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pfam03178: CPSF_A 
CPSF A subunit region
This family includes a region that lies towards the C-terminus of the cleavage and polyadenylation specificity factor (CPSF) A (160 kDa) subunit. CPSF is involved in mRNA polyadenylation and binds the AAUAAA conserved sequence in pre-mRNA. CPSF has also been found to be necessary for splicing of single-intron pre-mRNAs. The function of the aligned region is unknown but may be involved in RNA/DNA binding.
Statistics
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PSSM-Id: 251781
View PSSM: pfam03178
Aligned: 80 rows
Threshold Bit Score: 146.218
Threshold Setting Gi: 123455623
Created: 28-Mar-2013
Updated: 4-Apr-2013
Structure
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Aligned Rows:

pfam03178 is a member of the superfamily cl20247.
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75032529   869 SAAVPLLE------------------NERCVFLQTVRLD-----GgegggagerggepidvaasdsagvsEEewqhLLLI 925
gi 46395602   733 LSFLRVYEkntlsei----ahhkfneYEMVESIILMNd--------------------------------DK----RVVV 772
gi 74616958   792 HSSFKLVDeilfarvgkefmlgtssySELVEDVIRAELP-----Dsyg--------------------nlVE----RFIV 842
gi 121930128  765 LSHFKLVDeiqfkel----dtyalneEELVECVMRCDLA-----Dgsg--------------------gtAE----RFVI 811
gi 74598850   781 KSQFVLADeilfrrl----dafdlegEEIVECVIRAEAP-----Eskd-------------------geaKD----RFVV 828
gi 121738327  782 KSQFVLADeilfrrl----dafdlrsEELVESVIRAEFP-----Vgkdek---------------grdmfKD----RFVV 833
gi 156389050  801 iGSLLIIDqhtfevt----hahqlhdNEQATSLMSCTLS-----Dd-----------------------pHT----YYCV 844
gi 154286506  794 ASRFMLADeimfrel----diydlnkDELVESVIRAQFP-----Dgidre---------------gndlfKD----LFVV 845
gi 268536658  780 tSSFMILDqntfqvl----hahefgpFEAAVSCISGQFS-----Dd-----------------------aRQ----YYIV 823
gi 119471789  783 KSRFVLADeilfrrl----dafelrpEELVESVIRAEFPagkgaNdrd--------------------evKD----RFIV 834
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75032529   926 GSSFTFPDEQRARS---GRITWCALRE-EHqqqRLHLIASKDIGGAlqcCAAVPHYKGRIALGVNGCVCLYKWN-TEDq- 999
gi 46395602   773 GTGFNFPDQDAPDS---GRLMVFEMTSd----nNIEMQAEHKVQGS---VNTLVLYKHLIVAGINASVCIFEYE-HGT-- 839
gi 74616958   843 GTSFLEDPDRGAGTdkrGRILVFGIDSn----rDPYLVLKHELKGG---CRALAVMGSKIVAALHKTVVISQYE-ETSst 914
gi 121930128  812 GTAYLDDQNSTVER---GRILILEVTPe----rVLKLVTEIAVKGG---CRCLAMCEGKIVAALIKTIVVYDIE-YRTqs 880
gi 74598850   829 GSAYLGEDDG-DSTl--GYIRVFEVDNg----rKLAKVAQERVKGA---CRALAVMGDKIVAALVKTVVVFQVV-PRSgg 897
gi 121738327  834 GTAYLDEDEDRDSIr--GRILMFEVDNg----rKLTKVAELAVKGA---CRALAMLGDKVVAALVKTVVIYKVT-GNNfg 903
gi 156389050  845 GTAYVFPEEPEPKA---GRLLLFHLSEg-----KLVQVAEKEVKGA---VYSLVEFNGKVLAGINSTVSIFEWTaDKE-- 911
gi 154286506  846 GTSYLDDFGEGSIR---GRILAFEVTan----rQLAKVAEMPVKGA---CRALAIVQDKIVAALMKTVVVYTIS-KGQfa 914
gi 268536658  824 GTGLIYPDESDTKL---GRIIVFEVDDvERt--KLRRVHELVVRGS---PLALRILNGKLVAAINSSVRLFEWT-ADK-- 892
gi 119471789  835 GTAYLDDEGDESIR---GRILIFEVDNg----rKLTQVAELPVKGA---CRALAMLGDKIVAALVKTVVVYRVI-NNNfg 903
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75032529  1000 --tFVA-EERCRVGLtvtKLIPLYH-TSlaasVLVALDVRHSAFFIEVDT---------LQGsLKVLCRDAELRGVMDGH 1066
gi 46395602   840 ---MHV-RNSIRTPT---YTIDISVnQD----EIIAADLMKSITVLQFID----------DQ-LIEVARDYHPLWATSVE 897
gi 74616958   915 eahLVK-LASYRCTT---YPVDIAVhGN----MIAVADMMKSATLVEYVPaktggekseAPK-LVECARHRHSAWATAVA 985
gi 121930128  881 kpdLVK-AATFRCST---APIDITVnGT----QIAIADLMKSMVVVEYQRge-----tgLPDkLVEVARHFQVTWATAVA 947
gi 74598850   898 -lqLQR-LASYRTST---APVDITVtRN----VIAIADLMKSVCVVEYHEgen----gaPDK-LVEVARHFQTVWATGVT 963
gi 121738327  904 amkLEK-LASYRTST---APVDITVtDN----VIAVSDLMKSSCLVEYIEged----glPDS-LKEVARHFQTVWATGIA 970
gi 156389050  912 ---FRY-ECSYYDNI---LALYLKTkGD----FILVGDLMRSMTLLVYLP---------LEGsFQEIAHDFSPKWMTAIE 971
gi 154286506  915 dytLSK-TASYRTST---APIDIAVtGN----LIAVADLMKSVSIVEYQQgs-----ngLPDsLTEVARHFQTLWSTAVA 981
gi 268536658  893 ---VLRlECSNFNHI---VALDLKVmNE----EVAVADLMRSVSLLSYRM---------MEGnFEEVAKDWNSEWMVTCE 953
gi 119471789  904 amrLEK-LASYRTST---APVDVTVtGN----LIAVSDLMKSMCLVEYKEge-----ngTPDtMTEVARHFQTVWATGVA 970
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75032529  1067 IGSDAENLCLFDDSLNFTALRVVPlpveagdgdaaaaasvtaqyRFEVRAQCHLGDLVTCVRQGSF-AA--TslMEAPAS 1143
gi 46395602   898 IL-SErKYFVTEADGNAVILLRDnvspq-----------lsdrkKLRWYKKFYLGELINKTRHCTF-IE-----PQDKSL 959
gi 74616958   986 HV-EGeSWLEADANGNLIVLQRNaegvt-----------vedqrQLRITSELNLGEQVNKIRPIK--VE-----TSPNAI 1046
gi 121930128  948 EV-DEnTYLESDAEGNLLVLYRDPkgvtd-----------ddkrRLNVSSEMLLGEMVNRIRRIDV-AT--Ap-DAVVVP 1011
gi 74598850   964 SV-APdTYLESDAEGNLIVLRRNrsgve-----------eddrrRLEVTGEICLNEMVNRIRPVN--IQ-----QLPSAT 1024
gi 121738327  971 CI-APhTYLESDAEGNLIILRRNlsgve-----------eddkrRLEVTGEISLGEMVNRIRPVN--IQ-----QLASVT 1031
gi 156389050  972 IL-DDDTFLGAENSYNLFTCTKDsgatt-----------deeryHLQDAGQYHLGEFVNVFRHGSL-VMehP--GDASTP 1036
gi 154286506  982 HVAE-DTWLESDAEGNLVMLHRNvngvt-----------dddrrRLEVTSEILLGEMVNRIRPVNI-QG--S--QGAEAA 1044
gi 268536658  954 FITA-ESILGGEAHLNMFTVEVDKsrpit----------ddgryVLEPTGYWYLGELPKVMVRASLvVQ--P--EDSTIE 1018
gi 119471789  971 NIA-PDTFLESDAEGNLIVLHRNttgve-----------eddkrRLEVTGEISLGEMVNRIRPVNI-----Q--QLASVA 1031
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 75032529  1144 CasaqnrlllpgiagPQLVFATAHGGFGvVTP-VHAATYLVLRTLEASLVRTLQPLGGLSHQAF------REV-LRSgqe 1215
gi 46395602   960 Vt-------------PQLLCATVDGSLM-IVGdAGMSNTPLLLQLQDNIRKVIPSFGGLSHKEW------KEY-RGEn-- 1016
gi 74616958  1047 Ii-------------PRAFLATAEGGIY-MFGtIARE-QDLLLRFQDKLAAVIKTVGELDFNSY------RAF-RNAe-- 1102
gi 121930128 1012 ----------------RAFMGTVEGSIY-LFAlISQNYLDLLITLQSNLGNLVVSPGNMDFAKF------RAF-KNQv-- 1065
gi 74598850  1025 Vv-------------PRAFLATVEGSIY-LYAiINPDYQDFLMRLQATMASRADSLGGIPFTDY------RAF-RTMt-- 1081
gi 121738327 1032 Vt-------------PRAFLGTVEGSIY-LYAiINPEHQDFLMRLQATMAGKIESLGDMPFNEF------RGF-RSMv-- 1088
gi 156389050 1037 Fq-------------GCVLFGTVNGRIG-IVAqIAQDLFNFLIQVQKKLNKVIKSVGKIDHSLYpfphcsNLS-HSR--- 1098
gi 154286506 1045 Is-------------PRAFLGTVEGSIY-LFGiINPTYQDLLMRLQSAMAGMVVTPGGMPFNKF------RAF-RNT--- 1100
gi 268536658 1019 Ys-------------HPIMFGTNQGTIGmLVq-IDDKWKKFLVSIEKAISDSVKNCMQIEHSTY------RSFiFQK--- 1075
gi 119471789 1032 Vt-------------PRAFLGTVEGSIY-LFAiINPDHQDFLMRLQATIAGKVELVGNMPLNEF------RGF-RSMv-- 1088
                         410       420
                  ....*....|....*....|....*...
gi 75032529  1216 rgV--SYla--skTGCALTRERLRRYEP 1239
gi 46395602  1017 -eT--S-------PSDLIDGSLIESILG 1034
gi 74616958  1103 -rG--PEadgttgPVRFLDGELLERFLD 1127
gi 121930128 1066 -rT--EEe-----PNRFVDGELIERFLD 1085
gi 74598850  1082 -rQ--ATe-----PYRFVDGELIERFLT 1101
gi 121738327 1089 -rE--AKe-----PYRFVDGELIERFLT 1108
gi 156389050 1099 --K--MEp-----AHGFIDGDLIESFLD 1117
gi 154286506 1101 --IrqAEe-----PYRFVDGELIERFLS 1121
gi 268536658 1076 --R--IEp-----PSGFIDGDLVESILD 1094
gi 119471789 1089 -rE--AKe-----PYRFVDGELIERFLT 1108
Citing CDD
Marchler-Bauer A et al. (2013), "CDD: conserved domains and protein three-dimensional structure.", Nucleic Acids Res. 41(D1):D384-52.
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