5IFE


Conserved Protein Domain Family
CPSF_A

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pfam03178: CPSF_A 
Click on image for an interactive view with Cn3D
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: 335252
View PSSM: pfam03178
Aligned: 65 rows
Threshold Bit Score: 180.447
Threshold Setting Gi: 75032529
Created: 23-Mar-2017
Updated: 23-May-2017
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IFE_A        873 ASVIRVMNPiqGN-TL-DLVQLEQNEAAFSVAVCRFsnTGE--------------------DWYVLVGVAKDLILNPrSV 930
gi 74583567   990 QSGILLINP--KSwKViDKIDFPKNSVVNEMRSSMIqiNSKtk----------------rkREYIIAGVANATTEDTpPT 1051
gi 74609915   990 KSGVLLINP--KSwEViDELDLPDNSLVNDMKSSFIqiDTRtk----------------rkREYIIVGIGYATMEDVpPT 1051
gi 74695871   932 QSGIILLSP--KSwEIiDKIEYGKNSLINDMRTMMIqlNSNtk----------------rrREYLVVGNTYVRDEDIgGT 993
gi 74606921   934 KSGLLLINP--LTwNIiDRLDLSENSMVNDIKTMLIqlNSKtr----------------rkRELVIIGSSFVKEEDQpST 995
gi 74591422  1022 KGSIKLVSP--YNwTViETIELGDNEVGMTLKSMILdvGSEsgstlgsdpnslikkynkkkREYIVIGIGKYRMEDLaAN 1099
gi 150951283  976 KGSIKLISPfnWS-VI-DTIELADNELGMTVKSMILdvGSStkkf-------------khkKEFIVIGSGKYRMEDLsAN 1040
gi 149237256 1015 KSSIKLISPhnWT-VI-DSFDLEDNEVGMTVKSMILdrGSGaaslk----------kfkskREYIVIGTGKLRMEDLaAN 1082
gi 156847699  968 QAGILLVNPktWN-VI-DKIEFERNSLINDMRSMTIqvNSKtk----------------kkRELLVVGVASIGTEDL-PS 1028
gi 698996654 1012 rgVLKLLSGitWT-VI-DTVEMEPCETVLCVETLNLevSEStn----------------erKQLIAVGTALIKGEDLpTR 1073
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IFE_A        931 aGgFVYTYKLVNN------GE---KLEFLHKTPV-EEVPAAIAPF--QGRVLIGVGKLLRVYDLGKK-K-LLRKCEN-KH 995
gi 74583567  1052 -G-AFHIYDVIEVvpepgkPDtnyKLKEIFQEEV-SGTVSTVCEV--SGRFMISQSQKVLVRDIQED-NsVIPVAFLdIP 1125
gi 74609915  1052 -G-EFHIYDITEVvpepgkPNtnfKLKEIFKEDI-RGIVSVVNGI--SGRFLISQSQKIMVRDVQQD-NsVIPVAFLdVP 1125
gi 74695871   994 -G-SFYLYDITEVvpepgkPDtnyKFKDIFQEDI-RGTVSTVCEI--SGRFMISQSSKAMVRDIQED-NsVVPVAFLdMP 1067
gi 74606921   996 -G-CLLVLDITEVvaepgkPDsnfKFKQLFEEEI-RGSVNAVCEI--SGRFMIGQSSKALVRDMQED-NsAVPVAFLdMP 1069
gi 74591422  1100 -G-IFKIYEIIDIipepgkPEtnhKFKEIFKEET-RGAITSICEL--SGRFLVSQGQKVIVRDLQDD-G-TVPVAFLdTP 1172
gi 150951283 1041 -G-SFRIYEIIDIipepdrPEtnhKFKEVFKEDT-KGAVTSVCEV--SGRFLVSQGQKVIVRDLQDD-G-VVPVAFLdTA 1113
gi 149237256 1083 -G-SFKIYEIIDIipepgkPEtnhKFKEVFQEDA-RGAVTAICDL--SGRLMVGQGQKIIVRDIEDD-G-VVPVAFLdTS 1155
gi 156847699 1029 aG-SFHVIDINEVvpepgkPDtnyKFKEIFQETV-RGNVNSVCEI--SGRFMINQSQKLLVRDIQEDeS-VVPVAFLdVP 1103
gi 698996654 1074 -G-RVYVFDIADVipepgkPEtskKLKLVAKEDIpRGAVTALSEVgtQGLMLVAQGQKCMVRGLKED-GtLLPVAFMdMN 1150
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IFE_A        996 IanYISGIQTI--GHRVIVSDVQESFIWVRYKRNENqLIIFADDTYPRWVTTASLL--DY-D---TVAGADKFGNICVVR 1067
gi 74583567  1126 V--FVTDSKSF--GNLLIIGDAMQGFQFIGFDAEPYrMISLGRSMSKFQTMSLEFLv-NGgDm--YFAATDADRNVHVLK 1198
gi 74609915  1126 V--FVTSLKTF--GNLIVIGDAMQGIQFVGFDAEPYrMITLGSSITKFEVISVEFLv-NNgDi--YFLVTDRDSIMHVLK 1198
gi 74695871  1068 V--FITDAKSF--GNLMIIGDSMQGFSFLGFDAEPYrMLTLGKSVSKLETMCVEFLv-NNgDv--YFLVTDRNNLMHVLK 1140
gi 74606921  1070 V--FITDAKSF--SNLMIIGDSMQGFTFVGFDAEPYrMIVLGKSTSKFQVMNLEFLv-NNgNi--NFIVTDRQNHLHVLR 1142
gi 74591422  1173 V--YVSESKSF--GNLLILGDLLKGCWLVGFDAEPFrMIMLGKDTQHISVECADFIi-NDdEi--FVLVADNNNVLHLLN 1245
gi 150951283 1114 V--YVSEAKSF--GNMMILGDSLKSVWLVGFDAEPFrMIMLGKDLQGLDVNCADFI--TK-DeevFILIADNNNVLHLVQ 1186
gi 149237256 1156 V--YISEAKSF--GNLLILGDPLKSVWLVGFEAEPYrMVMLGKDRQHLDVECADFIikDE-Di--FILVADNNNCIHLIQ 1228
gi 156847699 1104 V--YVTDTKSF--SNLMIVGDSMQGFQFVGFDAEPYrMIPLGRSVSKFKTVALEFLvnNG-Di--FFIVSDRNDILHVLK 1176
gi 698996654 1151 C--YVTSVKELpgTGLCLMADAFKGVWFTGYTEEPYkMMLFGKSSTRMEVLNADFLp-DGkEl--YIVASDADGHIHILQ 1225
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IFE_A       1068 LPPNTNDEVDEDptgnkalwdrgllngasqKAEVIMNYHVGETVLSLqktTLIP---GGSES------------------ 1126
gi 74583567  1199 YAPDEPNSLSGQ------------------RLVHCSSFTLHSTNSCM---MLLPrn-eEFGSpqvp-------------- 1242
gi 74609915  1199 YAPDQPNTLSGQ------------------RLVHCSSFNLHSLNNCT---MLLPkn-dEFPRdqrys------------- 1243
gi 74695871  1141 YAPDEPNSLSGQ------------------RLVHCTSFNLHSTNTCM---RLIKkn-dEFGKvsrgfgi----------- 1187
gi 74606921  1143 YAPDEANSLSGQ------------------RLVHCNSFNMFTTNNYM---KLVRkh-vEFGSkts--------------- 1185
gi 74591422  1246 YDPDDPQSINGT------------------KLLTKASFELNSTISCL---RSLPlidIEESVqtdaltniavppplppnt 1304
gi 150951283 1187 YDPEDPTALNGQ------------------RLLSKSSFSINSFVTCL---KSLP---KTEEKydtg-------------- 1228
gi 149237256 1229 YDPDDPKSINGTi------------------LLNKASFELNSATTCLr---sIP---KGEkgd----------------- 1267
gi 156847699 1177 YAPDEPNSLSGQ------------------RLAHYSSFNIHSTNTSM---ILLP---SNNEFqsspng------------ 1220
gi 698996654 1226 FDPEHPKSLQGH------------------LLLHRTTFNTGAHHPTSs--LLLPavyPNPSslssnse------------ 1273
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5IFE_A       1127 ------LVYTTLSGGIGILVPfTSHEDHDFFQHVEMHLRSEHPPLCGRDHLSFR-----SYYf--------------pV- 1180
gi 74583567  1243 ---sfqNVGGQVDGSVFKIVP-LSEEKYRRLYVIQQQIIDRELQLGGLNPRMER-----LANdfyqm-----------gh 1302
gi 74609915  1244 --rsfqTITAQVDGSISKIVP-VKEETYRRLYFIQQQIIDKEPQLAGLNPRMER-----QDNkyyhl-----------gh 1304
gi 74695871  1188 ympsfqCIGSQADGTIFKVVP-LSEASYRSLYLIQQQLIDKEVQLCGLNPRMER-----LENpfyqm-----------gh 1250
gi 74606921  1186 ---nyiALGCQTDGSIFRMIP-LNEASYRRFYLVQQQLLDHEIPLAGFNTKMER-----LDNeyyhk-----------gh 1245
gi 74591422  1305 tsnyfqVIGSTQDGSFFNVFP-INEAAYRRMYILQQQLIDKEFHYCGLNPRLNR-----IGSiklqn-------netnT- 1370
gi 150951283 1229 ---nfqTIGSTIDGSFFSVVP-INEASYRRMYILQQQLTDKEYHYCGLNPRLNR-----FGGlsmta-------ndtnT- 1291
gi 149237256 1268 ----yqIIGSTLDGALYNVFP-VNEFTYRRMYILQQQISDKVYHFCGLNPRLNRfggsvTLRdre-----------tnT- 1330
gi 156847699 1221 -qatfqSVGSCVDGSIFKVIP-LDEDSFRRLYVIQQQVIDTEIQAGGLNPRMER-----LSNeyy-----------qlVh 1282
gi 698996654 1274 ensphiLLLASPTGVLATLRP-LQENAYRRLSSLAVQLTNGLPHPAGLNPKGYR-----LPSpsasasmqlpgvdagiG- 1346
                         410
                  ....*....|....
5IFE_A       1181 --KNVIDGDLCEQF 1192
gi 74583567  1303 smRPMLDFNVIRRF 1316
gi 74609915  1305 slRPMLDFNIIKRF 1318
gi 74695871  1251 ilRPMLDFTVLKRF 1264
gi 74606921  1246 slRPTLDSQVLKKY 1259
gi 74591422  1371 --KPILDYDLIRSF 1382
gi 150951283 1292 --KPILDYDVIRAY 1303
gi 149237256 1331 --KPILDYGLIRRF 1342
gi 156847699 1283 lmRPMLDFNIIRRF 1296
gi 698996654 1347 --RNIVDGKILERF 1358
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