SV=1	Back alignment and function desciption

 Score =  404 bits (1039), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 303/733 (41%), Positives = 391/733 (53%), Gaps = 145/733 (19%)

Query: 1   MDSYEATKLVFSRIKAIDPENASKIMGYLLIQDNGDKEMIRLAFGPETLLHNLIFKAKTH 60
           MD+YEATK+VFSRI+A+DP++A+KIMG+LLIQD+G+KEMIRLAFGPE LLH ++ KA+  
Sbjct: 1   MDAYEATKVVFSRIQALDPDHAAKIMGFLLIQDHGEKEMIRLAFGPEALLHTVMAKARKE 60

Query: 61  LSNASASASASATNPSSLSPSSAPWLPPASLSYANVVNGSSCSSTNAAASASESLYYSNI 120
           L    AS   +   P+S++ ++A    P  LS  N     +  S  + +S S        
Sbjct: 61  LGLLPASGPGT---PTSVAAAAAAAHSPFMLSRQNSGRCGTAPSPLSVSSPSSWAPPPVF 117

Query: 121 SNNNS----------------------------YASSDIADDFHQFQDHLSFLDESS--- 149
           S NNS                            +   D   D  Q QD L+FL+E     
Sbjct: 118 SRNNSISNGAGEEMVGLGDELISPANGGGPPSPFFGGDPLMDELQLQDQLAFLNEGGVPA 177

Query: 150 ----------ELASSTDADHHNHHHLLKRSLSLPVH------PNVCFGSDDDPNSGLGWK 193
                     E  S    D     + L  +   P H        +C G  D    GLGWK
Sbjct: 178 GHQMPMFDGGECRSPGGGDGGLFSYNLGWANGGPGHRRSASVSELCLGGAD----GLGWK 233

Query: 194 HCLYFAKGFCKNGTACKFHHIHSPEAATAAAIVGSPSKLSEFELSQELLLRSKASVQQRK 253
            CLY+A+G+CKNG+AC+F H   P+ A        PS + +    Q+ L+RSK+   QR 
Sbjct: 234 PCLYYARGYCKNGSACRFVHGGLPDDAAGKM---DPSAVEQ--QCQDFLIRSKS---QRL 285

Query: 254 LAAASQF--MGSFP-----YNKCMNFL-------NDTQRSAA---LMMGDELHNKFGTCS 296
            AAA  +   GS P       KC++ L       N++QR+AA   LM+G +  +KF    
Sbjct: 286 AAAAFPYSPTGSLPGSPSAATKCLSLLLQQQQQQNESQRAAAAAALMLGGDEAHKFMGRP 345

Query: 297 RPERNDFFGSMNPSARQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVT 356
           R ER DF   MNP +RQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVT
Sbjct: 346 RLERADFASMMNPGSRQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVT 405

Query: 357 FVYPETVKLILAKGNPHFVCDSRVLVKPYKEKGKVQEKKQQQHQQQMERGEYSSACSSPS 416
           FVYPETVKLILAKGNPHF+CD+RVLVKPYKEKGKV +K ++QHQ   ER ++SS C++P+
Sbjct: 406 FVYPETVKLILAKGNPHFICDARVLVKPYKEKGKVPDKYRKQHQPG-ERVDFSS-CTTPT 463

Query: 417 G-----PFDFH-FGGRMLYN----NQEMLRRK---LEEQADLQQAIEMQGRRLMNLQLHL 463
           G     PFD H  G RML +    N+ +LRRK    ++ A+LQQAIE+  RRLM LQL  
Sbjct: 464 GLDARDPFDMHQLGARMLQHSNSANEMLLRRKLEEQQQAAELQQAIELHSRRLMGLQL-- 521

Query: 464 KNNHLNHQFHHGLSNGSPIPSPTLSHSPNNRTRIFPFEGSDEEVPPEESGVSPVTDSQIT 523
               L+ +     S  +  P+P  +          PF  S        +G SP    ++ 
Sbjct: 522 ----LDFK-----SRAAAAPTPIGN----------PFSASQTAA--NATGESPPDSGELG 560

Query: 524 DHLFHREENRTSNHNKNNNSDGNDKEE------KPNSDENDLCDSLEHILPDNLFASPKK 577
                +       H K  N  G DKEE       PN+D +    S+EH LPD+ FASP K
Sbjct: 561 -----KGSGFLLAHKKAVN--GADKEESTGESSSPNTDSD---QSVEHNLPDSPFASPTK 610

Query: 578 SAGGHITVFSSASAEVDEKNTSSVTST-----------NNNTKLPSTSLNMSSLNSCLLQ 626
           SAG     F+   AE+    ++  ++T             N  LPS +L+M S       
Sbjct: 611 SAGFARDPFAPTEAEISATASTGCSATYVGINNGASNGGTNHLLPS-ALDMPSPKPYFFP 669

Query: 627 MSRFSSGQGTIGM 639
           MSR +S  G IGM
Sbjct: 670 MSRLASDHGAIGM 682

Oryza sativa subsp. japonica (taxid: 39947)

>sp\|Q10M00\|C3H22_ORYSJ Zinc finger CCCH domain-containing protein 22 OS=Oryza sativa subsp. japonica GN=Os03g0328900 PE=2 SV=2	Back alignment and function description

>sp\|Q10LZ9\|C3H23_ORYSJ Zinc finger CCCH domain-containing protein 23 OS=Oryza sativa subsp. japonica GN=Os03g0329200 PE=2 SV=1	Back alignment and function description

>sp\|Q9SV09\|C3H46_ARATH Zinc finger CCCH domain-containing protein 46 OS=Arabidopsis thaliana GN=At3g51950 PE=1 SV=1	Back alignment and function description

>sp\|Q94CJ8\|C3H55_ARATH Zinc finger CCCH domain-containing protein 55 OS=Arabidopsis thaliana GN=At5g12440 PE=2 SV=3	Back alignment and function description

>sp\|Q9SJ41\|C3H18_ARATH Zinc finger CCCH domain-containing protein 18 OS=Arabidopsis thaliana GN=At2g05160 PE=2 SV=1	Back alignment and function description

>sp\|Q6ZK57\|C3H54_ORYSJ Zinc finger CCCH domain-containing protein 54 OS=Oryza sativa subsp. japonica GN=Os08g0126700 PE=2 SV=2	Back alignment and function description

>sp\|Q84ZT0\|C3H51_ORYSJ Putative zinc finger CCCH domain-containing protein 51 OS=Oryza sativa subsp. japonica GN=Os07g0583300 PE=4 SV=1	Back alignment and function description

>sp\|Q54PB2\|MRD1_DICDI Multiple RNA-binding domain-containing protein 1 OS=Dictyostelium discoideum GN=mrd1 PE=3 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		639
224104191		685	predicted protein [Populus trichocarpa]	0.973	0.908	0.582	0.0
255544928		700	nucleic acid binding protein, putative [	0.978	0.892	0.593	0.0
225436555		695	PREDICTED: zinc finger CCCH domain-conta	0.971	0.893	0.561	1e-176
147807899		697	hypothetical protein VITISV_021251 [Viti	0.970	0.889	0.560	1e-175
297734950		615	unnamed protein product [Vitis vinifera]	0.907	0.943	0.560	1e-166
356542909		704	PREDICTED: zinc finger CCCH domain-conta	0.946	0.859	0.486	1e-151
356529848		696	PREDICTED: zinc finger CCCH domain-conta	0.959	0.880	0.494	1e-149
356542895		698	PREDICTED: zinc finger CCCH domain-conta	0.934	0.855	0.484	1e-148
356531625		700	PREDICTED: zinc finger CCCH domain-conta	0.945	0.862	0.488	1e-146
224072821		680	predicted protein [Populus trichocarpa]	0.921	0.866	0.471	1e-138

>gi\|224104191\|ref\|XP_002313352.1\| predicted protein [Populus trichocarpa] gi\|222849760\|gb\|EEE87307.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

 Score =  686 bits (1770), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 409/702 (58%), Positives = 492/702 (70%), Gaps = 80/702 (11%)

Query: 1   MDSYEATKLVFSRIKAIDPENASKIMGYLLIQDNGDKEMIRLAFGPETLLHNLIFKAKTH 60
           MDSYEAT +VFSRI++++PENASKIMGYLL+QD G+KEMIRLAFGPETLL NLI + KT 
Sbjct: 1   MDSYEATNIVFSRIQSLEPENASKIMGYLLLQDYGEKEMIRLAFGPETLLQNLILQTKTQ 60

Query: 61  L---SNASASAS-----ASATNPSSLSPSSAP-------------------WLPP---AS 90
           L   SN  ++ S     +S  +P  +S S  P                    L P    S
Sbjct: 61  LGFPSNTPSTPSPAFIPSSRPSPLYISSSRIPNNNGFDITNSSSPSTNSWPLLSPNSTTS 120

Query: 91  LSYANVVNGSS---CSSTNAAASASESLYYSNISNNNSYASSDIADDFHQFQDHLSFLDE 147
           LSYA+VVNG+S     ST    + S S  +S  SNNN  A+ D+ D++ + Q+  SFL++
Sbjct: 121 LSYASVVNGASNINAGSTPFQPTVSLSKAFS-YSNNNDNAN-DLVDEY-ELQERFSFLND 177

Query: 148 S---------SELASSTDADHHNHHHLLKRSLSLPVHPNVCFGSDDDPNSGLGWKHCLYF 198
           S          ELA S  A   N  H  KRS S+P    +CFGS+D  NSG GWK CLYF
Sbjct: 178 SKTDDLFDPRGELAMSPPAFGDNSLH--KRSFSVP---GMCFGSEDS-NSGFGWKPCLYF 231

Query: 199 AKGFCKNGTACKFHHIHSPEAATAAAIVGSPSKLSEFELSQELLLRSKASVQQRKLAAAS 258
           ++GFCKNGT C+F H    ++A +AAIVGSPS+L+EFE  QE+L RSKA+ QQRKLAAAS
Sbjct: 232 SRGFCKNGTGCRFVH---GDSADSAAIVGSPSELNEFEQCQEIL-RSKAAAQQRKLAAAS 287

Query: 259 QFMGS---FPYNKCMNFL----NDTQRSAA---LMMGDELHNKFGTCSRPERNDF----- 303
           QFM      P NKCMNFL    N++QRSAA   LMMGDE+H KFG   RPER+DF     
Sbjct: 288 QFMAGATFLPQNKCMNFLHQQQNESQRSAAAAALMMGDEIH-KFGRI-RPERSDFSQMGL 345

Query: 304 FGSMNPSARQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVTFVYPETV 363
            G+M+PSARQIYLTFPADSTFREEDVS+YFS YGPV DVRIPYQQKRMFGFVTFV+ ETV
Sbjct: 346 GGAMSPSARQIYLTFPADSTFREEDVSSYFSFYGPVQDVRIPYQQKRMFGFVTFVFAETV 405

Query: 364 KLILAKGNPHFVCDSRVLVKPYKEKGKVQEKKQQQHQQQMERGEYSSACSSPSG-----P 418
           KLILAKGNPHFVCDSRVLVKPYKEKGKV +KK QQ QQQ+ER EY SAC SPS      P
Sbjct: 406 KLILAKGNPHFVCDSRVLVKPYKEKGKVPDKKHQQ-QQQIEREEY-SACPSPSRINCREP 463

Query: 419 FDFHFGGRMLYNNQEMLRRKLEEQADLQQAIEMQGRRLMNLQLHLKNNHLNHQFHHGLSN 478
           FD H GGRM YN QEMLRRKLEE+ADLQQAIE+Q RRL+NLQL    NH  H++ HGLS 
Sbjct: 464 FDLHLGGRMFYNTQEMLRRKLEEEADLQQAIELQERRLLNLQLLDLKNHRQHRYFHGLST 523

Query: 479 GSPIPSPTLSHSPNNRTRIFPFEGSDEEVPPEESGVSPVTDSQITDHLFHREENRTSNHN 538
           GSP+PSPT+ HSPNN+T  FP +G D+EV   E+G +P   +         +E   + ++
Sbjct: 524 GSPLPSPTILHSPNNQTLFFPIDGIDKEVQHAENGSNPDAAAAQNAVADADQEVSPACNH 583

Query: 539 KNNNSDGNDKEEKPNSDENDLCDSLEHILPDNLFASPKKSAGGHITVFSSASAEVDEKNT 598
            + N +  DKEEK NSDE+DL ++LEHILPDNLF SPKKSAG ++TVFS+AS EVD+ ++
Sbjct: 584 NDGNGNNRDKEEKSNSDESDLNENLEHILPDNLFGSPKKSAGDNLTVFSTASVEVDDNSS 643

Query: 599 SSVTST-NNNTKLPSTSLNMSSLNSCLLQMSRFSSGQGTIGM 639
           S  TS+ N+N  +P+TSLNM+SL SC LQM R SSG GT+G+
Sbjct: 644 SLTTSSPNSNPLVPTTSLNMTSLKSCFLQMPRLSSGHGTVGI 685

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|255544928\|ref\|XP_002513525.1\| nucleic acid binding protein, putative [Ricinus communis] gi\|223547433\|gb\|EEF48928.1\| nucleic acid binding protein, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|225436555\|ref\|XP_002274487.1\| PREDICTED: zinc finger CCCH domain-containing protein 53-like [Vitis vinifera]	Back alignment and taxonomy information

>gi\|147807899\|emb\|CAN62156.1\| hypothetical protein VITISV_021251 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|297734950\|emb\|CBI17184.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|356542909\|ref\|XP_003539907.1\| PREDICTED: zinc finger CCCH domain-containing protein 53-like [Glycine max]	Back alignment and taxonomy information

>gi\|356529848\|ref\|XP_003533499.1\| PREDICTED: zinc finger CCCH domain-containing protein 53-like [Glycine max]	Back alignment and taxonomy information

>gi\|356542895\|ref\|XP_003539900.1\| PREDICTED: zinc finger CCCH domain-containing protein 53-like [Glycine max]	Back alignment and taxonomy information

>gi\|356531625\|ref\|XP_003534377.1\| PREDICTED: zinc finger CCCH domain-containing protein 53-like [Glycine max]	Back alignment and taxonomy information

>gi\|224072821\|ref\|XP_002303898.1\| predicted protein [Populus trichocarpa] gi\|222841330\|gb\|EEE78877.1\| predicted protein [Populus trichocarpa]	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		639
TAIR\|locus:2083740		540	AT3G51950 [Arabidopsis thalian	0.386	0.457	0.514	6.4e-79
TAIR\|locus:505006612		650	AT5G12440 [Arabidopsis thalian	0.482	0.473	0.463	1.7e-78
TAIR\|locus:2092970		602	AT3G21100 [Arabidopsis thalian	0.511	0.543	0.413	6e-71
TAIR\|locus:2033882		513	AT1G51520 [Arabidopsis thalian	0.295	0.368	0.462	7.6e-53
TAIR\|locus:2051239		536	AT2G05160 [Arabidopsis thalian	0.134	0.160	0.689	9.6e-41
TAIR\|locus:2085211		381	AT3G52980 [Arabidopsis thalian	0.109	0.183	0.690	6.3e-33

TAIR\|locus:2083740 AT3G51950 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 541 (195.5 bits), Expect = 6.4e-79, Sum P(3) = 6.4e-79
 Identities = 145/282 (51%), Positives = 162/282 (57%)

Query:   180 FGSDDDPNSGLGWKHCLYFAKGFCKNGTACKFHHIHSPEAATAAAIVGSPXXXXXXXXXX 239
             +G D D   G G   C YFA+GFCKNG +C+F  +HS   A    +VGSP          
Sbjct:   141 YGGDSD--LGFGGVPCSYFARGFCKNGASCRF--VHSDGGAD---LVGSPSRIELL---- 189

Query:   240 XXXXRSKASVQQRKLAAASQFMGSFPY--NKCMNFL-NDTQRSAA-LMMGDELHNKFGTC 295
                 RS  SV  R LA       S P    K +N   ND QR+AA LM+GDEL  K G  
Sbjct:   190 ----RSN-SVPPR-LAHHFMTRSSLPSFSTKGVNLQQNDVQRAAAALMIGDELQ-KLGRW 242

Query:   296 SRPERNDFFGSMNPSARQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFV 355
              RPER D      P++RQIYLTFPADS FREEDVSNYFS +GPV DVRIPYQQKRMFGFV
Sbjct:   243 -RPERIDLSAMACPASRQIYLTFPADSRFREEDVSNYFSTFGPVQDVRIPYQQKRMFGFV 301

Query:   356 TFVYPETVKLILAKGNPHFVCDSRVLVKPYXXXXXXXXXXXXXXXXXXXRGEYSSACSSP 415
             TFVYPETVK ILAKGNPHFVCDSRVLVKPY                     E S      
Sbjct:   302 TFVYPETVKSILAKGNPHFVCDSRVLVKPYKEKGKVPDKYRTNQTTER---ELSPT-GLD 357

Query:   416 SGPFDFHFGGRMLYNN-QEML-RRKLEEQADLQQAIEMQGRR 455
             S P D   GGR  YNN Q++L R K EE+      +E+Q RR
Sbjct:   358 SSPRDV-LGGRGFYNNTQDVLWRSKFEEEI-----LELQSRR 393

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0003723 "RNA binding" evidence=ISS

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=RCA

TAIR\|locus:505006612 AT5G12440 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2092970 AT3G21100 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2033882 AT1G51520 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2051239 AT2G05160 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2085211 AT3G52980 [Arabidopsis thaliana (taxid:3702)]	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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9SV09	C3H46_ARATH	3, ., 1, ., -, ., -	0.4283	0.8090	0.9574	yes	no
Q0D3J9	C3H53_ORYSJ	No assigned EC number	0.4133	0.9201	0.8621	yes	no

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		639
cd12458		70	cd12458, RRM_AtC3H46_like, RNA recognition motif i	1e-37
smart00360		73	smart00360, RRM, RNA recognition motif	1e-08
cd12328		73	cd12328, RRM2_hnRNPA_like, RNA recognition motif 2	1e-07
cd12322		71	cd12322, RRM2_TDP43, RNA recognition motif 2 in TA	4e-07
cd00590		72	cd00590, RRM_SF, RNA recognition motif (RRM) super	3e-06
cd12325		72	cd12325, RRM1_hnRNPA_hnRNPD_like, RNA recognition	5e-06
pfam14259		69	pfam14259, RRM_6, RNA recognition motif (a	1e-05
cd12297		78	cd12297, RRM2_Prp24, RNA recognition motif 2 in fu	4e-05
cd12407		76	cd12407, RRM_FOX1_like, RNA recognition motif in v	4e-05
cd12574		82	cd12574, RRM1_DAZAP1, RNA recognition motif 1 in D	6e-05
cd12323		74	cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-	7e-05
cd12595		70	cd12595, RRM1_SRSF5, RNA recognition motif 1 in ve	8e-05
cd12321		77	cd12321, RRM1_TDP43, RNA recognition motif 1 in TA	8e-05
cd12229		81	cd12229, RRM_G3BP, RNA recognition motif (RRM) in	1e-04
cd12412		80	cd12412, RRM_DAZL_BOULE, RNA recognition motif in	2e-04
cd12329		75	cd12329, RRM2_hnRNPD_like, RNA recognition motif 2	2e-04
cd12327		80	cd12327, RRM2_DAZAP1, RNA recognition motif 2 in D	2e-04
cd12552		77	cd12552, RRM_Nop15p, RNA recognition motif in yeas	2e-04
smart00356		27	smart00356, ZnF_C3H1, zinc finger	2e-04
pfam00076		70	pfam00076, RRM_1, RNA recognition motif	8e-04
cd12307		74	cd12307, RRM_NIFK_like, RNA recognition motif in n	0.001
cd12399		78	cd12399, RRM_HP0827_like, RNA recognition motif in	0.001
cd12363		78	cd12363, RRM_TRA2, RNA recognition motif in transf	0.002
pfam13893		56	pfam13893, RRM_5, RNA recognition motif	0.002
cd12357		89	cd12357, RRM_PPARGC1A_like, RNA recognition motif	0.002
cd12673		81	cd12673, RRM_BOULE, RNA recognition motif in prote	0.003
cd12316		74	cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition mot	0.004
cd12567		79	cd12567, RRM3_RBM19, RNA recognition motif 3 in RN	0.004

>gnl\|CDD\|240904 cd12458, RRM_AtC3H46_like, RNA recognition motif in Arabidopsis thaliana zinc finger CCCH domain-containing protein 46 (AtC3H46) and similar proteins	Back alignment and domain information

 Score =  133 bits (336), Expect = 1e-37
 Identities = 55/70 (78%), Positives = 58/70 (82%)

Query: 314 IYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVTFVYPETVKLILAKGNPH 373
           IYLTFPADS F EEDVS YF  +GPV DVRIPYQQKRMFGFVTF   ETVK IL+KGNPH
Sbjct: 1   IYLTFPADSRFTEEDVSEYFGQFGPVLDVRIPYQQKRMFGFVTFENAETVKRILSKGNPH 60

Query: 374 FVCDSRVLVK 383
           F+C SRV VK
Sbjct: 61  FICGSRVRVK 70

This subfamily corresponds to the RRM domain in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity. . Length = 70

>gnl\|CDD\|214636 smart00360, RRM, RNA recognition motif	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\|240768 cd12322, RRM2_TDP43, RNA recognition motif 2 in TAR DNA-binding protein 43 (TDP-43) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240668 cd00590, RRM_SF, RNA recognition motif (RRM) superfamily	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\|222631 pfam14259, RRM_6, RNA recognition motif (a	Back alignment and domain information

>gnl\|CDD\|240743 cd12297, RRM2_Prp24, RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) 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\|241018 cd12574, RRM1_DAZAP1, RNA recognition motif 1 in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins	Back alignment and domain information

>gnl\|CDD\|240769 cd12323, RRM2_MSI, RNA recognition motif 2 in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins	Back alignment and domain information

>gnl\|CDD\|241039 cd12595, RRM1_SRSF5, RNA recognition motif 1 in vertebrate serine/arginine-rich splicing factor 5 (SRSF5)	Back alignment and domain information

>gnl\|CDD\|240767 cd12321, RRM1_TDP43, RNA recognition motif 1 in TAR DNA-binding protein 43 (TDP-43) and similar proteins	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\|240858 cd12412, RRM_DAZL_BOULE, RNA recognition motif in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE	Back alignment and domain information

>gnl\|CDD\|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins	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\|240996 cd12552, RRM_Nop15p, RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins	Back alignment and domain information

>gnl\|CDD\|214632 smart00356, ZnF_C3H1, zinc finger	Back alignment and domain information

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

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

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

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

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

>gnl\|CDD\|240803 cd12357, RRM_PPARGC1A_like, RNA recognition motif in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators	Back alignment and domain information

>gnl\|CDD\|241117 cd12673, RRM_BOULE, RNA recognition motif in protein BOULE	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\|241011 cd12567, RRM3_RBM19, RNA recognition motif 3 in RNA-binding protein 19 (RBM19) 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		639
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	99.57
PLN03134		144	glycine-rich RNA-binding protein 4; Provisional	99.55
KOG0153		377	consensus Predicted RNA-binding protein (RRM super	99.48
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.44
KOG0125		376	consensus Ataxin 2-binding protein (RRM superfamil	99.38
TIGR01661		352	ELAV_HUD_SF ELAV/HuD family splicing factor. These	99.37
PF00076		70	RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or	99.34
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	99.3
KOG0149		247	consensus Predicted RNA-binding protein SEB4 (RRM	99.28
PLN03120		260	nucleic acid binding protein; Provisional	99.28
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	99.27
KOG0111		298	consensus Cyclophilin-type peptidyl-prolyl cis-tra	99.23
TIGR01659		346	sex-lethal sex-lethal family splicing factor. This	99.2
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	99.16
smart00362		72	RRM_2 RNA recognition motif.	99.14
KOG0122		270	consensus Translation initiation factor 3, subunit	99.13
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	99.13
PF14259		70	RRM_6: RNA recognition motif (a.k.a. RRM, RBD, or	99.13
PLN03121		243	nucleic acid binding protein; Provisional	99.11
TIGR01645		612	half-pint poly-U binding splicing factor, half-pin	99.11
PF13893		56	RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or	99.11
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.1
KOG4207		256	consensus Predicted splicing factor, SR protein su	99.09
KOG0107		195	consensus Alternative splicing factor SRp20/9G8 (R	99.08
KOG0148		321	consensus Apoptosis-promoting RNA-binding protein	99.07
PLN03213		759	repressor of silencing 3; Provisional	99.07
TIGR01628		562	PABP-1234 polyadenylate binding protein, human typ	99.07
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	99.06
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	99.06
KOG0113		335	consensus U1 small nuclear ribonucleoprotein (RRM	99.05
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	99.04
COG0724		306	RNA-binding proteins (RRM domain) [General functio	99.04
smart00360		71	RRM RNA recognition motif.	99.03
TIGR01649		481	hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor	99.01
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.01
TIGR01648		578	hnRNP-R-Q heterogeneous nuclear ribonucleoprotein	99.0
TIGR01622		457	SF-CC1 splicing factor, CC1-like family. A homolog	99.0
smart00361		70	RRM_1 RNA recognition motif.	98.97
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.97
cd00590		74	RRM RRM (RNA recognition motif), also known as RBD	98.96
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	98.88
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	98.86
KOG0126		219	consensus Predicted RNA-binding protein (RRM super	98.83
KOG0108		435	consensus mRNA cleavage and polyadenylation factor	98.79
KOG0117		506	consensus Heterogeneous nuclear ribonucleoprotein	98.79
KOG0121		153	consensus Nuclear cap-binding protein complex, sub	98.79
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.76
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	98.74
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.74
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	98.74
KOG0114		124	consensus Predicted RNA-binding protein (RRM super	98.74
KOG0132		894	consensus RNA polymerase II C-terminal domain-bind	98.73
KOG0145		360	consensus RNA-binding protein ELAV/HU (RRM superfa	98.71
KOG0105		241	consensus Alternative splicing factor ASF/SF2 (RRM	98.71
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	98.7
KOG0144		510	consensus RNA-binding protein CUGBP1/BRUNO (RRM su	98.69
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	98.69
KOG4205		311	consensus RNA-binding protein musashi/mRNA cleavag	98.62
TIGR01642		509	U2AF_lg U2 snRNP auxilliary factor, large subunit,	98.6
KOG0130		170	consensus RNA-binding protein RBM8/Tsunagi (RRM su	98.55
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	98.52
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	98.51
KOG0127		678	consensus Nucleolar protein fibrillarin NOP77 (RRM	98.48
KOG0131		203	consensus Splicing factor 3b, subunit 4 [RNA proce	98.39
KOG4208		214	consensus Nucleolar RNA-binding protein NIFK [Gene	98.39
KOG0415		479	consensus Predicted peptidyl prolyl cis-trans isom	98.34
KOG0146		371	consensus RNA-binding protein ETR-3 (RRM superfami	98.32
KOG0123		369	consensus Polyadenylate-binding protein (RRM super	98.32
KOG0109		346	consensus RNA-binding protein LARK, contains RRM a	98.27
KOG0124		544	consensus Polypyrimidine tract-binding protein PUF	98.22
KOG4661		940	consensus Hsp27-ERE-TATA-binding protein/Scaffold	98.2
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	98.16
KOG0110		725	consensus RNA-binding protein (RRM superfamily) [G	98.14
KOG0151		877	consensus Predicted splicing regulator, contains R	98.01
KOG4212		608	consensus RNA-binding protein hnRNP-M [RNA process	97.94
KOG0116		419	consensus RasGAP SH3 binding protein rasputin, con	97.94
KOG4454		267	consensus RNA binding protein (RRM superfamily) [G	97.78
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	97.76
KOG0533		243	consensus RRM motif-containing protein [RNA proces	97.67
KOG0226		290	consensus RNA-binding proteins [General function p	97.55
KOG4209		231	consensus Splicing factor RNPS1, SR protein superf	97.55
KOG2135		526	consensus Proteins containing the RNA recognition	97.35
KOG4660		549	consensus Protein Mei2, essential for commitment t	97.33
PF00642		27	zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and si	97.22
PF14605		53	Nup35_RRM_2: Nup53/35/40-type RNA recognition moti	97.06
KOG0147		549	consensus Transcriptional coactivator CAPER (RRM s	96.98
KOG1190		492	consensus Polypyrimidine tract-binding protein [RN	96.96
smart00356		27	ZnF_C3H1 zinc finger.	96.77
KOG1457		284	consensus RNA binding protein (contains RRM repeat	96.75
KOG1548		382	consensus Transcription elongation factor TAT-SF1	96.64
KOG4211		510	consensus Splicing factor hnRNP-F and related RNA-	96.63
KOG0106		216	consensus Alternative splicing factor SRp55/B52/SR	96.6
KOG1548		382	consensus Transcription elongation factor TAT-SF1	96.56
PF05172		100	Nup35_RRM: Nup53/35/40-type RNA recognition motif;	96.55
PF04059		97	RRM_2: RNA recognition motif 2; InterPro: IPR00720	96.46
KOG4210		285	consensus Nuclear localization sequence binding pr	96.34
COG5175		480	MOT2 Transcriptional repressor [Transcription]	96.31
KOG1456		494	consensus Heterogeneous nuclear ribonucleoprotein	96.16
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	96.08
PF00658		72	PABP: Poly-adenylate binding protein, unique domai	95.84
smart00517		64	PolyA C-terminal domain of Poly(A)-binding protein	95.74
PF11608		90	Limkain-b1: Limkain b1; InterPro: IPR024582 This e	95.73
PF14608		19	zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	95.54
KOG2314		698	consensus Translation initiation factor 3, subunit	95.03
PF08777		105	RRM_3: RNA binding motif; InterPro: IPR014886 This	95.01
KOG4211		510	consensus Splicing factor hnRNP-F and related RNA-	94.85
KOG0120		500	consensus Splicing factor U2AF, large subunit (RRM	94.69
KOG2185		486	consensus Predicted RNA-processing protein, contai	94.55
KOG1855		484	consensus Predicted RNA-binding protein [General f	94.52
PF08952		146	DUF1866: Domain of unknown function (DUF1866) ; In	94.38
KOG1995		351	consensus Conserved Zn-finger protein [General fun	94.06
KOG4307		944	consensus RNA binding protein RBM12/SWAN [General	93.99
KOG3152		278	consensus TBP-binding protein, activator of basal	93.93
KOG1677		332	consensus CCCH-type Zn-finger protein [General fun	93.58
KOG1456		494	consensus Heterogeneous nuclear ribonucleoprotein	92.96
KOG4206		221	consensus Spliceosomal protein snRNP-U1A/U2B [RNA	92.88
KOG2202		260	consensus U2 snRNP splicing factor, small subunit,	92.06
KOG1457		284	consensus RNA binding protein (contains RRM repeat	91.79
KOG1996		378	consensus mRNA splicing factor [RNA processing and	91.58
KOG0129		520	consensus Predicted RNA-binding protein (RRM super	91.05
KOG0129		520	consensus Predicted RNA-binding protein (RRM super	89.17
KOG4285		350	consensus Mitotic phosphoprotein [Cell cycle contr	89.0
PF08675		87	RNA_bind: RNA binding domain; InterPro: IPR014789	88.59
KOG1039		344	consensus Predicted E3 ubiquitin ligase [Posttrans	87.83
KOG1190		492	consensus Polypyrimidine tract-binding protein [RN	87.41
KOG4676		479	consensus Splicing factor, arginine/serine-rich [R	86.61
PF04847		184	Calcipressin: Calcipressin; InterPro: IPR006931 Ca	85.99
PF03880		74	DbpA: DbpA RNA binding domain ; InterPro: IPR00558	85.48
KOG4849		498	consensus mRNA cleavage factor I subunit/CPSF subu	85.44
KOG2068		327	consensus MOT2 transcription factor [Transcription	84.4
KOG4307		944	consensus RNA binding protein RBM12/SWAN [General	82.27
PF15023		166	DUF4523: Protein of unknown function (DUF4523)	82.24
KOG0112		975	consensus Large RNA-binding protein (RRM superfami	81.95

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

Probab=99.57  E-value=1.6e-15  Score=162.08  Aligned_cols=132  Identities=23%  Similarity=0.269  Sum_probs=97.9

Q ss_pred             HhcchhHHHHHHHHHhhhccCCCCcccccCCCCHHHHHHHHhhhhhcccccCCCC----------CCccccccCCCCCCC
Q 041390          242 LLRSKASVQQRKLAAASQFMGSFPYNKCMNFLNDTQRSAALMMGDELHNKFGTCS----------RPERNDFFGSMNPSA  311 (639)
Q Consensus       242 lLrsk~~~qq~~l~~~~~~~~~lp~~K~~~~lte~qr~aa~~L~~~~~~kf~~~~----------R~eR~df~G~~~~~s  311 (639)
                      ++|||.+++                .|+|+|++...|..|..+...+||++..++          -.||..     ....
T Consensus        66 l~kDk~t~~----------------s~gcCFv~~~trk~a~~a~~Alhn~ktlpG~~~pvqvk~Ad~E~er-----~~~e  124 (510)
T KOG0144|consen   66 LIKDKSTGQ----------------SKGCCFVKYYTRKEADEAINALHNQKTLPGMHHPVQVKYADGERER-----IVEE  124 (510)
T ss_pred             eecccccCc----------------ccceEEEEeccHHHHHHHHHHhhcccccCCCCcceeecccchhhhc-----cccc
Confidence            689988654                588999988888877777666776443331          111111     1234


Q ss_pred             ceEEEeCCCCCCCCHHHHHHHhhcCCCeeEEEeecc---CCCceEEEEECCHHHHHHHHHhCCCeE-E--cCeEEEEEec
Q 041390          312 RQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQ---QKRMFGFVTFVYPETVKLILAKGNPHF-V--CDSRVLVKPY  385 (639)
Q Consensus       312 r~IYV~~~~d~~~TEedLre~FsqFG~V~dVrIp~D---ksRGFGFVtF~~~E~Ae~Al~~mng~~-L--~GR~I~Vk~a  385 (639)
                      +.+||+-+.. ..||.+|+++|++||.|++|+|++|   .+||||||+|.++|.|..||+.||+.. +  |..+|.|++|
T Consensus       125 ~KLFvg~lsK-~~te~evr~iFs~fG~Ied~~ilrd~~~~sRGcaFV~fstke~A~~Aika~ng~~tmeGcs~PLVVkFA  203 (510)
T KOG0144|consen  125 RKLFVGMLSK-QCTENEVREIFSRFGHIEDCYILRDPDGLSRGCAFVKFSTKEMAVAAIKALNGTQTMEGCSQPLVVKFA  203 (510)
T ss_pred             hhhhhhhccc-cccHHHHHHHHHhhCccchhhheecccccccceeEEEEehHHHHHHHHHhhccceeeccCCCceEEEec
Confidence            5555553333 8999999999999999999999996   999999999999999999999999754 4  5578999999


Q ss_pred             ccCC-cchHHH
Q 041390          386 KEKG-KVQEKK  395 (639)
Q Consensus       386 ~~K~-k~~~k~  395 (639)
                      ..++ |..+++
T Consensus       204 Dtqkdk~~~~l  214 (510)
T KOG0144|consen  204 DTQKDKDGKRL  214 (510)
T ss_pred             ccCCCchHHHH
Confidence            6544 444444

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

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

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

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

>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor	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

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

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

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

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

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

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

>smart00362 RRM_2 RNA recognition motif	Back alignment and domain information

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

>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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>smart00360 RRM RNA recognition motif	Back alignment and domain information

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

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

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

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

>smart00361 RRM_1 RNA recognition motif	Back alignment and domain information

>KOG0131 consensus Splicing factor 3b, subunit 4 [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

>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

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

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

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

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

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

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

>KOG0146 consensus RNA-binding protein ETR-3 (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

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

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

>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

>KOG0145 consensus RNA-binding protein ELAV/HU (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

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

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

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

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

>KOG0130 consensus RNA-binding protein RBM8/Tsunagi (RRM superfamily) [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

>KOG4212 consensus RNA-binding protein hnRNP-M [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

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

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

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

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

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

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

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

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

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

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

>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [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

>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

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

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

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

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

>KOG2135 consensus Proteins containing the RNA recognition motif [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

>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

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

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

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

>smart00356 ZnF_C3H1 zinc finger	Back alignment and domain information

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

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

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

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

>KOG1548 consensus Transcription elongation factor TAT-SF1 [Transcription]	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

>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

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

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

>KOG1456 consensus Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [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

>PF00658 PABP: Poly-adenylate binding protein, unique domain; InterPro: IPR002004 The polyadenylate-binding protein (PABP) has a conserved C-terminal domain (PABC), which is also found in the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains (IPR000569 from INTERPRO) []	Back alignment and domain information

>smart00517 PolyA C-terminal domain of Poly(A)-binding protein	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

>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type	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

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

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

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

>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]	Back alignment and domain information

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

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

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

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

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

>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]	Back alignment and domain information

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

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

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

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

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

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

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

>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

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

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

>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

>PF03880 DbpA: DbpA RNA binding domain ; InterPro: IPR005580 This RNA binding domain is found at the C terminus of a number of DEAD helicase proteins []	Back alignment and domain information

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

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

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

>PF15023 DUF4523: Protein of unknown function (DUF4523)	Back alignment and domain information

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

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		639
2e5g_A		94	U6 snRNA-specific terminal uridylyltransferase 1;	8e-14
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	2e-11
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	1e-06
1s79_A		103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	2e-10
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	3e-10
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	9e-07
1iqt_A		75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	4e-10
1wf0_A		88	TDP-43, TAR DNA-binding protein-43; structural gen	8e-10
3d2w_A		89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	1e-09
2mss_A		75	Protein (musashi1); RNA-binding domain, RNA bindin	7e-09
2dgs_A		99	DAZ-associated protein 1; RRM domain, structural g	2e-08
3lqv_A		115	PRE-mRNA branch site protein P14; cysless mutant,	8e-08
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
3ucg_A		89	Polyadenylate-binding protein 2; ferredoxin-like,	2e-07
2xs2_A		102	Deleted in azoospermia-like; RNA binding protein-R	3e-07
2do4_A		100	Squamous cell carcinoma antigen recognized by T- c	3e-07
3mdf_A		85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	5e-07
1uaw_A		77	Mouse-musashi-1; RNP-type structure, RNA binding p	7e-07
2cq4_A		114	RNA binding motif protein 23; RRM domain, structur	8e-07
2rs2_A		109	Musashi-1, RNA-binding protein musashi homolog 1;	1e-06
2fy1_A		116	RNA-binding motif protein, Y chromosome, family 1	1e-06
1x4b_A		116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	2e-06
2dnm_A		103	SRP46 splicing factor; RRM domain, RBD, structural	2e-06
2dh8_A		105	DAZ-associated protein 1; RRM domain, structural g	3e-06
3u1l_A		240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	3e-06
1whw_A		99	Hypothetical protein riken cDNA 1200009A02; RNA re	4e-06
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	4e-06
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	6e-04
2jwn_A		124	Embryonic polyadenylate-binding protein 2-B; epabp	5e-06
2cqg_A		103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	9e-06
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	1e-05
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	4e-04
3s7r_A		87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	2e-05
1x4a_A		109	Splicing factor, arginine/serine-rich 1 (splicing	2e-05
2hvz_A		101	Splicing factor, arginine/serine-rich 7; RRM, RNA	2e-05
2lea_A		135	Serine/arginine-rich splicing factor 2; SR protein	3e-05
2kn4_A		158	Immunoglobulin G-binding protein G, splicing FACT	3e-05
2x1f_A		96	MRNA 3'-END-processing protein RNA15; transcriptio	3e-05
2kvi_A		96	Nuclear polyadenylated RNA-binding protein 3; RNA-	4e-05
2e5h_A		94	Zinc finger CCHC-type and RNA-binding motif- conta	4e-05
2jvo_A		108	Nucleolar protein 3; nucleus, phosphorylation, rib	4e-05
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	4e-05
3s8s_A		110	Histone-lysine N-methyltransferase SETD1A; chromat	4e-05
2i2y_A		150	Fusion protein consists of immunoglobin G- binding	4e-05
2kxn_B		129	Transformer-2 protein homolog beta; SR protein, RR	5e-05
2cph_A		107	RNA binding motif protein 19; RNA recognition moti	5e-05
2cqd_A		116	RNA-binding region containing protein 1; RNA recog	5e-05
2voo_A		193	Lupus LA protein; RNA-binding protein, RNA recogni	5e-05
2dnl_A		114	Cytoplasmic polyadenylation element binding protei	5e-05
2cqc_A		95	Arginine/serine-rich splicing factor 10; RNA recog	6e-05
2xnq_A		97	Nuclear polyadenylated RNA-binding protein 3; tran	6e-05
1p1t_A		104	Cleavage stimulation factor, 64 kDa subunit; RNA r	6e-05
1x5s_A		102	Cold-inducible RNA-binding protein; structure geno	6e-05
2ytc_A		85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	7e-05
1x4h_A		111	RNA-binding protein 28; structural genomics, RRM d	7e-05
2dgt_A		92	RNA-binding protein 30; RRM domain, structural gen	8e-05
1x5u_A		105	Splicing factor 3B subunit 4 (spliceosome associat	1e-04
2cpj_A		99	Non-POU domain-containing octamer-binding protein;	1e-04
2cqb_A		102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	2e-04
4a8x_A		88	RNA-binding protein with serine-rich domain 1; tra	2e-04
2dnq_A		90	RNA-binding protein 4B; RRM domain,RBD, structural	2e-04
1fje_B		175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	2e-04
2cq0_A		103	Eukaryotic translation initiation factor 3 subunit	2e-04
2ki2_A		90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	3e-04
2e5j_A		97	Methenyltetrahydrofolate synthetase domain contain	3e-04
2j76_E		100	EIF-4B, EIF4B, eukaryotic translation initiation f	3e-04
2dnp_A		90	RNA-binding protein 14; RRM domain, RBD, structura	3e-04
2ku7_A		140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	4e-04
2cq3_A		103	RNA-binding protein 9; RRM domain, structural geno	4e-04
2ywk_A		95	Putative RNA-binding protein 11; RRM-domain, struc	4e-04
2db1_A		118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	4e-04
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	4e-04
2dhx_A		104	Poly (ADP-ribose) polymerase family, member 10 var	5e-04
2la4_A		101	Nuclear and cytoplasmic polyadenylated RNA-bindin	5e-04
2dnz_A		95	Probable RNA-binding protein 23; RNA recognition m	7e-04
2err_A		109	Ataxin-2-binding protein 1; protein-RNA complex, R	8e-04
1wf1_A		110	RNA-binding protein RALY; structural genomics, RRM	8e-04
3ex7_B		126	RNA-binding protein 8A; protein-RNA complex, mRNA	8e-04

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

 Score = 66.6 bits (163), Expect = 8e-14
 Identities = 20/94 (21%), Positives = 41/94 (43%), Gaps = 5/94 (5%)

Query: 306 SMNPSARQIYLT-FPADSTFREEDVSNYFSIYGPVHDVRIPYQQKRMFGFVTFVYPETVK 364
           S +   R ++++ FP         +S YF  +GPV  V +  + K +F  V        +
Sbjct: 3   SGSSGLRSVFVSGFPRGVD--SAQLSEYFLAFGPVASVVMD-KDKGVFAIVEMGDVGARE 59

Query: 365 LILAKGNPHFVCDSRVLVKPYKEKGKVQEKKQQQ 398
            +L++ + H +   R+ V+P ++K       +  
Sbjct: 60  AVLSQ-SQHSLGGHRLRVRPREQKEFQSPASKSP 92

PyMOL of 2e5g

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196	Back alignment and structure

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A Length = 196	Back alignment and structure

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

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

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

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

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

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

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A Length = 75	Back alignment and structure

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 99	Back alignment and structure

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

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

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

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A Length = 89	Back alignment and structure

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

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

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

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 Length = 77	Back alignment and structure

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 114	Back alignment and structure

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus} Length = 109	Back alignment and structure

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

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116	Back alignment and structure

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

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} Length = 105	Back alignment and structure

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A Length = 240	Back alignment and structure

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

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

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

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis} Length = 124	Back alignment and structure

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

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

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

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A Length = 87	Back alignment and structure

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

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

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

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

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

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

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

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

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

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

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

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

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

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 116	Back alignment and structure

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

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

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

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

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 Length = 104	Back alignment and structure

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

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

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

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

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

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

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

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

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

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

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

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori} Length = 90	Back alignment and structure

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

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens} Length = 100	Back alignment and structure

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

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

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

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

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} Length = 118	Back alignment and structure

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

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 104	Back alignment and structure

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

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

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

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

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		639
3u1l_A		240	PRE-mRNA-splicing factor CWC2; CSMP, zinc finger;	99.87
4f25_A		115	Polyadenylate-binding protein 1; RRM fold, transla	99.68
3s8s_A		110	Histone-lysine N-methyltransferase SETD1A; chromat	99.67
4fxv_A		99	ELAV-like protein 1; RNA recognition motif, putati	99.67
2lxi_A		91	RNA-binding protein 10; NMR {Homo sapiens}	99.65
3mdf_A		85	Peptidyl-prolyl CIS-trans isomerase E; RRM domain,	99.63
1whw_A		99	Hypothetical protein riken cDNA 1200009A02; RNA re	99.62
3md1_A		83	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.61
3bs9_A		87	Nucleolysin TIA-1 isoform P40; RNA recognition mot	99.61
2e5h_A		94	Zinc finger CCHC-type and RNA-binding motif- conta	99.61
2x1f_A		96	MRNA 3'-END-processing protein RNA15; transcriptio	99.6
2cqb_A		102	Peptidyl-prolyl CIS-trans isomerase E; RNA recogni	99.6
2cqi_A		103	Nucleolysin TIAR; RNA recognition motif, RRM, RNA	99.6
2cq3_A		103	RNA-binding protein 9; RRM domain, structural geno	99.6
4a8x_A		88	RNA-binding protein with serine-rich domain 1; tra	99.6
2dgs_A		99	DAZ-associated protein 1; RRM domain, structural g	99.6
2dnz_A		95	Probable RNA-binding protein 23; RNA recognition m	99.6
1x4a_A		109	Splicing factor, arginine/serine-rich 1 (splicing	99.59
1x5t_A		96	Splicing factor 3B subunit 4; structure genomics,	99.59
2do4_A		100	Squamous cell carcinoma antigen recognized by T- c	99.59
1sjq_A		105	Polypyrimidine tract-binding protein 1; babbab mot	99.59
2cq0_A		103	Eukaryotic translation initiation factor 3 subunit	99.59
1x5u_A		105	Splicing factor 3B subunit 4 (spliceosome associat	99.59
2wbr_A		89	GW182, gawky, LD47780P; DNA-binding protein, RRM,	99.59
2dgo_A		115	Cytotoxic granule-associated RNA binding protein 1	99.59
2cpf_A		98	RNA binding motif protein 19; RNA recognition moti	99.58
2jvr_A		111	Nucleolar protein 3; RNA recognition motif, nucleu	99.58
2cpz_A		115	CUG triplet repeat RNA-binding protein 1; RRM doma	99.58
1x4h_A		111	RNA-binding protein 28; structural genomics, RRM d	99.58
2dgx_A		96	KIAA0430 protein; RRM domain, structural genomics,	99.58
2cqc_A		95	Arginine/serine-rich splicing factor 10; RNA recog	99.58
1x5s_A		102	Cold-inducible RNA-binding protein; structure geno	99.58
2lkz_A		95	RNA-binding protein 5; RRM; NMR {Homo sapiens}	99.57
1x5p_A		97	Negative elongation factor E; structure genomics,	99.57
1oo0_B		110	CG8781-PA, drosophila Y14; RNA recognition motif,	99.57
2err_A		109	Ataxin-2-binding protein 1; protein-RNA complex, R	99.57
2ytc_A		85	PRE-mRNA-splicing factor RBM22; RRM domain, RBD, s	99.57
2ywk_A		95	Putative RNA-binding protein 11; RRM-domain, struc	99.57
1p27_B		106	RNA-binding protein 8A; nuclear protein, mRNA spli	99.57
2la4_A		101	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.57
2dgv_A		92	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.57
2d9p_A		103	Polyadenylate-binding protein 3; RRM domain, struc	99.57
2e5j_A		97	Methenyltetrahydrofolate synthetase domain contain	99.56
3r27_A		100	HnRNP L, heterogeneous nuclear ribonucleoprotein L	99.56
2dnh_A		105	Bruno-like 5, RNA binding protein; RRM domain, RBD	99.56
2dnm_A		103	SRP46 splicing factor; RRM domain, RBD, structural	99.56
3ucg_A		89	Polyadenylate-binding protein 2; ferredoxin-like,	99.56
1nu4_A		97	U1A RNA binding domain; RNA recognition motif, U1	99.56
3ns6_A		100	Eukaryotic translation initiation factor 3 subuni;	99.56
2rs2_A		109	Musashi-1, RNA-binding protein musashi homolog 1;	99.56
2cpi_A		111	CCR4-NOT transcription complex subunit 4; RNA reco	99.56
1s79_A		103	Lupus LA protein; RRM, alpha/beta, RNA binding pro	99.55
2cqd_A		116	RNA-binding region containing protein 1; RNA recog	99.55
2cph_A		107	RNA binding motif protein 19; RNA recognition moti	99.55
2cq1_A		101	PTB-like protein L; RRM domain, structural genomic	99.55
1u6f_A		139	Tcubp1, RNA-binding protein UBP1; trypanosome, mRN	99.55
2do0_A		114	HnRNP M, heterogeneous nuclear ribonucleoprotein M	99.55
3n9u_C		156	Cleavage and polyadenylation specificity factor S;	99.55
1x4d_A		102	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.55
3p5t_L		90	Cleavage and polyadenylation specificity factor S;	99.55
2dnq_A		90	RNA-binding protein 4B; RRM domain,RBD, structural	99.55
1p1t_A		104	Cleavage stimulation factor, 64 kDa subunit; RNA r	99.55
2dgp_A		106	Bruno-like 4, RNA binding protein; RRM domain, str	99.55
3s7r_A		87	Heterogeneous nuclear ribonucleoprotein A/B; ferre	99.55
2khc_A		118	Testis-specific RNP-type RNA binding protein; RRM,	99.55
1x4g_A		109	Nucleolysin TIAR; structural genomics, RRM domain,	99.54
2dh8_A		105	DAZ-associated protein 1; RRM domain, structural g	99.54
2div_A		99	TRNA selenocysteine associated protein; structural	99.54
2fy1_A		116	RNA-binding motif protein, Y chromosome, family 1	99.54
1why_A		97	Hypothetical protein riken cDNA 1810017N16; RNA re	99.54
2cpe_A		113	RNA-binding protein EWS; RNA recognition motif, RR	99.54
2cpj_A		99	Non-POU domain-containing octamer-binding protein;	99.54
1x4c_A		108	Splicing factor, arginine/serine-rich 1; structura	99.54
2a3j_A		127	U1 small nuclear ribonucleoprotein A; computationa	99.54
2dng_A		103	Eukaryotic translation initiation factor 4H; RRM d	99.53
2jrs_A		108	RNA-binding protein 39; RNA binding motif of RBM39	99.53
2cq4_A		114	RNA binding motif protein 23; RRM domain, structur	99.53
3ulh_A		107	THO complex subunit 4; nuclear protein, RNA bindin	99.53
1x4b_A		116	Heterogeneous nuclear ribonucleoproteins A2/B1; st	99.53
1wi8_A		104	EIF-4B, eukaryotic translation initiation factor 4	99.53
2ku7_A		140	MLL1 PHD3-CYP33 RRM chimeric protein; transcriptio	99.53
2kxn_B		129	Transformer-2 protein homolog beta; SR protein, RR	99.53
2dgt_A		92	RNA-binding protein 30; RRM domain, structural gen	99.53
2nlw_A		105	Eukaryotic translation initiation factor 3 subunit	99.53
3lqv_A		115	PRE-mRNA branch site protein P14; cysless mutant,	99.53
2cqp_A		98	RNA-binding protein 12; RNA recognition motif, RRM	99.53
2ad9_A		119	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.52
2dhg_A		104	TRNA selenocysteine associated protein (SECP43); R	99.52
2la6_A		99	RNA-binding protein FUS; structural genomics, nort	99.52
2kt5_A		124	RNA and export factor-binding protein 2; chaperone	99.52
2dgw_A		91	Probable RNA-binding protein 19; RRM domain, struc	99.52
1wex_A		104	Hypothetical protein (riken cDNA 2810036L13); stru	99.52
3ex7_B		126	RNA-binding protein 8A; protein-RNA complex, mRNA	99.52
1whx_A		111	Hypothetical protein riken cDNA 1200009A02; RNA re	99.51
2jvo_A		108	Nucleolar protein 3; nucleus, phosphorylation, rib	99.51
2dnp_A		90	RNA-binding protein 14; RRM domain, RBD, structura	99.51
2mss_A		75	Protein (musashi1); RNA-binding domain, RNA bindin	99.51
2kn4_A		158	Immunoglobulin G-binding protein G, splicing FACT	99.51
2hvz_A		101	Splicing factor, arginine/serine-rich 7; RRM, RNA	99.51
2cqg_A		103	TDP-43, TAR DNA-binding protein-43; RNA recognitio	99.51
1h2v_Z		156	20 kDa nuclear CAP binding protein; CAP-binding-co	99.51
2dgu_A		103	Heterogeneous nuclear ribonucleoprotein Q; RRM dom	99.51
2dis_A		109	Unnamed protein product; structural genomics, RRM	99.51
2cpy_A		114	RNA-binding protein 12; RRM domain, structural gen	99.51
2ki2_A		90	SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA	99.51
2ek1_A		95	RNA-binding protein 12; RNA recognition motif, dim	99.51
1uaw_A		77	Mouse-musashi-1; RNP-type structure, RNA binding p	99.51
2krb_A		81	Eukaryotic translation initiation factor 3 subunit	99.51
2jwn_A		124	Embryonic polyadenylate-binding protein 2-B; epabp	99.5
2j76_E		100	EIF-4B, EIF4B, eukaryotic translation initiation f	99.5
1x4f_A		112	Matrin 3; structural genomics, RRM domain, NPPSFA,	99.5
3d2w_A		89	TAR DNA-binding protein 43; DP-43 proteinopathy, T	99.5
1x4e_A		85	RNA binding motif, single-stranded interacting pro	99.5
2i2y_A		150	Fusion protein consists of immunoglobin G- binding	99.5
2fc9_A		101	NCL protein; structure genomics, RRM_1 domain, str	99.5
2m2b_A		131	RNA-binding protein 10; T-cell, JCSG, MPP, PSI-bio	99.49
2cqh_A		93	IGF-II mRNA-binding protein 2 isoform A; RNA recog	99.49
2xnq_A		97	Nuclear polyadenylated RNA-binding protein 3; tran	99.49
2cpx_A		115	Hypothetical protein FLJ11016; RRM domain, structu	99.48
2cpd_A		99	Apobec-1 stimulating protein; RNA recognition moti	99.48
4f02_A		213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.48
2j8a_A		136	Histone-lysine N-methyltransferase, H3 lysine-4 sp	99.48
1wg1_A		88	KIAA1579 protein, homolog EXC-7; RBD, structural g	99.48
2bz2_A		121	Negative elongation factor E; NELF E, RNA recognit	99.47
1fjc_A		96	Nucleolin RBD2, protein C23; RNP, RRM, RNA binding	99.47
1wg5_A		104	Heterogeneous nuclear ribonucleoprotein H; structu	99.47
2cq2_A		114	Hypothetical protein LOC91801; RRM domain, structu	99.47
1wf1_A		110	RNA-binding protein RALY; structural genomics, RRM	99.47
1rk8_A		165	CG8781-PA, CG8781-PA protein; mRNA processing, RRM	99.47
2db1_A		118	Heterogeneous nuclear ribonucleoprotein F; RRM dom	99.47
2lea_A		135	Serine/arginine-rich splicing factor 2; SR protein	99.46
2hgl_A		136	HNRPF protein, heterogeneous nuclear ribonucleopro	99.46
1x5o_A		114	RNA binding motif, single-stranded interacting pro	99.46
1fj7_A		101	Nucleolin RBD1, protein C23; RNP, RRM, RNA binding	99.46
2kvi_A		96	Nuclear polyadenylated RNA-binding protein 3; RNA-	99.46
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.46
2dnn_A		109	RNA-binding protein 12; RRM domain, RBD, structura	99.45
2e44_A		96	Insulin-like growth factor 2 mRNA binding protein	99.45
1wf0_A		88	TDP-43, TAR DNA-binding protein-43; structural gen	99.45
1wez_A		102	HnRNP H', FTP-3, heterogeneous nuclear ribonucleop	99.44
1iqt_A		75	AUF1, heterogeneous nuclear ribonucleoprotein D0;	99.44
2xs2_A		102	Deleted in azoospermia-like; RNA binding protein-R	99.44
3q2s_C		229	Cleavage and polyadenylation specificity factor S;	99.44
2hzc_A		87	Splicing factor U2AF 65 kDa subunit; RNA splicing,	99.43
1wel_A		124	RNA-binding protein 12; structural genomics, NPPSF	99.43
3egn_A		143	RNA-binding protein 40; RNA recognition motif (RRM	99.42
2fc8_A		102	NCL protein; structure genomics, RRM_1 domain, str	99.42
2e5g_A		94	U6 snRNA-specific terminal uridylyltransferase 1;	99.42
2lcw_A		116	RNA-binding protein FUS; RRM, nucleic acid binding	99.14
1sjr_A		164	Polypyrimidine tract-binding protein 1; extended b	99.42
2pe8_A		105	Splicing factor 45; RRM, protein binding; 2.00A {H	99.42
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.42
2dit_A		112	HIV TAT specific factor 1 variant; structural geno	99.41
2lmi_A		107	GRSF-1, G-rich sequence factor 1; G-rich RNA seque	99.41
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	99.41
3md3_A		166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.4
4f02_A		213	Polyadenylate-binding protein 1; mRNA, eukaryotic	99.4
3md3_A		166	Nuclear and cytoplasmic polyadenylated RNA-bindin	99.4
2f3j_A		177	RNA and export factor binding protein 2; RRM domai	99.39
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.39
2dha_A		123	FLJ20171 protein; RRM domain, structural genomics,	99.38
3beg_B		115	Splicing factor, arginine/serine-rich 1; kinase, S	99.38
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.38
3zzy_A		130	Polypyrimidine tract-binding protein 1; protein bi	99.37
2hgn_A		139	Heterogeneous nuclear ribonucleoprotein F; RNA rec	99.37
2yh0_A		198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.37
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.36
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	99.36
2dnl_A		114	Cytoplasmic polyadenylation element binding protei	99.36
1l3k_A		196	Heterogeneous nuclear ribonucleoprotein A1; nuclea	99.36
2qfj_A		216	FBP-interacting repressor; protein-DNA complex; HE	99.35
2e5i_A		124	Heterogeneous nuclear ribonucleoprotein L-like; RR	99.35
2hgm_A		126	HNRPF protein, heterogeneous nuclear ribonucleopro	99.34
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.34
3pgw_A		282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.34
2voo_A		193	Lupus LA protein; RNA-binding protein, RNA recogni	99.33
3pgw_S		437	U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM	99.33
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	99.32
1fje_B		175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.32
2d9o_A		100	DNAJ (HSP40) homolog, subfamily C, member 17; RRM	99.31
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.3
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.3
2cjk_A		167	Nuclear polyadenylated RNA-binding protein 4; HRP1	99.3
3pgw_A		282	U1-A; protein-RNA complex, U1 snRNA, SM fold, SM c	99.3
3nmr_A		175	Cugbp ELAV-like family member 1; RRM, PRE-mRNA spl	99.29
1b7f_A		168	Protein (SXL-lethal protein), RNA (5'-R(PGPUP*UP	99.29
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	99.28
2diu_A		96	KIAA0430 protein; structural genomics, RRM domain,	99.27
1fxl_A		167	Paraneoplastic encephalomyelitis antigen HUD; prot	99.26
3v4m_A		105	Splicing factor U2AF 65 kDa subunit; canonical RNA	99.26
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.24
3s6e_A		114	RNA-binding protein 39; ferredoxin-like, structura	99.23
1jmt_A		104	Splicing factor U2AF 35 kDa subunit; RRM, RNA spli	99.23
2g4b_A		172	Splicing factor U2AF 65 kDa subunit; protein-RNA c	99.22
3sde_A		261	Paraspeckle component 1; RRM, anti parallel right	99.22
2yh0_A		198	Splicing factor U2AF 65 kDa subunit; PRE-mRNA spli	99.21
3ue2_A		118	Poly(U)-binding-splicing factor PUF60; RNA recogni	99.19
2adc_A		229	Polypyrimidine tract-binding protein 1; RBD, RRM,	99.18
1fje_B		175	Nucleolin RBD12, protein C23; RNP, RRM, RNA bindin	99.18
1qm9_A		198	Polypyrimidine tract-binding protein; ribonucleopr	99.17
3smz_A		284	Protein raver-1, ribonucleoprotein PTB-binding 1;	99.16
3tht_A		345	Alkylated DNA repair protein ALKB homolog 8; struc	99.16
2ghp_A		292	U4/U6 snRNA-associated splicing factor PRP24; RNA	99.14
3tyt_A		205	Heterogeneous nuclear ribonucleoprotein L; ferredo	99.13
2dnr_A		91	Synaptojanin-1; RRM domain, RBD, structural genomi	98.84
3dxb_A		222	Thioredoxin N-terminally fused to PUF60(UHM); spli	98.6
1ufw_A		95	Synaptojanin 2; RNP domain, structural genomics, r	98.54
1owx_A		121	Lupus LA protein, SS-B, LA; RRM, transcription; NM	98.44
2l9w_A		117	U4/U6 snRNA-associated-splicing factor PRP24; RRM,	97.1
2dhx_A		104	Poly (ADP-ribose) polymerase family, member 10 var	96.94
1wwh_A		119	Nucleoporin 35, nucleoporin; structural genomics,	96.55
2rhk_C		72	Cleavage and polyadenylation specificity factor su	95.91
3p3d_A		132	Nucleoporin 53; structural genomics, PSI-2, protei	95.8
2d9n_A		77	Cleavage and polyadenylation specificity factor, 3	95.78
1i2t_A		61	HYD protein; four alpha-helical domain, ligase; 1.	95.64
2d9m_A		69	Zinc finger CCCH-type domain containing protein 7A	95.52
1wey_A		104	Calcipressin 1; structural genomics, RRM domain, r	95.48
1m9o_A		77	Tristetraproline; Cys3His type zinc finger, metal	95.33
2cqe_A		98	KIAA1064 protein; CCCH zinc-finger, structural gen	95.28
3d2q_A		70	Muscleblind-like protein 1; tandem zinc finger dom	95.04
3kuj_A		88	Polyadenylate-binding protein 1; protein-protein c	94.98
1nmr_A		85	Poly(A)-binding protein; all helical domain, pepti	94.97
2cqe_A		98	KIAA1064 protein; CCCH zinc-finger, structural gen	94.73
2dyd_A		85	Poly(A)-binding protein; alpha helical protein, RN	94.71
1m9o_A		77	Tristetraproline; Cys3His type zinc finger, metal	94.41
3d2q_A		70	Muscleblind-like protein 1; tandem zinc finger dom	94.31
1ifw_A		92	Polyadenylate-binding protein, cytoplasmic and nuc	94.22
3d2n_A		83	Muscleblind-like protein 1; tandem zinc finger dom	94.13
3pq1_A		464	Poly(A) RNA polymerase; nucleotidyl transferase, R	93.95
2e5s_A		98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	93.41
2kn4_A		158	Immunoglobulin G-binding protein G, splicing FACT	93.18
2e5s_A		98	Otthump00000018578; ZF-CCCHX2 domain, muscleblind-	92.9
2rpp_A		89	Muscleblind-like protein 2; zinc finger domain, C3	92.88
1whv_A		100	Poly(A)-specific ribonuclease; RNA recognition mot	92.83
1g9l_A		144	Polyadenylate-binding protein 1; all-helical domai	92.66
3d2n_A		83	Muscleblind-like protein 1; tandem zinc finger dom	91.89
2d9n_A		77	Cleavage and polyadenylation specificity factor, 3	91.7
2rhk_C		72	Cleavage and polyadenylation specificity factor su	91.22
3ctr_A		101	Poly(A)-specific ribonuclease PARN; protein-RNA-co	91.14
2i2y_A		150	Fusion protein consists of immunoglobin G- binding	88.61
2rpp_A		89	Muscleblind-like protein 2; zinc finger domain, C3	87.73
1uw4_A		91	UPF3X; nonsense mediated mRNA decay protein, RNA-b	85.54

>3u1l_A PRE-mRNA-splicing factor CWC2; CSMP, zinc finger; 1.64A {Saccharomyces cerevisiae} PDB: 3u1m_A 3tp2_A	Back alignment and structure

Probab=99.87  E-value=7.9e-23  Score=206.62  Aligned_cols=85  Identities=20%  Similarity=0.272  Sum_probs=71.1

Q ss_pred             CCCCCCCceEEEeCCCCCCC---------CHHHHHHHhhcCCCeeEEEeeccCCCceEEEEECCHHHHHHHHHhCCCeEE
Q 041390          305 GSMNPSARQIYLTFPADSTF---------REEDVSNYFSIYGPVHDVRIPYQQKRMFGFVTFVYPETVKLILAKGNPHFV  375 (639)
Q Consensus       305 G~~~~~sr~IYV~~~~d~~~---------TEedLre~FsqFG~V~dVrIp~DksRGFGFVtF~~~E~Ae~Al~~mng~~L  375 (639)
                      |......++|||+++.. .+         +|++|+++|++||+|++|+|+.  +||||||+|.+.++|++|++.|++..|
T Consensus       128 gs~~~~~rtLfVgnL~~-~~~~~~~~~~~tEe~L~~~F~~fG~I~~v~v~~--~kG~AFV~F~~~~~Ae~A~~am~g~~l  204 (240)
T 3u1l_A          128 GSFRKKNKTLYVGGIDG-ALNSKHLKPAQIESRIRFVFSRLGDIDRIRYVE--SKNCGFVKFKYQANAEFAKEAMSNQTL  204 (240)
T ss_dssp             ---CCCCCEEEEECTTG-GGTTCCCCHHHHHHHHHHHHHTTSCEEEEEEEG--GGTEEEEEESSHHHHHHHHHHHTTCCC
T ss_pred             CccccCCceeecCCCCh-hhhcccccccCcHHHHHHHHHccCCEEEEEEEC--CCCEEEEEeCCHHHHHHHHHHhCCCEE
Confidence            34466889999997654 55         7999999999999999999998  899999999999999999999999999


Q ss_pred             ------------cCeEEEEEecccCCcch
Q 041390          376 ------------CDSRVLVKPYKEKGKVQ  392 (639)
Q Consensus       376 ------------~GR~I~Vk~a~~K~k~~  392 (639)
                                  .|+.|.|+|+.++....
T Consensus       205 ~~~~~~e~~~~~~gr~L~V~wA~~~pnp~  233 (240)
T 3u1l_A          205 LLPSDKEWDDRREGTGLLVKWANEDPDPA  233 (240)
T ss_dssp             CCTTSTTGGGGGGSCCCEEEECC------
T ss_pred             eccccccccccCCCCEEEEEEccCCCCHH
Confidence                        89999999998765443

PyMOL of 3u1l

>4f25_A Polyadenylate-binding protein 1; RRM fold, translation initiation, RNA-binding, EIF4G-binding translation; 1.90A {Homo sapiens} PDB: 4f26_A 2k8g_A	Back alignment and structure

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

>4fxv_A ELAV-like protein 1; RNA recognition motif, putative RNA-binding domain, transcri structural genomics, joint center for structural genomics; 1.90A {Homo sapiens}	Back alignment and structure

>2lxi_A RNA-binding protein 10; NMR {Homo sapiens}	Back alignment and structure

>3mdf_A Peptidyl-prolyl CIS-trans isomerase E; RRM domain, PHD finger, CYP33, MLL, RNA binding protein, ISO mRNA processing, mRNA splicing, nucleus; 1.85A {Homo sapiens} SCOP: d.58.7.1 PDB: 2kyx_A 3lpy_A*	Back alignment and structure

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

>3md1_A Nuclear and cytoplasmic polyadenylated RNA-bindin PUB1; RRM, RBD, RNP, poly(U) binding, nucleus, RNA-binding, binding protein; 1.60A {Saccharomyces cerevisiae} SCOP: d.58.7.0	Back alignment and structure

>3bs9_A Nucleolysin TIA-1 isoform P40; RNA recognition motif, RRM, RNA binding domain, RBD, RNA splicing, apoptosis, phosphoprotein, RNA-binding; 1.95A {Homo sapiens}	Back alignment and structure

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

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

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

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

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

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

>2dgs_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

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

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

>1x5t_A Splicing factor 3B subunit 4; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

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

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

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

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

>2wbr_A GW182, gawky, LD47780P; DNA-binding protein, RRM, RBD, TNRC6A, mirnas, P-bodies, argonaute, mRNA decay; NMR {Drosophila melanogaster}	Back alignment and structure

>2dgo_A Cytotoxic granule-associated RNA binding protein 1; RRM domain, structural genomics, NPPSFA; NMR {Mus musculus} PDB: 2rne_A 2dh7_A	Back alignment and structure

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

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

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

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

>2dgx_A KIAA0430 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

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

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

>2lkz_A RNA-binding protein 5; RRM; NMR {Homo sapiens}	Back alignment and structure

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

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

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

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

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

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

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

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

>2d9p_A Polyadenylate-binding protein 3; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

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

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

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

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

>3ucg_A Polyadenylate-binding protein 2; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: PGE; 1.95A {Homo sapiens} PDB: 3b4d_A 3b4m_A	Back alignment and structure

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

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

>2rs2_A Musashi-1, RNA-binding protein musashi homolog 1; protein-RNA complex, RRM, RBD, RNA binding protein- complex; NMR {Mus musculus}	Back alignment and structure

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

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

>2cqd_A RNA-binding region containing protein 1; RNA recognition motif, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

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

>2cq1_A PTB-like protein L; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1u6f_A Tcubp1, RNA-binding protein UBP1; trypanosome, mRNA-binding protein, GU-rich RNA, structure; NMR {Trypanosoma cruzi} SCOP: d.58.7.1	Back alignment and structure

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

>3n9u_C Cleavage and polyadenylation specificity factor S; protein-protein complex, coexpression, heterotetramer, mRNA maturation, mRNA cleavage; 1.92A {Homo sapiens}	Back alignment and structure

>1x4d_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>3p5t_L Cleavage and polyadenylation specificity factor S; RRM domain, poly(A) site recognition, RNA, nuclear, RNA BIND protein; 2.70A {Homo sapiens} PDB: 3p6y_C	Back alignment and structure

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

>1p1t_A Cleavage stimulation factor, 64 kDa subunit; RNA recognition motif, C-terminal helix, N-terminal helix, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

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

>3s7r_A Heterogeneous nuclear ribonucleoprotein A/B; ferredoxin-like, structural genomics, joint center for struc genomics, JCSG; 2.15A {Homo sapiens} PDB: 1hd0_A 1hd1_A	Back alignment and structure

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

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

>2dh8_A DAZ-associated protein 1; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2div_A TRNA selenocysteine associated protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

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

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

>2cpe_A RNA-binding protein EWS; RNA recognition motif, RRM, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

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

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

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

>2dng_A Eukaryotic translation initiation factor 4H; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}	Back alignment and structure

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

>2cq4_A RNA binding motif protein 23; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

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

>1x4b_A Heterogeneous nuclear ribonucleoproteins A2/B1; structure genomics, RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1wi8_A EIF-4B, eukaryotic translation initiation factor 4B; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

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

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

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

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

>3lqv_A PRE-mRNA branch site protein P14; cysless mutant, PRE-mRNA splicing, adenine, mRNA processing, nucleus, phosphoprotein, RNA-binding; HET: ADE; 2.38A {Homo sapiens} SCOP: d.58.7.1 PDB: 2f9d_A 2f9j_A 2fho_B	Back alignment and structure

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

>2ad9_A Polypyrimidine tract-binding protein 1; RBD, RRM, protein-RNA complex, RNA binding protein/RNA complex; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2dhg_A TRNA selenocysteine associated protein (SECP43); RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2la6_A RNA-binding protein FUS; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, RNA recognition; NMR {Homo sapiens}	Back alignment and structure

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

>2dgw_A Probable RNA-binding protein 19; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

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

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

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

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

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

>2mss_A Protein (musashi1); RNA-binding domain, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2mst_A	Back alignment and structure

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

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

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

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

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

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

>2cpy_A RNA-binding protein 12; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2ki2_A SS-DNA binding protein 12RNP2; HP0827, RRM, SS-DNA binding proteins, RNA binding protein/SS-DNA binding protein complex; NMR {Helicobacter pylori}	Back alignment and structure

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

>1uaw_A Mouse-musashi-1; RNP-type structure, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

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

>2jwn_A Embryonic polyadenylate-binding protein 2-B; epabp2, poly(A) binding, structural genomics, protein structure initiative, PSI-2; NMR {Xenopus laevis}	Back alignment and structure

>2j76_E EIF-4B, EIF4B, eukaryotic translation initiation factor 4B; protein biosynthesis, RNA recognition motif, RNA binding domain, RRM, RBD, RNP; NMR {Homo sapiens}	Back alignment and structure

>1x4f_A Matrin 3; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

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

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

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

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

>2m2b_A RNA-binding protein 10; T-cell, JCSG, MPP, PSI-biology; NMR {Homo sapiens}	Back alignment and structure

>2cqh_A IGF-II mRNA-binding protein 2 isoform A; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

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

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

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

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*	Back alignment and structure

>2j8a_A Histone-lysine N-methyltransferase, H3 lysine-4 specific; histone methyltransferase, RRM fold, telomere, nuclear protein; 3.0A {Saccharomyces cerevisiae}	Back alignment and structure

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

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

>1wg5_A Heterogeneous nuclear ribonucleoprotein H; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2cq2_A Hypothetical protein LOC91801; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

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

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

>2db1_A Heterogeneous nuclear ribonucleoprotein F; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}	Back alignment and structure

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

>2hgl_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative, splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kfy_A	Back alignment and structure

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

>1fj7_A Nucleolin RBD1, protein C23; RNP, RRM, RNA binding domain, nucleolus, structural protein; NMR {Mesocricetus auratus} SCOP: d.58.7.1	Back alignment and structure

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

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

>2dnn_A RNA-binding protein 12; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

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

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

>1wez_A HnRNP H', FTP-3, heterogeneous nuclear ribonucleoprotein H'; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

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

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

>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25, CFIM68, CPSF5, CPSF6, CPSF, 3' END processing, processing, cleavage factor; 2.90A {Homo sapiens} PDB: 3q2t_C	Back alignment and structure

>2hzc_A Splicing factor U2AF 65 kDa subunit; RNA splicing, RRM, RNA recognition, alternative conformation binding protein; HET: P6G; 1.47A {Homo sapiens} PDB: 1u2f_A	Back alignment and structure

>1wel_A RNA-binding protein 12; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

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

>2fc8_A NCL protein; structure genomics, RRM_1 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

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

>2lcw_A RNA-binding protein FUS; RRM, nucleic acid binding protein; NMR {Homo sapiens}	Back alignment and structure

>1sjr_A Polypyrimidine tract-binding protein 1; extended babbab motif, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1 PDB: 2adb_A	Back alignment and structure

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

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

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

>2lmi_A GRSF-1, G-rich sequence factor 1; G-rich RNA sequence binding factor, RNA binding domain, STRU genomics, joint center for structural genomics, JCSG; NMR {Homo sapiens}	Back alignment and structure

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

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

>4f02_A Polyadenylate-binding protein 1; mRNA, eukaryotic initiation factors PAIP1 and PAIP2, translation-RNA complex; 2.00A {Homo sapiens} PDB: 1cvj_A*	Back alignment and structure

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

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

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

>2dha_A FLJ20171 protein; RRM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

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

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A	Back alignment and structure

>3zzy_A Polypyrimidine tract-binding protein 1; protein binding, peptide binding, RNA recognition motif; 1.40A {Homo sapiens} PDB: 3zzz_A	Back alignment and structure

>2hgn_A Heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg1_A	Back alignment and structure

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

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

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

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

>1l3k_A Heterogeneous nuclear ribonucleoprotein A1; nuclear protein hnRNP A1, RNA-recognition motif, RNA- binding, UP1, RNA binding protein; 1.10A {Homo sapiens} SCOP: d.58.7.1 d.58.7.1 PDB: 1u1k_A* 1u1l_A* 1u1m_A* 1u1n_A* 1u1o_A 1u1p_A* 1u1q_A 1u1r_A* 1pgz_A* 1ha1_A 1po6_A* 2up1_A* 1up1_A	Back alignment and structure

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

>2e5i_A Heterogeneous nuclear ribonucleoprotein L-like; RRM domain, RBD, structural genomics, NPPSFA; NMR {Mus musculus}	Back alignment and structure

>2hgm_A HNRPF protein, heterogeneous nuclear ribonucleoprotein F; RNA recognition motif, G-tract, G-quadruplex, alternative splicing, RNA binding protein; NMR {Homo sapiens} PDB: 2kg0_A	Back alignment and structure

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

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

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

>3pgw_S U1-70K; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens} PDB: 3cw1_K 2l5i_A 2l5j_A*	Back alignment and structure

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

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

>2d9o_A DNAJ (HSP40) homolog, subfamily C, member 17; RRM domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

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

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E	Back alignment and structure

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

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

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

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

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

>2diu_A KIAA0430 protein; structural genomics, RRM domain, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

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

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

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

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

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

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

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

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

>3ue2_A Poly(U)-binding-splicing factor PUF60; RNA recognition motif, RRM, RNA binding domain, ST genomics, joint center for structural genomics, JCSG; HET: MSE; 1.23A {Homo sapiens} SCOP: d.58.7.0 PDB: 3us5_A 2dny_A	Back alignment and structure

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

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

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

>3smz_A Protein raver-1, ribonucleoprotein PTB-binding 1; RNA binding, RNA recognition motif, vincu alpha-actinin, nucleus, RNA binding protein; 1.99A {Homo sapiens} PDB: 3vf0_B* 3h2u_B 3h2v_E	Back alignment and structure

>3tht_A Alkylated DNA repair protein ALKB homolog 8; structural genomics, PSI-biology, northeast structural genom consortium, NESG; HET: AKG; 3.01A {Homo sapiens} PDB: 3thp_A*	Back alignment and structure

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

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

>2dnr_A Synaptojanin-1; RRM domain, RBD, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3dxb_A Thioredoxin N-terminally fused to PUF60(UHM); splicing, FBP interacting repressor, RRM, electron TRAN redox-active center, transport; 2.20A {Escherichia coli O157}	Back alignment and structure

>1ufw_A Synaptojanin 2; RNP domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>1owx_A Lupus LA protein, SS-B, LA; RRM, transcription; NMR {Homo sapiens} SCOP: d.58.7.1	Back alignment and structure

>2l9w_A U4/U6 snRNA-associated-splicing factor PRP24; RRM, U6 snRNP, RNA binding protein; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>2dhx_A Poly (ADP-ribose) polymerase family, member 10 variant; RRM domain, RNA- binding, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1wwh_A Nucleoporin 35, nucleoporin; structural genomics, MPPN, riken structural genomics/proteomics initiative, RSGI, protein transport; 2.70A {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}	Back alignment and structure

>3p3d_A Nucleoporin 53; structural genomics, PSI-2, protein structure initiative, NE structural genomix research consortium, nysgxrc; 2.35A {Pichia guilliermondii}	Back alignment and structure

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1i2t_A HYD protein; four alpha-helical domain, ligase; 1.04A {Homo sapiens} SCOP: a.144.1.1 PDB: 3ntw_A	Back alignment and structure

>2d9m_A Zinc finger CCCH-type domain containing protein 7A; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>1wey_A Calcipressin 1; structural genomics, RRM domain, riken structural genomics/proteomics initiative, RSGI, RNA binding protein; NMR {Mus musculus} SCOP: d.58.7.1	Back alignment and structure

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A	Back alignment and structure

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1	Back alignment and structure

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A	Back alignment and structure

>3kuj_A Polyadenylate-binding protein 1; protein-protein complex, methylation, mRNA processing, mRNA nucleus, phosphoprotein, RNA-binding, spliceosome; 1.40A {Homo sapiens} PDB: 3ktr_A 3kui_A 3ktp_A 3kus_A* 3kut_A 3pkn_A 2rqg_B 2rqh_B 3kur_A 3pth_A 2x04_A	Back alignment and structure

>1nmr_A Poly(A)-binding protein; all helical domain, peptide binding protein; NMR {Trypanosoma cruzi} SCOP: a.144.1.1	Back alignment and structure

>2cqe_A KIAA1064 protein; CCCH zinc-finger, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.66.1.1 g.66.1.1	Back alignment and structure

>2dyd_A Poly(A)-binding protein; alpha helical protein, RNA binding protein; NMR {Triticum aestivum}	Back alignment and structure

>1m9o_A Tristetraproline; Cys3His type zinc finger, metal binding protein; NMR {Mus musculus} SCOP: g.66.1.1 PDB: 1rgo_A	Back alignment and structure

>3d2q_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 1.50A {Homo sapiens} PDB: 3d2s_A	Back alignment and structure

>1ifw_A Polyadenylate-binding protein, cytoplasmic and nuclear; all-helical domain, RNA binding protein; NMR {Saccharomyces cerevisiae} SCOP: a.144.1.1	Back alignment and structure

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens}	Back alignment and structure

>3pq1_A Poly(A) RNA polymerase; nucleotidyl transferase, RNP-type RNA binding domain, poly(A polymerase, mitochondria, transferase; 3.10A {Homo sapiens}	Back alignment and structure

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

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

>2e5s_A Otthump00000018578; ZF-CCCHX2 domain, muscleblind-like 2, isoform 1, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}	Back alignment and structure

>1whv_A Poly(A)-specific ribonuclease; RNA recognition motif, RRM, RNA binding domain, RBD, RNP, PARN, structural genomics; NMR {Mus musculus} SCOP: d.58.7.1 PDB: 2rok_A*	Back alignment and structure

>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A 1jh4_A	Back alignment and structure

>3d2n_A Muscleblind-like protein 1; tandem zinc finger domain, alternative splicing, metal- binding, nucleus, RNA-binding, zinc, zinc-finger, metal binding; 2.70A {Homo sapiens}	Back alignment and structure

>2d9n_A Cleavage and polyadenylation specificity factor, 30 kDa subunit; CCCH zinc-finger, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2rhk_C Cleavage and polyadenylation specificity factor subunit 4; influenza A, nonstructural protein, viral protein: HOST complex, Zn finger; 1.95A {Homo sapiens}	Back alignment and structure

>3ctr_A Poly(A)-specific ribonuclease PARN; protein-RNA-complex, M7G-CAP, M7GTP, RNA recognition motif, RRM, cytoplasm, exonuclease, hydrolase, magnesium; HET: MGP; 2.10A {Homo sapiens}	Back alignment and structure

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

>2rpp_A Muscleblind-like protein 2; zinc finger domain, C3H, alternative splicing, cytoplasm, metal-binding, nucleus, RNA-binding, zinc, zinc-finger; NMR {Homo sapiens}	Back alignment and structure

>1uw4_A UPF3X; nonsense mediated mRNA decay protein, RNA-binding protein, N domain, MIF4G domain; 1.95A {Homo sapiens} SCOP: d.58.7.4	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		639
d2f9da1		114	d.58.7.1 (A:12-125) Pre-mRNA branch site protein p	3e-07
d2dita1		99	d.58.7.1 (A:8-106) HIV Tat-specific factor 1 {Huma	1e-05
d1x0fa1		75	d.58.7.1 (A:183-257) Nuclear ribonucleoprotein D0	2e-05
d2cpfa1		85	d.58.7.1 (A:362-446) Probable RNA-binding protein	2e-05
d2cpha1		94	d.58.7.1 (A:454-547) Probable RNA-binding protein	1e-04
d1wf0a_		88	d.58.7.1 (A:) TAR DNA-binding protein 43, TDP-43 {	2e-04
d1wwha1		81	d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus mu	2e-04
d1wf2a_		98	d.58.7.1 (A:) Heterogeneous nuclear ribonucleoprot	4e-04
d1cvja2		89	d.58.7.1 (A:91-179) Poly(A)-binding protein {Human	4e-04
d1cvja1		80	d.58.7.1 (A:11-90) Poly(A)-binding protein {Human	5e-04
d1uawa_		77	d.58.7.1 (A:) Musashi-1 {Mouse (Mus musculus) [Tax	0.002
d1no8a_		78	d.58.7.1 (A:) Nuclear factor Aly {Mouse (Mus muscu	0.002
d1l3ka1		84	d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RN	0.002
d1x4ba1		103	d.58.7.1 (A:8-110) Heterogeneous nuclear ribonucle	0.003
d2cq4a1		101	d.58.7.1 (A:132-232) RNA binding protein 23 {Human	0.003

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


class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Pre-mRNA branch site protein p14
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.3 bits (112), Expect = 3e-07
 Identities = 15/86 (17%), Positives = 35/86 (40%), Gaps = 1/86 (1%)

Query: 321 DSTFREEDVSNYFSIYGPVHDVRIPYQ-QKRMFGFVTFVYPETVKLILAKGNPHFVCDSR 379
                 E++ + F  YGP+  +R+    + R   +V +      K      +   VC+  
Sbjct: 16  PYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRY 75

Query: 380 VLVKPYKEKGKVQEKKQQQHQQQMER 405
           ++V  Y      Q+   ++ ++Q++ 
Sbjct: 76  LVVLYYNANRAFQKMDTKKKEEQLKL 101

PyMOL of d2f9da1

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

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

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

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

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

>d1wwha1 d.58.7.1 (A:169-249) Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090]} Length = 81	Back information, alignment and structure

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

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

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

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

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

>d1l3ka1 d.58.7.1 (A:8-91) Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human (Homo sapiens) [TaxId: 9606]} Length = 84	Back information, alignment and structure

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

>d2cq4a1 d.58.7.1 (A:132-232) RNA binding protein 23 {Human (Homo sapiens) [TaxId: 9606]} Length = 101	Back information, alignment and structure

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		639
d2cqba1		89	Peptidyl-prolyl cis-trans isomerase E, N-terminal	99.67
d1b7fa1		82	Sex-lethal protein {Drosophila melanogaster [TaxId	99.67
d1fxla1		82	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.66
d1cvja2		89	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.66
d1whwa_		99	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.65
d1rk8a_		88	RNA-binding protein 8 {Fruit fly (Drosophila melan	99.65
d2f9da1		114	Pre-mRNA branch site protein p14 {Human (Homo sapi	99.65
d1x5ua1		93	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.65
d2cqia1		90	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.64
d2cq3a1		93	RNA-binding protein 9 {Human (Homo sapiens) [TaxId	99.64
d2cq0a1		90	Eukaryotic translation initiation factor 3 subunit	99.64
d2cpfa1		85	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.64
d1h2vz_		93	CBP20, 20KDa nuclear cap-binding protein {Human (H	99.64
d2cqga1		90	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.63
d1p1ta_		104	Cleavage stimulation factor, 64 kda subunit {Human	99.63
d2ghpa3		86	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.62
d1u6fa1		139	RNA-binding protein UBP1 {Trypanosoma cruzi [TaxId	99.62
d2cpza1		102	CUG triplet repeat RNA-binding protein 1 {Human (H	99.62
d2cpha1		94	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.62
d1x4ba1		103	Heterogeneous nuclear ribonucleoproteins A2/B1 {Hu	99.62
d1cvja1		80	Poly(A)-binding protein {Human (Homo sapiens) [Tax	99.62
d2cqda1		103	RNA-binding region containing protein 1 {Human (Ho	99.61
d2u2fa_		85	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.61
d1l3ka1		84	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.61
d1x4ga1		96	Nucleolysin TIAR {Human (Homo sapiens) [TaxId: 960	99.61
d2bz2a1		79	Negative elongation factor E, NELF-E {Human (Homo	99.61
d2cqca1		83	Arginine/serine-rich splicing factor 10 {Human (Ho	99.61
d1x5sa1		90	Cold-inducible RNA-binding protein {Human (Homo sa	99.6
d2adca1		109	Polypyrimidine tract-binding protein {Human (Homo	99.6
d1x5ta1		83	Splicing factor 3B subunit 4 {Human (Homo sapiens)	99.6
d1no8a_		78	Nuclear factor Aly {Mouse (Mus musculus) [TaxId: 1	99.59
d2cq4a1		101	RNA binding protein 23 {Human (Homo sapiens) [TaxI	99.59
d1fxla2		85	Hu antigen D (Hud) {Human (Homo sapiens) [TaxId: 9	99.59
d1hd0a_		75	Heterogeneous nuclear ribonucleoprotein d0 {Human	99.59
d1x4aa1		95	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.59
d1whxa_		111	Probable RNA-binding protein 19, Rbm19 {Mouse (Mus	99.59
d1b7fa2		85	Sex-lethal protein {Drosophila melanogaster [TaxId	99.59
d1x4ha1		98	RNA-binding protein 28 {Mouse (Mus musculus) [TaxI	99.58
d1wf0a_		88	TAR DNA-binding protein 43, TDP-43 {Human (Homo sa	99.58
d1uawa_		77	Musashi-1 {Mouse (Mus musculus) [TaxId: 10090]}	99.58
d1nu4a_		91	Splicesomal U1A protein {Human (Homo sapiens) [Tax	99.58
d2cpda1		86	APOBEC1 stimulating protein {Human (Homo sapiens)	99.57
d2ghpa1		81	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.57
d1l3ka2		79	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.57
d1wf2a_		98	Heterogeneous nuclear ribonucleoproteins C1/C2 {Hu	99.57
d1fjeb1		91	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.56
d2cqha1		80	IGF-II mRNA-binding protein 2 isoform A {Human (Ho	99.56
d2cpja1		86	Non-POU domain-containing octamer-binding protein,	99.55
d1x0fa1		75	Nuclear ribonucleoprotein D0 (AUF1) {Human (Homo s	99.55
d2adca2		88	Polypyrimidine tract-binding protein {Human (Homo	99.54
d1zh5a2		85	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.54
d2cpea1		101	RNA-binding protein EWS {Human (Homo sapiens) [Tax	99.53
d2b0ga1		83	Splicesomal U1A protein {Drosophila melanogaster [	99.53
d1wg1a_		88	Probable RNA-binding protein KIAA1579 {Human (Homo	99.53
d2ghpa2		75	U4/U6 snRNA-associated-splicing factor PRP24 {Bake	99.52
d2msta_		75	Neural RNA-binding protein Musashi-1 {Mouse (Mus m	99.52
d2cpia1		89	E3 ubiquitin protein ligase CNOT4 {Mouse (Mus musc	99.52
d2cpxa1		102	RNA-binding protein 41, RBM41 {Human (Homo sapiens	99.51
d1fjca_		96	Nucleolin {Golden hamster (Mesocricetus auratus) [	99.5
d1x5oa1		101	RNA-binding motif, single-stranded-interacting pro	99.5
d1wi8a_		104	Eukaryotic translation initiation factor 4B {Human	99.5
d2cq1a1		88	Polypyrimidine tract-binding protein 2, PTBP2 {Hum	99.49
d2disa1		96	Hypothetical protein FLJ20273 {Human (Homo sapiens	99.48
d1whya_		97	Putative RNA-binding protein 15B, Rbm15b {Mouse (M	99.48
d1x4da1		89	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.47
d2adba1		108	Polypyrimidine tract-binding protein {Human (Homo	99.47
d1x4fa1		99	Matrin 3 {Mouse (Mus musculus) [TaxId: 10090]}	99.46
d3begb1		87	Splicing factor, arginine/serine-rich 1, SFRS1 {Hu	99.46
d1wg4a_		98	Splicing factor, arginine/serine-rich 9 (SFRS9) {M	99.45
d1wi6a1		75	Ribonucleoprotein PTB-binding 1, Raver-1 {Mouse (M	99.45
d2cqpa1		86	RNA-binding protein 12 {Mouse (Mus musculus) [TaxI	99.44
d2cpya1		103	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.44
d1x4ea1		72	RNA-binding motif, single-stranded-interacting pro	99.42
d1weya_		104	Calcipressin-1 {Mouse (Mus musculus) [TaxId: 10090	99.41
d1wexa_		104	Heterogeneous nuclear ribonucleoprotein L-like {Mo	99.41
d1weza_		102	Heterogeneous nuclear ribonucleoprotein H' {Human	99.39
d1u1qa_		183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.38
d1wg5a_		104	Heterogeneous nuclear ribonucleoprotein H' {Human	99.35
d1u2fa_		90	Splicing factor U2AF 65 KDa subunit {Human (Homo s	99.29
d2dita1		99	HIV Tat-specific factor 1 {Human (Homo sapiens) [T	99.28
U2AF35 (35 KDa subunit) {Human (Homo sapiens) [TaxId: 9606]}" target="_blank" href="http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sid=d1jmta_">d1jmta_		104	U2	99.28
d1owxa_		113	Lupus LA protein {Human (Homo sapiens) [TaxId: 960	99.25
d1wela1		112	RNA-binding protein 12 {Human (Homo sapiens) [TaxI	99.24
d2cq2a1		101	Alkylation repair AlkB homolog 8, ALKBH8 {Human (H	99.22
d1wwha1		81	Nucleoporin 35 {Mouse (Mus musculus) [TaxId: 10090	99.16
d1u1qa_		183	Nuclear ribonucleoprotein A1 (RNP A1, UP1) {Human	99.11
d1o0pa_		104	Splicing factor U2AF 65 KDa subunit {Human (Homo s	98.96
d2cqea2		29	Zinc finger CCCH domain-containing protein C19orf7	97.18
d1m9oa_		40	Tristetraproline (ttp, tis11, nup475) {Mouse (Mus	96.94
d1rgoa1		36	Butyrate response factor 2 (Tis11D) {Human (Homo s	96.56
d2cqea1		56	Zinc finger CCCH domain-containing protein C19orf7	96.42
d1i2ta_		61	hyperplastic discs protein {Human (Homo sapiens) [	96.32
d1rgoa2		34	Butyrate response factor 2 (Tis11D) {Human (Homo s	96.29
d2dgxa1		73	Limkain-b1, LKAP {Human (Homo sapiens) [TaxId: 960	96.27
d1ufwa_		95	Synaptojanin 2 {Human (Homo sapiens) [TaxId: 9606]	95.72
d1g9la_		144	poly(A) binding protein {Human (Homo sapiens) [Tax	95.36
d1nmra_		85	poly(A) binding protein {Protozoan (Trypanosoma cr	95.28
d1ifwa_		92	poly(A) binding protein {Baker's yeast (Saccharomy	94.68
d1uw4a_		91	RNA processing protein UPF3x, RRM domain {Human (H	84.91

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

class: Alpha and beta proteins (a+b)
fold: Ferredoxin-like
superfamily: RNA-binding domain, RBD
family: Canonical RBD
domain: Peptidyl-prolyl cis-trans isomerase E, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=5.2e-17  Score=137.06  Aligned_cols=80  Identities=21%  Similarity=0.333  Sum_probs=73.8

Q ss_pred             CCCceEEEeCCCCCCCCHHHHHHHhhcCCCeeEEEeecc----CCCceEEEEECCHHHHHHHHHhCCCeEEcCeEEEEEe
Q 041390          309 PSARQIYLTFPADSTFREEDVSNYFSIYGPVHDVRIPYQ----QKRMFGFVTFVYPETVKLILAKGNPHFVCDSRVLVKP  384 (639)
Q Consensus       309 ~~sr~IYV~~~~d~~~TEedLre~FsqFG~V~dVrIp~D----ksRGFGFVtF~~~E~Ae~Al~~mng~~L~GR~I~Vk~  384 (639)
                      ...++|||++++. ++||++|+++|++||+|.+|+|++|    ++||||||+|.+.++|++|++.+|+..|+|+.|.|++
T Consensus         3 ~~~~tlfV~nLp~-~~te~~l~~~F~~~G~i~~v~i~~d~~~~~~kg~afV~f~~~~~A~~ai~~l~~~~i~g~~l~v~~   81 (89)
T d2cqba1           3 TTKRVLYVGGLAE-EVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL   81 (89)
T ss_dssp             CCCSCEEEESCCS-SCCHHHHHHHHTTTSCCCCEECCCCSSSCCCSSEEEECCSSHHHHHHHHHHHTTEEETTEEEEEEE
T ss_pred             CCCcEEEEeCCCC-cCCHHHHHHHHhhCCeEEecccccccccccccceeEEEECCHHHHHHHHHHcCCCEECCEEEEEEE
Confidence            4578999997765 8999999999999999999999875    8899999999999999999999999999999999999


Q ss_pred             cccCC
Q 041390          385 YKEKG  389 (639)
Q Consensus       385 a~~K~  389 (639)
                      ++++.
T Consensus        82 a~p~~   86 (89)
T d2cqba1          82 AKPMR   86 (89)
T ss_dssp             CCCCC
T ss_pred             eCCCC
Confidence            98654

PyMOL of d2cqba1

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

>d2cqea2 g.66.1.1 (A:429-457) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1m9oa_ g.66.1.1 (A:) Tristetraproline (ttp, tis11, nup475) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1rgoa1 g.66.1.1 (A:151-186) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2cqea1 g.66.1.1 (A:458-513) Zinc finger CCCH domain-containing protein C19orf7 (KIAA1064) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1i2ta_ a.144.1.1 (A:) hyperplastic discs protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1rgoa2 g.66.1.1 (A:187-220) Butyrate response factor 2 (Tis11D) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

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

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

>d1g9la_ a.144.1.1 (A:) poly(A) binding protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1nmra_ a.144.1.1 (A:) poly(A) binding protein {Protozoan (Trypanosoma cruzi) [TaxId: 5693]}	Back information, alignment and structure

>d1ifwa_ a.144.1.1 (A:) poly(A) binding protein {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

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