RNA Polymerase II Transcription (Homo sapiens)

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371427, 331221, 28, 30, 3337363412343733373710, 24148363, 34141227, 3337373321, 3334372, 9, 19, 21374, 6, 16, 20, 22...345, 73326nucleoplasmPOLR2K U7 snRNA GTF2B NELFACCNH CTDP1 Pol II transcriptioncomplex containingextruded transcriptto +30POLR2C TAF13 POLR2G NELFE GTF2H1 NELFCD TAF1L ATP GTF2H2 POLR2L ERCC3 POLR2H GTF2F2 ERCC2 GTF2H4 SNRPB POLR2K TAF1 TAF13 TAF5 POLR2I TAF5 CCNT2 PPiPOLR2L GTF2F2 Elongating transcript in processive Pol II mediated elongation POLR2E POLR2F TAF6 UTP POLR2B GTF2F1 POLR2G SNRPE POLR2D TAF1 SNRPD3 GTF2H4 CDK9 DNA containing RNA Polymerase II promoter TCEB2 TAF6 POLR2B GTF2A1(275-376) POLR2L CDK9 GTF2F1 Capped IntronlessHistonepre-mRNA:CBC:ZFP100ComplexCDK7 POLR2H POLR2H POLR2G ERCC3 SUPT4H1 DHX38 POLR2L CF I - 72 kDa subunit MNAT1 POLR2B POLR2B SNRPF POLR2D GTF2H1 TAF6 CDK9 template:capped transcript hybrid GTF2BTAF1L GTF2F2 ELL POLR2F POLR2G GTF2A1(1-274) TAF9B POLR2I TCEB2 pol II openpre-initiationcomplexPOLR2A CCNT1 Elongating transcript in processive Pol II mediated elongation TAF4B GTF2H3 ERCC2 CF I - 72 kDa subunit Mature Intronless transcript derived Histone mRNA GTP RNMT GTF2H5 POLR2G POLR2J GTF2H3 GTF2H3 POLR2F GTF2E2 template:capped transcript hybrid SUPT16H Aborted elongationcomplex afterarrestCCNH POLR2K POLR2D POLR2E ERCC3 RNMTUTP NELFB ERCC2 TAF6 TAF5 SNRPG RNGTTTAF3 POLR2E POLR2C TAF1L GTF2F1 POLR2I ERCC3 CTDP1 GTF2H2 CF I - 68 kDa subunit polIIpromoter:TFIID:TFIIA:TFIIB complexGTF2E1 POLR2J PPiERCC2 NCBP1 GTF2H3 GTF2H4 mRNA 3'-end cleavagefactorPOLR2H GTF2H2 TBP CCNH CCNH PPiCDK7 NCBP2 TAF4 ERCC3 GTF2H3 GTF2A1(1-274) POLR2J Mature Intronless transcript derived Histone mRNA POLR2D pol II transcriptioncomplexERCC2 POLR2D TAF6 SSRP1 GTF2F2 GTP GTF2H1 TAF12 POLR2F GTF2F1 POLR2D POLR2I POLR2D POLR2D TFIIHPOLR2L MNAT1 ELL NELFB CPSF1 NELFB POLR2G POLR2I NELFECDK9 GTF2F1 POLR2D Elongating transcript prior to separation POLR2B POLR2G NELFE GTF2BTAF4B POLR2K MNAT1 TCEB1 SRRM1 TAF4B POLR2G POLR2F SUPT4H1 GTF2H2 TCEB3 POLR2D GTF2F2 mRNA with spliced exons POLR2C GTF2H1 POLR2F UTP ZNF473 MNAT1 TCEA1 GTF2A1(1-274) POLR2K PCF11 NCBP1 Cap Binding Complex(CBC)SRSF5 NFX.1 TFIIFPOLR2D GTF2H1 TCEB2 Aborted earlyelongation complexcapped pre-mRNA GTF2F1 TAF4 TAF6 POLR2D RNPS1 POLR2A TAF5 NUDT21 POLR2E GTF2A1(275-376) capped pre-mRNA POLR2E TAF11 POLR2C CCNT1 POLR2H CDK7 NCBP1 CDK7 GTF2A1(1-274) TAF1L MNAT1 NELFA POLR2J GTF2H3 TCEB1 pol IIpromoter:TFIIDcomplexp-S2,S5-POLR2A NCBP1 TCEA1 CDK7 POLR2L POLR2H GTF2H1 POLR2G TCEA1 POLR2K ERCC2 POLR2H TCEA1 RBM8A POLR2C POLR2E NTPPOLR2L TAF1L CTDP1 TAF3 POLR2C CF IELL GTF2A2 SRSF6 GTF2F1 TAF10 POLR2B Capped intronless pre-mRNA NELFA CPSF2 CSTF2 TAF5 GTF2E1 TAF2 NTPERCC2 TCEB2 CCNH GTF2H3 TCEB3 GTF2F2 POLR2D GTF2A1(1-274) GTF2H5 CDK9 DNA containing RNA Polymerase II promoter CstFPOLR2F CSTF3 POLR2F POLR2I TAF10 POLR2E NELFA SSRP1 SRSF7 GTF2F2 GTF2H1 NELFA SLBP CDK9 TAF3 GTF2H3 POLR2J GTF2F2 upstream intronless mRNA fragment CCNT1 GTF2F2 ATP TFIIANCBP2 SUPT4H1 ATP POLR2B TCEB1 POLR2H GTF2F2 TAF6 CCNH NELFA POLR2J TAF12 SUPT4H1 GTF2F1 POLR2B TAF9 ERCC2 CCNT2 TAF1 SNRPD3 ELL POLR2H template DNA:4 nucleotide transcript hybrid NTPERCC3 PABPN1 POLR2G TAF5 Open DNA -10 to +2 containing RNA Polymerase II promoter TAF3 CCNT1 p-S5-POLR2A GTF2A1(275-376) POLR2L TCEB1 PPiGTF2F2 POLR2C CCNH GTF2F1 CDK9 GTF2H1 POLR2L GTF2H4 POLR2I GTF2A1(1-274) TAF2 CTP GTF2H3 POLR2J NELFE POLR2D POLR2G NELFB CDK7 TAF2 CLP1 CTP POLR2A TAF9 CTP UPF3B GTF2E2 TAF11 GTF2H5 p-S2,S5-POLR2A POLR2H POLR2K GTF2E2 GTF2H1 GTF2A1(275-376) SRSF9 GTF2H1 NELFCD GTF2E1 GTF2H4 SRSF4 CCNT2 GTF2A1(1-274) POLR2G RNGTT TAF12 CTDP1 POLR2E CCNT1 CLP1 ATP ALYREF CTP POLR2D POLR2F TAF11 SRSF11 TAF10 POLR2L NCBP1 POLR2E damaged DNAsubstrate:nascentmRNA hybridCDK7 CPSF4 - 30 kDa subunit GTF2A2 GTF2B POLR2E GTF2H1 NELFCD TAF11 POLR2G CTP p-SUPT5H MAGOH POLR2F POLR2E ATP GTF2F2 UTP CTP CPSF1 POLR2L GTF2H3 TAF9 TAF3 MNAT1 NCBP1 GTF2A1(1-274) GTF2F2 GTF2H5 TCEB2 POLR2J POLR2J GTF2A1(275-376) capped pre-mRNA ERCC3 Mature intronlesstranscript derivedHistonepre-mRNA:CBCcomplexTAF11 UTP RNPS1 GTP GTF2H3 POLR2C UTP GTF2E2 POLR2I CCNH ERCC3 POLR2E NTPTAF10 POLR2I TAF9B ERCC2 ALYREF TAF9B SRSF9 SSRP1 TAF2 TAF3 POLR2D SNRPD3 GTF2H5 SSRP1 POLR2H POLR2A ATP SSRP1 U2AF1 ERCC2 Elongation complexprior to separationTAF1 TAF9B ERCC3 TBP TAF13 POLR2L POLR2K GTF2H2 CDK7 GTP POLR2C p-S2,S5-POLR2A POLR2D TAF2 CPSF7 POLR2A NUDT21 POLR2F Elongating transcript prior to cleavage p-S5-POLR2A TAF4B GTF2H4 CCNH SUPT4H1 POLR2F TAF12 POLR2G template DNA:4-9 nucleotide transcript hybrid POLR2L GTF2F2 POLR2K PAPOLA GTF2H5 GTF2H4 TAF9B TAF4 pol II transcriptioncomplex containing9 nucleotide longtranscriptNELFE GTF2H1 CTP SUPT16H POLR2G CDC40 POLR2D FACT complexSUPT16H POLR2G POLR2G POLR2C TAF5 POLR2A TAF9B POLR2D POLR2B p-SUPT5H POLR2K POLR2B CTP POLR2I POLR2I MNAT1 GTF2H2 TAF12 POLR2G GTF2F2 GTF2H4 TAF11 POLR2I GTF2F2 p-S5-POLR2A SUPT16H ATP POLR2E NELFA GTF2H2 TAF4 POLR2I POLR2E POLR2L ATP SNRPE CTP GTF2A1(275-376) POLR2A NELFE LSM10 CF I - 68 kDa subunit POLR2C TCEB2ERCC2 POLR2H PPiTAF9B RNA Pol II withphosphorylated CTD:CE complex withactivated GTERCC3 GTF2B GTF2H1 TAF10 SNRPG GTF2H5 CDK9 POLR2E GTF2E1 GTF2F2 TAF9B NTPNELFCD TAF9 Elongating transcript in processive Pol II mediated elongation TAF10 p-S5-POLR2A ERCC3 TAF6 SNRPB ERCC3 NELFB ERCC2 CCNH Pol II initiationcomplexGTP template DNA:30 nt transcript hybrid TAF4 NELF complexTAF1L TCEA1 CDK7 RNAPolymeraseIIholoenzymecomplex(hyperphosphorylated)POLR2E CPSF3 POLR2F TBP GTF2F2 ATP POLR2E TAF13 TBP CCNH POLR2C GTF2H4 TAF13 POLR2H POLR2L SRSF3 CCNT1CE:Pol II CTD:Spt5complexNELFB CDK7 POLR2F TFIIHGTF2H5 CCNT2 CPSF7 SUPT4H1 GTF2A1(1-274) POLR2D CPSF3 CCNT2 POLR2B GTF2F1 GTP POLR2E ERCC3 POLR2A Paused processiveelongation complexERCC2 POLR2D GTF2H1 CappedIntronlessHistonepre-mRNA:CBP80:CBP20:SLBP:ZFP100 ComplexCTP POLR2A NCBP2 template DNA with first transcript dinucleotide, opened to +8 position p-SUPT5H TAF11 CTDP1 GTF2E2 GTF2H4 GTF2H4 ERCC2 TFIIHTAF5 GTF2H4 TAF1L ATP TAF10 TAF1L p-S2,S5-POLR2A SRRM1 GTF2E1 POLR2H POLR2E POLR2L Ligated exoncontaining complexTAF3 POLR2J TAF2 POLR2I TAF2 CTDP1GTF2H5 CTP POLR2B POLR2F LSM10 POLR2B ERCC3 GTF2A1(275-376) NELFA TAF2 CCNT2 POLR2F GTF2H4 POLR2C MatureIntronlesstranscriptderivedHistonemRNA:SLBP:CBP80:CBP20TAF12 GTF2B POLR2D POLR2K GTF2E1 POLR2L POLR2H POLR2D POLR2A POLR2E GTP POLR2G GTF2F1 CLP1 3' end cleaved,ligated exoncontaining complexPOLR2K GTF2F1 POLR2E hTra2 TAF1L ERCC3 POLR2G POLR2J SNRPE TAF12 GTF2H4 POLR2D POLR2F GTF2F1 POLR2I CTDP1 POLR2C POLR2B POLR2B POLR2I CPSF7 GTF2H5 POLR2D POLR2L GTF2F2 CSTF1 TAF9 TCEA1 SUPT16H template DNA:30 nt transcript hybrid TCEB3 CSTF3 GTF2F1 CCNT2 POLR2D GTF2E1 TAF13 UPF3B POLR2F POLR2K CCNT2 CDK7 ERCC2 GTF2A1(275-376) CPSF2 POLR2J POLR2F POLR2B ERCC3 TAF12 CTDP1 TAF11 TCEB1 ERCC2 POLR2C POLR2K MNAT1 TFIIENELFA GTF2H3 MNAT1 POLR2G GTF2F1 POLR2L POLR2H GTF2A2 POLR2H POLR2I POLR2F TAF5 POLR2C POLR2L POLR2I POLR2H GTP POLR2I POLR2I Intronless Histone pre-mRNA POLR2H DSIF complexp-SUPT5H MNAT1 POLR2H POLR2K POLR2B POLR2B CDK7 GTF2H3 POLR2F POLR2G POLR2L PCF11 GTF2H2 LSM10 TAF1 POLR2F CCNH CDK7 template DNA:30 nt transcript hybrid TAF4B GTF2F2 POLR2K CCNH template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end POLR2F POLR2K CPSF7 GTF2H4 POLR2F U2AF1 ATPPOLR2E GTF2H2 U7 snRNA POLR2C SSRP1 DNA containing RNAPolymerase IIpromoterPOLR2F ZNF473 template DNA:3 nucleotide transcript hybrid POLR2D Pol II Initiationcomplex withphosphodiester-PPiintermediate3'-end cleaved mRNA with spliced exons GTP NELFB Processiveelongation complexElongation complexwith separated anduncleavedtranscriptGTF2E2 GTF2F1 U2AF2 ATP TAF5 TBP TCEB1 TCEA1TAF9 GTF2B POLR2K POLR2B TAF4B TAF5 polIIpromoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complexTAF11 NELFBU2AF2 RNGTT TAF11 TAF6 TAF4 GTF2E1 GTF2H5 POLR2L GTF2E2 POLR2C TAF4 POLR2I GTP UTP GTF2F2 GTF2H5 NELFE CPSF2 CF IIGTF2E2 template DNA withfirst transcriptdinucleotide,opened to +8positionGTF2H2 POLR2B TAF9B POLR2B CDK7 GTF2H5 Elongin B:C complexGTF2H5 NTPCPSF1 POLR2J POLR2B pol II closedpre-initiationcomplexPOLR2I TCEB1POLR2G GTF2H3 TCEB1 POLR2H POLR2J TAF3 RNGTT POLR2H p-S2,S5-POLR2A POLR2H ERCC2 SUPT16H GTF2F2 SRSF11 Elongation complexp-SUPT5H POLR2H POLR2F POLR2J CSTF2 GTF2E1 p-SUPT5H p-S2,S5-POLR2A TAF11 CCNH TAF3 GTF2H1 POLR2L p-S2,S5-POLR2A POLR2I GTF2F1 POLR2F CDK7 TAF3 GTF2H3 GTF2H2 TAF13 TAF2 CDK7 NELFA p-SUPT5H TAF3 TCEB3 POLR2K GTF2A1(275-376) POLR2E GTF2H3 SUPT4H1 SSRP1 CPSF3 SUPT4H1 CCNT1 POLR2L GTF2H1 NCBP1 Intronless Histone pre-mRNA NELFCD POLR2E MNAT1 p-SUPT5H CDK7 TAF1L POLR2E p-SUPT5H NTPPOLR2B p-S5-POLR2A TAF9 POLR2J NELFB CSTF3 TFIIDPOLR2C CCNH GTF2H5 pol II transcriptioncomplex containing11 nucleotide longtranscriptUTP DNA containing Pol II promoter with transcript with 2 or 3 nucleotides POLR2B SUPT4H1 POLR2J TAF1L SUPT16H NUDT21 TAF10 TBP p-SUPT5H GTF2H5 POLR2E GTP GTF2H5 POLR2K TCEB1 TAF4 ERCC3 CTP POLR2J TFIIHCDK9 POLR2L MNAT1 CF I - 72 kDa subunit ATP POLR2G POLR2J GTF2H4 TAF6 GTF2H1 TAF4 POLR2K GTF2H1 ELL GTF2A2 TAF13 POLR2B POLR2K CTDP1 GTF2A1(1-274) TAF9 SUPT16H POLR2E TAF4B CF I - 68 kDa subunit TAF9 GTP CPSF4 - 30 kDa subunit TAF9B TAF11 TAF6 TAF1 POLR2I TAF4B POLR2A Pol II transcriptioncomplex containingtranscript to +30POLR2A GTF2F1 TAF2 POLR2I GTP MNAT1 SRSF1 NTPGTF2H4 SUPT4H1 ATP template DNA:9 nucleotide transcript hybrid PAPOLA PAPOLA TAF9B TCEB3 POLR2H GTF2H1 POLR2K PABPN1 GTF2A1(1-274) POLR2D GTF2A2 GTF2F2 TAF10 GTF2E1 GTF2H3 NELFCD TAF9B CTP POLR2J POLR2C SUPT16HPOLR2E NCBP2 TCEB1 POLR2C TAF12 NELFB GTF2F2 p-S5-POLR2A POLR2B GTF2H5 CCNT1 RNAPolII(hypophosphorylated):capped pre-mRNA complexNTPTFIIDTAF2 DNA containing PolII promoter withtranscript with 2or 3 nucleotidesNUDT21 TAF4B POLR2A POLR2J POLR2H TAF1L NCBP1 POLR2B TBP GTF2E2 GTF2H2 ADPCPSF3 TAF1 UTP MNAT1 GTF2H5 NCBP1 NCBP1 POLR2E POLR2C cappedpre-mRNA:CBC:RNAPol II(phosphorylated)complexPOLR2K CDK7 POLR2G CCNH CCNH SRSF4 SSRP1 POLR2A MNAT1 p-S5-POLR2A TAF4 CCNH NCBP2 GTF2H5 POLR2B CDK9U7 snRNA POLR2K POLR2I DHX38 TCEB3 GTF2A2 GTF2A1(1-274) RNAPolymeraseII(unphosphorylated):TFIIF complexU7 snRNP:ZNF473CCNH POLR2J POLR2B TAF9 template DNA:4-9nucleotidetranscript hybridPOLR2F GTF2H2 POLR2H GTF2F1 GTF2F2 p-S2,S5-POLR2A POLR2F CCNT1 GTF2F2 POLR2C NELFCD GTF2H3 NTPUTP POLR2C MNAT1 POLR2G POLR2L PAPOLA NCBP1 GTF2E2 ERCC3 GTF2A2 GTP CTP Elongating transcript in processive Pol II mediated elongation MNAT1 GTF2H2 ERCC2 TAF1 GTF2F2 TAF3 TAF12 POLR2L POLR2C TAF6 SUPT4H1 NELFCD GTF2F1 TAF1 GTF2F1 TBP TCEB2 TAF12 POLR2E NCBP2 GTF2F1 TAF1 TAF2 POLR2H POLR2J NCBP2 GTF2A1(275-376) intronless pre-mRNAcleavage complexATP POLR2F NTPcapped pre-mRNA UTP CTDP1 POLR2D polIIpromoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complexPOLR2A CCNT2 GTF2H2 GTF2F2 POLR2J GTF2B SNRPF NELFCD CCNH TAF11 GTF2F2 TAF4B POLR2F POLR2H POLR2J GTF2F1 SRSF2 SLBP POLR2C GTF2H1 CPSF2 upstreammRNAfragment:CPSF:PAP:PABPN1 complexTFIIAPOLR2K POLR2C LSM11 POLR2K ERCC3 GTF2F1 TAF5 TAF4 TAF4 POLR2G TAF6 NELFB TBP template DNA:30 nt transcript hybrid TAF5 TAF2 TFIIEPOLR2J POLR2C GTF2H2 NCBP1 pol II transcriptioncomplex containing3 Nucleotide longtranscriptPOLR2C TAF4 POLR2K UTP NCBP2 TAF9 GTF2B POLR2B TAF9B MNAT1 NCBP2 GTF2E2 TAF10 TAF3 p-SUPT5H NELFCD POLR2H p-SUPT5H Pol II transcriptioncomplex with (ser5)phosphorylated CTDcontaining extrudedtranscript to +30CDK7 GTF2B POLR2C GTF2A1(275-376) GTF2F2 MNAT1 SSRP1NCBP2 POLR2J SNRPG TAF9 CTDP1 hSLU7 MNAT1 CPSF4 - 30 kDa subunit POLR2G CDK7 GTF2F2 POLR2K GTF2F2 p-SUPT5H DNA containing RNA Polymerase II promoter ERCC3 POLR2F MAGOH TAF1 GTF2F1 CDK7 POLR2L CCNH TAF9 GTF2E2 GTF2E1 POLR2H ERCC2 TBP GTF2A2 TBP POLR2E TAF4B POLR2L Elongin ComplexTAF11 GTF2H2 GTF2H4 CTDP1 MNAT1 hSLU7 POLR2I NELFE POLR2B MNAT1 TAF13 ERCC3 CPSF1 LSM11 RBM8A GTF2A2 CCNH NCBP2 TAF1 NCBP2 RNA Pol II withphosphorylated CTD:CE complexPiTCEB2 POLR2I GTF2H3 PABPN1 TAF6 GTF2F1 POLR2K POLR2C TAF10 TAF10 GTF2F1 p-S5-POLR2A GTF2H2 p-S5-POLR2A TAF12 NELFE POLR2J POLR2J GTF2H2 POLR2I CPSF4 - 30 kDa subunit GTF2H2 P-TEFb complexCF I - 68 kDa subunit NELFA TAF10 POLR2H GTF2A2 GTF2A2 MNAT1 TCEB3 GTF2H3 POLR2J TAF4B SRSF3 GTF2A1(275-376) POLR2L POLR2E TFIIHTAF4 TCEA1 SUPT4H1POLR2D SRSF7 POLR2J ERCC3 TAF4B GTF2H5 NELFE CCNT1 POLR2A POLR2J PCF11 POLR2D SRSF5 UTP NELFE GTF2H5 POLR2H POLR2E POLR2J ELLNELFCD TAF1L TAF13 GTF2F1 POLR2I CTP POLR2I TAF9B ELL POLR2K POLR2G GTF2A1(275-376) TAF10 template DNA:30 nt transcript hybrid POLR2C pol II transcriptioncomplex containing4 nucleotide longtranscriptGTF2B NCBP2 POLR2H TAF1 capped pre-mRNA TAF12 SNRPB TCEB3CDK7 PABPN1 TAF5 Arrested processiveelongation complexERCC3 TCEB2 CDK7 POLR2K GTF2H4 p-SUPT5HNCBP1 NFX.1 POLR2D CTDP1 UTP TAF4B POLR2B TAF3 GTF2A1(1-274) POLR2G GTF2H2 DNA containing RNA Polymerase II promoter POLR2B GTF2F1 GTF2F1 POLR2G TCEB3 GTF2F1 TAF13 GTF2H4 POLR2F NELFE GTF2H3 POLR2L NELFB NCBP1 GTF2A2 POLR2K SRSF1 ZNF473 POLR2G GTF2H3 POLR2D GTF2F1 GTF2H3 SUPT4H1 GTF2E1 POLR2J GTP TCEB2 template DNA:11 nucleotide transcript hybrid pol II transcriptioncomplex containing4-9 nucleotide longtranscriptTBP UTP ATP POLR2L ERCC2 GTF2H5 TBP GTF2H4 GTF2F1 CSTF1 Early elongationcomplex withhyperphosphorylatedPol II CTDPOLR2K POLR2D CDC40 POLR2F UTP ERCC2 ERCC2 GTF2H4 NELFA p-S2,S5-POLR2A POLR2I CSTF1 GTF2F2 TAF13 Template DNA hybrid with phosphodiester-PPi intermediate GTF2H1 POLR2I downstreamintronless mRNAfragmentTAF2 POLR2C TAF1L ERCC2 CLP1 RNAPolII(hypophosphorylated) complex bound to DSIF proteinCF I - 72 kDa subunit GTF2H2 POLR2I TAF12 POLR2G POLR2E NELFCDGTF2F1 SRSF6 POLR2B GTF2H2 CCNH LSM11 TAF13 POLR2L ELL DSIF:NELF:earlyelongation complexPPiGTF2A2 DNA containing RNA Polymerase II promoter GTP template DNA:30 nt transcript hybrid GTF2H1 TAF9 GTF2H1 PCF11 CTP ATP TAF13 Pol II PromoterEscape ComplexCSTF2 TAF1 NCBP2 GTF2B POLR2C POLR2G POLR2L TBP GTF2H4 CCNT2GTF2F2 SRSF2 SNRPF 323517, 18, 25, 31231, 13, 151, 13, 151, 13, 15111, 13, 1517, 18, 25, 311, 13, 15


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  28. Gangloff YG, Pointud JC, Thuault S, Carré L, Romier C, Muratoglu S, Brand M, Tora L, Couderc JL, Davidson I.; ''The TFIID components human TAF(II)140 and Drosophila BIP2 (TAF(II)155) are novel metazoan homologues of yeast TAF(II)47 containing a histone fold and a PHD finger.''; PubMed Europe PMC Scholia
  29. Jacob GA, Luse SW, Luse DS.; ''Abortive initiation is increased only for the weakest members of a set of down mutants of the adenovirus 2 major late promoter.''; PubMed Europe PMC Scholia
  30. Kamakaka RT, Bulger M, Kadonaga JT.; ''Potentiation of RNA polymerase II transcription by Gal4-VP16 during but not after DNA replication and chromatin assembly.''; PubMed Europe PMC Scholia
  31. Frontini M, Soutoglou E, Argentini M, Bole-Feysot C, Jost B, Scheer E, Tora L.; ''TAF9b (formerly TAF9L) is a bona fide TAF that has unique and overlapping roles with TAF9.''; PubMed Europe PMC Scholia
  32. Yamaguchi Y, Takagi T, Wada T, Yano K, Furuya A, Sugimoto S, Hasegawa J, Handa H.; ''NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation.''; PubMed Europe PMC Scholia
  33. Chen J, Wagner EJ.; ''snRNA 3' end formation: the dawn of the Integrator complex.''; PubMed Europe PMC Scholia
  34. O'Reilly D, Kuznetsova OV, Laitem C, Zaborowska J, Dienstbier M, Murphy S.; ''Human snRNA genes use polyadenylation factors to promote efficient transcription termination.''; PubMed Europe PMC Scholia
  35. Takagaki Y, Manley JL.; ''Complex protein interactions within the human polyadenylation machinery identify a novel component.''; PubMed Europe PMC Scholia
  36. Zhao J, Hyman L, Moore C.; ''Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis.''; PubMed Europe PMC Scholia
  37. Schultz P, Fribourg S, Poterszman A, Mallouh V, Moras D, Egly JM.; ''Molecular structure of human TFIIH.''; PubMed Europe PMC Scholia
  38. Zhou Z, Licklider LJ, Gygi SP, Reed R.; ''Comprehensive proteomic analysis of the human spliceosome.''; PubMed Europe PMC Scholia
  39. Egloff S, Dienstbier M, Murphy S.; ''Updating the RNA polymerase CTD code: adding gene-specific layers.''; PubMed Europe PMC Scholia
  40. Orphanides G, Lagrange T, Reinberg D.; ''The general transcription factors of RNA polymerase II.''; PubMed Europe PMC Scholia
  41. Hu D, Smith ER, Garruss AS, Mohaghegh N, Varberg JM, Lin C, Jackson J, Gao X, Saraf A, Florens L, Washburn MP, Eissenberg JC, Shilatifard A.; ''The little elongation complex functions at initiation and elongation phases of snRNA gene transcription.''; PubMed Europe PMC Scholia
  42. Barolo S, Posakony JW.; ''Three habits of highly effective signaling pathways: principles of transcriptional control by developmental cell signaling.''; PubMed Europe PMC Scholia
  43. Giglia-Mari G, Giglia-Mari G, Coin F, Ranish JA, Hoogstraten D, Theil A, Wijgers N, Jaspers NG, Raams A, Argentini M, van der Spek PJ, Botta E, Stefanini M, Egly JM, Aebersold R, Hoeijmakers JH, Vermeulen W.; ''A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A.''; PubMed Europe PMC Scholia
  44. Morris DP, Michelotti GA, Schwinn DA.; ''Evidence that phosphorylation of the RNA polymerase II carboxyl-terminal repeats is similar in yeast and humans.''; PubMed Europe PMC Scholia
  45. Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, Bjorklund S, Blackwell TK, Borggrefe T, Carey M, Carlson M, Conaway JW, Conaway RC, Emmons SW, Fondell JD, Freedman LP, Fukasawa T, Gustafsson CM, Han M, He X, Herman PK, Hinnebusch AG, Holmberg S, Holstege FC, Jaehning JA, Kim YJ, Kuras L, Leutz A, Lis JT, Meisterernest M, Naar AM, Nasmyth K, Parvin JD, Ptashne M, Reinberg D, Ronne H, Sadowski I, Sakurai H, Sipiczki M, Sternberg PW, Stillman DJ, Strich R, Struhl K, Svejstrup JQ, Tuck S, Winston F, Roeder RG, Kornberg RD.; ''A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II.''; PubMed Europe PMC Scholia
  46. Egloff S, Murphy S.; ''Role of the C-terminal domain of RNA polymerase II in expression of small nuclear RNA genes.''; PubMed Europe PMC Scholia
  47. Aso T, Lane WS, Conaway JW, Conaway RC.; ''Elongin (SIII): a multisubunit regulator of elongation by RNA polymerase II.''; PubMed Europe PMC Scholia
  48. Cramer P.; ''Structure and function of RNA polymerase II.''; PubMed Europe PMC Scholia
  49. Baillat D, Wagner EJ.; ''Integrator: surprisingly diverse functions in gene expression.''; PubMed Europe PMC Scholia
  50. Woudstra EC, Gilbert C, Fellows J, Jansen L, Brouwer J, Erdjument-Bromage H, Tempst P, Svejstrup JQ.; ''A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage.''; PubMed Europe PMC Scholia
  51. Rachez C, Lemon BD, Suldan Z, Bromleigh V, Gamble M, Näär AM, Erdjument-Bromage H, Tempst P, Freedman LP.; ''Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex.''; PubMed Europe PMC Scholia
  52. Louvi A, Artavanis-Tsakonas S.; ''Notch signalling in vertebrate neural development.''; PubMed Europe PMC Scholia
  53. Wada T, Takagi T, Yamaguchi Y, Ferdous A, Imai T, Hirose S, Sugimoto S, Yano K, Hartzog GA, Winston F, Buratowski S, Handa H.; ''DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs.''; PubMed Europe PMC Scholia
  54. Goodrich JA, Tjian R.; ''Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II.''; PubMed Europe PMC Scholia
  55. Conaway JW, Florens L, Sato S, Tomomori-Sato C, Parmely TJ, Yao T, Swanson SK, Banks CA, Washburn MP, Conaway RC.; ''The mammalian Mediator complex.''; PubMed Europe PMC Scholia
  56. Shilatifard A, Conaway RC, Conaway JW.; ''The RNA polymerase II elongation complex.''; PubMed Europe PMC Scholia
  57. Fiedler U, Marc Timmers HT.; ''Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II.''; PubMed Europe PMC Scholia
  58. Bunick D, Zandomeni R, Ackerman S, Weinmann R.; ''Mechanism of RNA polymerase II--specific initiation of transcription in vitro: ATP requirement and uncapped runoff transcripts.''; PubMed Europe PMC Scholia
  59. Chen Y, Yamaguchi Y, Tsugeno Y, Yamamoto J, Yamada T, Nakamura M, Hisatake K, Handa H.; ''DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation.''; PubMed Europe PMC Scholia
  60. Lin X, Taube R, Fujinaga K, Peterlin BM.; ''P-TEFb containing cyclin K and Cdk9 can activate transcription via RNA.''; PubMed Europe PMC Scholia
  61. Conaway RC, Conaway JW.; ''ATP activates transcription initiation from promoters by RNA polymerase II in a reversible step prior to RNA synthesis.''; PubMed Europe PMC Scholia
  62. Blazek E, Mittler G, Meisterernst M.; ''The mediator of RNA polymerase II.''; PubMed Europe PMC Scholia
  63. Wang W, Carey M, Gralla JD.; ''Polymerase II promoter activation: closed complex formation and ATP-driven start site opening.''; PubMed Europe PMC Scholia
  64. Hoffmann A, Roeder RG.; ''Cloning and characterization of human TAF20/15. Multiple interactions suggest a central role in TFIID complex formation.''; PubMed Europe PMC Scholia
  65. Gonatopoulos-Pournatzis T, Cowling VH.; ''Cap-binding complex (CBC).''; PubMed Europe PMC Scholia
  66. Rossignol M, Kolb-Cheynel I, Egly JM.; ''Substrate specificity of the cdk-activating kinase (CAK) is altered upon association with TFIIH.''; PubMed Europe PMC Scholia
  67. Orphanides G, LeRoy G, Chang CH, Luse DS, Reinberg D.; ''FACT, a factor that facilitates transcript elongation through nucleosomes.''; PubMed Europe PMC Scholia
  68. Egloff S, O'Reilly D, Murphy S.; ''Expression of human snRNA genes from beginning to end.''; PubMed Europe PMC Scholia
  69. Pavelitz T, Bailey AD, Elco CP, Weiner AM.; ''Human U2 snRNA genes exhibit a persistently open transcriptional state and promoter disassembly at metaphase.''; PubMed Europe PMC Scholia
  70. Malik S, Roeder RG.; ''Dynamic regulation of pol II transcription by the mammalian Mediator complex.''; PubMed Europe PMC Scholia
  71. Dominski Z, Erkmann JA, Yang X, Sànchez R, Marzluff WF.; ''A novel zinc finger protein is associated with U7 snRNP and interacts with the stem-loop binding protein in the histone pre-mRNP to stimulate 3'-end processing.''; PubMed Europe PMC Scholia
  72. Archambault J, Pan G, Dahmus GK, Cartier M, Marshall N, Zhang S, Dahmus ME, Greenblatt J.; ''FCP1, the RAP74-interacting subunit of a human protein phosphatase that dephosphorylates the carboxyl-terminal domain of RNA polymerase IIO.''; PubMed Europe PMC Scholia
  73. Buratowski S.; ''Progression through the RNA polymerase II CTD cycle.''; PubMed Europe PMC Scholia
  74. Schweisguth F.; ''Regulation of notch signaling activity.''; PubMed Europe PMC Scholia
  75. Aso T, Yamazaki K, Amimoto K, Kuroiwa A, Higashi H, Matsuda Y, Kitajima S, Hatakeyama M.; ''Identification and characterization of Elongin A2, a new member of the Elongin family of transcription elongation factors, specifically expressed in the testis.''; PubMed Europe PMC Scholia
  76. Pal M, Luse DS.; ''Strong natural pausing by RNA polymerase II within 10 bases of transcription start may result in repeated slippage and reextension of the nascent RNA.''; PubMed Europe PMC Scholia
  77. Parvin JD, Sharp PA.; ''DNA topology and a minimal set of basal factors for transcription by RNA polymerase II.''; PubMed Europe PMC Scholia
  78. Fiedler U, Timmers HT.; ''Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation.''; PubMed Europe PMC Scholia
  79. Lin C, Smith ER, Takahashi H, Lai KC, Martin-Brown S, Florens L, Washburn MP, Conaway JW, Conaway RC, Shilatifard A.; ''AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia.''; PubMed Europe PMC Scholia
  80. Bernstein LB, Manser T, Weiner AM.; ''Human U1 small nuclear RNA genes: extensive conservation of flanking sequences suggests cycles of gene amplification and transposition.''; PubMed Europe PMC Scholia
  81. Kugel JF, Goodrich JA.; ''Translocation after synthesis of a four-nucleotide RNA commits RNA polymerase II to promoter escape.''; PubMed Europe PMC Scholia
  82. Hernandez N.; ''TBP, a universal eukaryotic transcription factor?''; PubMed Europe PMC Scholia
  83. Näär AM, Lemon BD, Tjian R.; ''Transcriptional coactivator complexes.''; PubMed Europe PMC Scholia
  84. Zawel L, Kumar KP, Reinberg D.; ''Recycling of the general transcription factors during RNA polymerase II transcription.''; PubMed Europe PMC Scholia
  85. Cramer P, Bushnell DA, Kornberg RD.; ''Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution.''; PubMed Europe PMC Scholia
  86. Schaeffer L, Roy R, Humbert S, Moncollin V, Vermeulen W, Hoeijmakers JH, Chambon P, Egly JM.; ''DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor.''; PubMed Europe PMC Scholia

History

View all...
CompareRevisionActionTimeUserComment
115030view16:57, 25 January 2021ReactomeTeamReactome version 75
113475view11:55, 2 November 2020ReactomeTeamReactome version 74
112674view16:06, 9 October 2020ReactomeTeamReactome version 73
101591view11:46, 1 November 2018ReactomeTeamreactome version 66
101127view21:31, 31 October 2018ReactomeTeamreactome version 65
100655view20:04, 31 October 2018ReactomeTeamreactome version 64
100205view16:49, 31 October 2018ReactomeTeamreactome version 63
99756view15:15, 31 October 2018ReactomeTeamreactome version 62 (2nd attempt)
99318view12:47, 31 October 2018ReactomeTeamreactome version 62
93793view13:36, 16 August 2017ReactomeTeamreactome version 61
93329view11:20, 9 August 2017ReactomeTeamreactome version 61
86414view09:17, 11 July 2016ReactomeTeamreactome version 56
83471view13:23, 18 November 2015ReactomeTeamVersion54
81416view12:56, 21 August 2015ReactomeTeamVersion53
76887view08:16, 17 July 2014ReactomeTeamFixed remaining interactions
76592view11:57, 16 July 2014ReactomeTeamFixed remaining interactions
75625view10:49, 10 June 2014ReactomeTeamReactome 48 Update
74980view13:50, 8 May 2014AnweshaFixing comment source for displaying WikiPathways description
74624view08:40, 30 April 2014ReactomeTeamReactome46
45042view18:59, 6 October 2011ThomasOntology Term : 'RNA Polymerase II transcription pathway' added !
42122view21:58, 4 March 2011MaintBotAutomatic update
39932view05:57, 21 January 2011MaintBotNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
3' end cleaved,

ligated exon

containing complex		ComplexR-HSA-72177 (Reactome)
3'-end cleaved mRNA with spliced exons R-NUL-71998 (Reactome)
ADPMetaboliteCHEBI:16761 (ChEBI)
ALYREF ProteinQ86V81 (Uniprot-TrEMBL)
ATP MetaboliteCHEBI:15422 (ChEBI)
ATPMetaboliteCHEBI:15422 (ChEBI)
Aborted early elongation complexComplexR-HSA-113410 (Reactome)
Aborted elongation

complex after

arrest		ComplexR-HSA-113722 (Reactome)
Arrested processive elongation complexComplexR-HSA-113721 (Reactome)
CCNH ProteinP51946 (Uniprot-TrEMBL)
CCNT1 ProteinO60563 (Uniprot-TrEMBL)
CCNT1ProteinO60563 (Uniprot-TrEMBL)
CCNT2 ProteinO60583 (Uniprot-TrEMBL)
CCNT2ProteinO60583 (Uniprot-TrEMBL)
CDC40 ProteinO60508 (Uniprot-TrEMBL)
CDK7 ProteinP50613 (Uniprot-TrEMBL)
CDK9 ProteinP50750 (Uniprot-TrEMBL)
CDK9ProteinP50750 (Uniprot-TrEMBL)
CE:Pol II CTD:Spt5 complexComplexR-HSA-77061 (Reactome) Spt5 reacts with Guanyl Transferase (GT) of the capping enzyme (CE).
CF I - 68 kDa subunit R-HSA-72013 (Reactome)
CF I - 72 kDa subunit R-HSA-72014 (Reactome)
CF IIComplexR-HSA-72020 (Reactome)
CF IComplexR-HSA-72015 (Reactome)
CLP1 ProteinQ92989 (Uniprot-TrEMBL)
CPSF1 ProteinQ10570 (Uniprot-TrEMBL)
CPSF2 ProteinQ9P2I0 (Uniprot-TrEMBL)
CPSF3 ProteinQ9UKF6 (Uniprot-TrEMBL)
CPSF4 - 30 kDa subunit R-NUL-71994 (Reactome)
CPSF7 ProteinQ8N684 (Uniprot-TrEMBL)
CSTF1 ProteinQ05048 (Uniprot-TrEMBL)
CSTF2 ProteinP33240 (Uniprot-TrEMBL)
CSTF3 ProteinQ12996 (Uniprot-TrEMBL)
CTDP1 ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTDP1ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTP MetaboliteCHEBI:17677 (ChEBI)
Cap Binding Complex (CBC)ComplexR-HSA-77088 (Reactome)
Capped

Intronless Histone

pre-mRNA:CBP80:CBP20:SLBP:ZFP100 Complex		ComplexR-HSA-110766 (Reactome)
Capped Intronless

Histone pre-mRNA:CBC:ZFP100

Complex		ComplexR-HSA-112045 (Reactome)
Capped intronless pre-mRNA R-NUL-112158 (Reactome)
CstFComplexR-HSA-72006 (Reactome)
DHX38 ProteinQ92620 (Uniprot-TrEMBL)
DNA containing Pol

II promoter with transcript with 2

or 3 nucleotides		R-NUL-110068 (Reactome)
DNA containing Pol II promoter with transcript with 2 or 3 nucleotides R-NUL-110068 (Reactome)
DNA containing RNA

Polymerase II

promoter		R-NUL-109627 (Reactome)
DNA containing RNA Polymerase II promoter R-NUL-109627 (Reactome)
DSIF complexComplexR-HSA-112420 (Reactome)
DSIF:NELF:early elongation complexComplexR-HSA-113408 (Reactome)
ELL ProteinP55199 (Uniprot-TrEMBL)
ELLProteinP55199 (Uniprot-TrEMBL)
ERCC2 ProteinP18074 (Uniprot-TrEMBL)
ERCC3 ProteinP19447 (Uniprot-TrEMBL)
Early elongation

complex with hyperphosphorylated

Pol II CTD		ComplexR-HSA-113426 (Reactome)
Elongating transcript in processive Pol II mediated elongation R-NUL-113717 (Reactome)
Elongating transcript prior to cleavage R-NUL-113725 (Reactome)
Elongating transcript prior to separation R-NUL-113714 (Reactome)
Elongation complex prior to separationComplexR-HSA-113724 (Reactome)
Elongation complex

with separated and uncleaved

transcript		ComplexR-HSA-113726 (Reactome)
Elongation complexComplexR-HSA-112433 (Reactome)
Elongin B:C complexComplexR-HSA-112424 (Reactome)
Elongin ComplexComplexR-HSA-112425 (Reactome)
FACT complexComplexR-HSA-112417 (Reactome)
GTF2A1(1-274) ProteinP52655 (Uniprot-TrEMBL)
GTF2A1(275-376) ProteinP52655 (Uniprot-TrEMBL)
GTF2A2 ProteinP52657 (Uniprot-TrEMBL)
GTF2B ProteinQ00403 (Uniprot-TrEMBL)
GTF2BProteinQ00403 (Uniprot-TrEMBL)
GTF2E1 ProteinP29083 (Uniprot-TrEMBL)
GTF2E2 ProteinP29084 (Uniprot-TrEMBL)
GTF2F1 ProteinP35269 (Uniprot-TrEMBL)
GTF2F2 ProteinP13984 (Uniprot-TrEMBL)
GTF2H1 ProteinP32780 (Uniprot-TrEMBL)
GTF2H2 ProteinQ13888 (Uniprot-TrEMBL)
GTF2H3 ProteinQ13889 (Uniprot-TrEMBL)
GTF2H4 ProteinQ92759 (Uniprot-TrEMBL)
GTF2H5 ProteinQ6ZYL4 (Uniprot-TrEMBL)
GTP MetaboliteCHEBI:15996 (ChEBI)
Intronless Histone pre-mRNA R-NUL-110756 (Reactome)
LSM10 ProteinQ969L4 (Uniprot-TrEMBL)
LSM11 ProteinP83369 (Uniprot-TrEMBL)
Ligated exon containing complexComplexR-HSA-72157 (Reactome)
MAGOH ProteinP61326 (Uniprot-TrEMBL)
MNAT1 ProteinP51948 (Uniprot-TrEMBL)
Mature

Intronless transcript derived Histone

mRNA:SLBP:CBP80:CBP20		ComplexR-HSA-111682 (Reactome)
Mature Intronless transcript derived Histone mRNA R-NUL-111676 (Reactome)
Mature intronless

transcript derived Histone pre-mRNA:CBC

complex		ComplexR-HSA-156959 (Reactome)
NCBP1 ProteinQ09161 (Uniprot-TrEMBL)
NCBP2 ProteinP52298 (Uniprot-TrEMBL)
NELF complexComplexR-HSA-112432 (Reactome)
NELFA ProteinQ9H3P2 (Uniprot-TrEMBL)
NELFAProteinQ9H3P2 (Uniprot-TrEMBL)
NELFB ProteinQ8WX92 (Uniprot-TrEMBL)
NELFBProteinQ8WX92 (Uniprot-TrEMBL)
NELFCD ProteinQ8IXH7 (Uniprot-TrEMBL)
NELFCDProteinQ8IXH7 (Uniprot-TrEMBL)
NELFE ProteinP18615 (Uniprot-TrEMBL)
NELFEProteinP18615 (Uniprot-TrEMBL)
NFX.1 ProteinO43831 (Uniprot-TrEMBL)
NTPComplexR-HSA-R-ALL-30595 (Reactome)
NUDT21 ProteinO43809 (Uniprot-TrEMBL)
Open DNA -10 to +2 containing RNA Polymerase II promoter R-NUL-109875 (Reactome)
P-TEFb complexComplexR-HSA-112431 (Reactome)
PABPN1 ProteinQ86U42 (Uniprot-TrEMBL)
PAPOLA ProteinP51003 (Uniprot-TrEMBL)
PCF11 ProteinO94913 (Uniprot-TrEMBL)
POLR2A ProteinP24928 (Uniprot-TrEMBL)
POLR2B ProteinP30876 (Uniprot-TrEMBL)
POLR2C ProteinP19387 (Uniprot-TrEMBL)
POLR2D ProteinO15514 (Uniprot-TrEMBL)
POLR2E ProteinP19388 (Uniprot-TrEMBL)
POLR2F ProteinP61218 (Uniprot-TrEMBL)
POLR2G ProteinP62487 (Uniprot-TrEMBL)
POLR2H ProteinP52434 (Uniprot-TrEMBL)
POLR2I ProteinP36954 (Uniprot-TrEMBL)
POLR2J ProteinP52435 (Uniprot-TrEMBL)
POLR2K ProteinP53803 (Uniprot-TrEMBL)
POLR2L ProteinP62875 (Uniprot-TrEMBL)
PPiMetaboliteCHEBI:29888 (ChEBI)
Paused processive elongation complexComplexR-HSA-113720 (Reactome)
PiMetaboliteCHEBI:18367 (ChEBI)
Pol II Initiation

complex with phosphodiester-PPi

intermediate		ComplexR-HSA-83601 (Reactome)
Pol II Promoter Escape ComplexComplexR-HSA-75859 (Reactome)
Pol II initiation complexComplexR-HSA-83551 (Reactome)
Pol II transcription

complex containing extruded transcript

to +30		ComplexR-HSA-157171 (Reactome)
Pol II transcription

complex containing

transcript to +30		ComplexR-HSA-111261 (Reactome)
Pol II transcription

complex with (ser5) phosphorylated CTD containing extruded

transcript to +30		ComplexR-HSA-157174 (Reactome)
Processive elongation complexComplexR-HSA-113719 (Reactome)
RBM8A ProteinQ9Y5S9 (Uniprot-TrEMBL)
RNA

Pol II

(hypophosphorylated) complex bound to DSIF protein		ComplexR-HSA-113406 (Reactome)
RNA

Pol II

(hypophosphorylated):capped pre-mRNA complex		ComplexR-HSA-113715 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex		ComplexR-HSA-71307 (Reactome)
RNA

Polymerase II holoenzyme complex

(hyperphosphorylated)		ComplexR-HSA-109909 (Reactome)
RNA Pol II with

phosphorylated CTD: CE complex with

activated GT		ComplexR-HSA-77056 (Reactome)
RNA Pol II with

phosphorylated CTD:

CE complex		ComplexR-HSA-77053 (Reactome)
RNGTT ProteinO60942 (Uniprot-TrEMBL)
RNGTTProteinO60942 (Uniprot-TrEMBL)
RNMT ProteinO43148 (Uniprot-TrEMBL)
RNMTProteinO43148 (Uniprot-TrEMBL)
RNPS1 ProteinQ15287 (Uniprot-TrEMBL)
SLBP ProteinQ14493 (Uniprot-TrEMBL)
SNRPB ProteinP14678 (Uniprot-TrEMBL)
SNRPD3 ProteinP62318 (Uniprot-TrEMBL)
SNRPE ProteinP62304 (Uniprot-TrEMBL)
SNRPF ProteinP62306 (Uniprot-TrEMBL)
SNRPG ProteinP62308 (Uniprot-TrEMBL)
SRRM1 ProteinQ8IYB3 (Uniprot-TrEMBL)
SRSF1 ProteinQ07955 (Uniprot-TrEMBL)
SRSF11 ProteinQ05519 (Uniprot-TrEMBL)
SRSF2 ProteinQ01130 (Uniprot-TrEMBL)
SRSF3 ProteinP84103 (Uniprot-TrEMBL)
SRSF4 ProteinQ08170 (Uniprot-TrEMBL)
SRSF5 ProteinQ13243 (Uniprot-TrEMBL)
SRSF6 ProteinQ13247 (Uniprot-TrEMBL)
SRSF7 ProteinQ16629 (Uniprot-TrEMBL)
SRSF9 ProteinQ13242 (Uniprot-TrEMBL)
SSRP1 ProteinQ08945 (Uniprot-TrEMBL)
SSRP1ProteinQ08945 (Uniprot-TrEMBL)
SUPT16H ProteinQ9Y5B9 (Uniprot-TrEMBL) DSIF is a heterodimer consisting of hSPT4 (human homolog of yeast Spt4- p14) and hSPT5 (human homolog of yeast Spt5-p160). DSIF association with Pol II may be enabled by Spt5 binding to Pol II creating a scaffold for NELF binding (Wada et al.,1998). Spt5 subunit of DSIF can be phosphorylated by P-TEFb.
SUPT16HProteinQ9Y5B9 (Uniprot-TrEMBL) DSIF is a heterodimer consisting of hSPT4 (human homolog of yeast Spt4- p14) and hSPT5 (human homolog of yeast Spt5-p160). DSIF association with Pol II may be enabled by Spt5 binding to Pol II creating a scaffold for NELF binding (Wada et al.,1998). Spt5 subunit of DSIF can be phosphorylated by P-TEFb.
SUPT4H1 ProteinP63272 (Uniprot-TrEMBL)
SUPT4H1ProteinP63272 (Uniprot-TrEMBL)
TAF1 ProteinP21675 (Uniprot-TrEMBL)
TAF10 ProteinQ12962 (Uniprot-TrEMBL)
TAF11 ProteinQ15544 (Uniprot-TrEMBL)
TAF12 ProteinQ16514 (Uniprot-TrEMBL)
TAF13 ProteinQ15543 (Uniprot-TrEMBL)
TAF1L ProteinQ8IZX4 (Uniprot-TrEMBL)
TAF2 ProteinQ6P1X5 (Uniprot-TrEMBL)
TAF3 ProteinQ5VWG9 (Uniprot-TrEMBL)
TAF4 ProteinO00268 (Uniprot-TrEMBL)
TAF4B ProteinQ92750 (Uniprot-TrEMBL)
TAF5 ProteinQ15542 (Uniprot-TrEMBL)
TAF6 ProteinP49848 (Uniprot-TrEMBL)
TAF9 ProteinQ16594 (Uniprot-TrEMBL)
TAF9B ProteinQ9HBM6 (Uniprot-TrEMBL)
TBP ProteinP20226 (Uniprot-TrEMBL)
TCEA1 ProteinP23193 (Uniprot-TrEMBL)
TCEA1ProteinP23193 (Uniprot-TrEMBL)
TCEB1 ProteinQ15369 (Uniprot-TrEMBL)
TCEB1ProteinQ15369 (Uniprot-TrEMBL)
TCEB2 ProteinQ15370 (Uniprot-TrEMBL)
TCEB2ProteinQ15370 (Uniprot-TrEMBL)
TCEB3 ProteinQ14241 (Uniprot-TrEMBL)
TCEB3ProteinQ14241 (Uniprot-TrEMBL)
TFIIAComplexR-HSA-109629 (Reactome)
TFIIDComplexR-HSA-109626 (Reactome)
TFIIEComplexR-HSA-109633 (Reactome)
TFIIFComplexR-HSA-109631 (Reactome)
TFIIHComplexR-HSA-109634 (Reactome)
Template DNA hybrid with phosphodiester-PPi intermediate R-NUL-83602 (Reactome)
U2AF1 ProteinQ01081 (Uniprot-TrEMBL)
U2AF2 ProteinP26368 (Uniprot-TrEMBL)
U7 snRNA R-NUL-110761 (Reactome)
U7 snRNP:ZNF473ComplexR-HSA-110765 (Reactome)
UPF3B ProteinQ9BZI7 (Uniprot-TrEMBL)
UTP MetaboliteCHEBI:15713 (ChEBI)
ZNF473 ProteinQ8WTR7 (Uniprot-TrEMBL)
capped

pre-mRNA:CBC:RNA Pol II (phosphorylated)

complex		ComplexR-HSA-77089 (Reactome)
capped pre-mRNA R-NUL-72085 (Reactome)
damaged DNA

substrate:nascent

mRNA hybrid		R-NUL-110291 (Reactome)
downstream

intronless mRNA

fragment		R-NUL-112165 (Reactome)
hSLU7 R-NUL-72073 (Reactome)
hTra2 R-HSA-72063 (Reactome)
intronless pre-mRNA cleavage complexComplexR-HSA-112162 (Reactome)
mRNA 3'-end cleavage factorComplexR-HSA-72075 (Reactome)
mRNA with spliced exons R-NUL-72156 (Reactome)
p-S2,S5-POLR2A ProteinP24928 (Uniprot-TrEMBL)
p-S5-POLR2A ProteinP24928 (Uniprot-TrEMBL)
p-SUPT5H ProteinO00267 (Uniprot-TrEMBL)
p-SUPT5HProteinO00267 (Uniprot-TrEMBL)
pol

II

promoter:TFIID:TFIIA:TFIIB complex		ComplexR-HSA-109630 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complex		ComplexR-HSA-109632 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complex		ComplexR-HSA-75871 (Reactome)
pol II

promoter:TFIID

complex		ComplexR-HSA-109628 (Reactome)
pol II closed

pre-initiation

complex		ComplexR-HSA-109635 (Reactome)
pol II open

pre-initiation

complex		ComplexR-HSA-109876 (Reactome)
pol II transcription

complex containing 11 nucleotide long

transcript		ComplexR-HSA-75902 (Reactome)
pol II transcription

complex containing 3 Nucleotide long

transcript		ComplexR-HSA-75878 (Reactome)
pol II transcription

complex containing 4 nucleotide long

transcript		ComplexR-HSA-75881 (Reactome)
pol II transcription

complex containing 4-9 nucleotide long

transcript		ComplexR-HSA-75890 (Reactome)
pol II transcription

complex containing 9 nucleotide long

transcript		ComplexR-HSA-75882 (Reactome)
pol II transcription complexComplexR-HSA-109878 (Reactome)
template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end R-NUL-71063 (Reactome)
template DNA with

first transcript dinucleotide, opened to +8

position		R-NUL-109877 (Reactome)
template DNA with first transcript dinucleotide, opened to +8 position R-NUL-109877 (Reactome)
template DNA:11 nucleotide transcript hybrid R-NUL-75901 (Reactome)
template DNA:3 nucleotide transcript hybrid R-NUL-75858 (Reactome)
template DNA:30 nt transcript hybrid R-NUL-111260 (Reactome)
template DNA:4 nucleotide transcript hybrid R-NUL-75884 (Reactome)
template DNA:4-9

nucleotide

transcript hybrid		R-NUL-75897 (Reactome)
template DNA:4-9 nucleotide transcript hybrid R-NUL-75897 (Reactome)
template DNA:9 nucleotide transcript hybrid R-NUL-75888 (Reactome)
template:capped transcript hybrid R-NUL-113424 (Reactome)
upstream

mRNA

fragment:CPSF:PAP:PABPN1 complex		ComplexR-HSA-112164 (Reactome)
upstream intronless mRNA fragment R-NUL-112163 (Reactome)

Annotated Interactions

View all...
SourceTargetTypeDatabase referenceComment
3' end cleaved,

ligated exon

containing complex		ArrowR-HSA-72180 (Reactome)
ADPArrowR-HSA-75949 (Reactome)
ATPR-HSA-75949 (Reactome)
Aborted early elongation complexArrowR-HSA-113409 (Reactome)
Aborted elongation

complex after

arrest		ArrowR-HSA-112395 (Reactome)
Arrested processive elongation complexArrowR-HSA-113414 (Reactome)
Arrested processive elongation complexR-HSA-112395 (Reactome)
Arrested processive elongation complexR-HSA-113413 (Reactome)
CCNT1R-HSA-112430 (Reactome)
CCNT2R-HSA-112430 (Reactome)
CDK9R-HSA-112430 (Reactome)
CE:Pol II CTD:Spt5 complexArrowR-HSA-77073 (Reactome)
CF IArrowR-HSA-72180 (Reactome)
CF IArrowR-HSA-77592 (Reactome)
CF IIArrowR-HSA-72180 (Reactome)
CF IIArrowR-HSA-77592 (Reactome)
CTDP1ArrowR-HSA-113429 (Reactome)
CTDP1R-HSA-112383 (Reactome)
CTDP1mim-catalysisR-HSA-112383 (Reactome)
Cap Binding Complex (CBC)ArrowR-HSA-112381 (Reactome)
Capped

Intronless Histone

pre-mRNA:CBP80:CBP20:SLBP:ZFP100 Complex		R-HSA-77586 (Reactome)
Capped Intronless

Histone pre-mRNA:CBC:ZFP100

Complex		R-HSA-111437 (Reactome)
CstFArrowR-HSA-72180 (Reactome)
CstFArrowR-HSA-77592 (Reactome)
DNA containing Pol

II promoter with transcript with 2

or 3 nucleotides		ArrowR-HSA-75856 (Reactome)
DNA containing RNA

Polymerase II

promoter		R-HSA-109636 (Reactome)
DSIF complexArrowR-HSA-112434 (Reactome)
DSIF complexArrowR-HSA-113429 (Reactome)
DSIF complexR-HSA-113407 (Reactome)
DSIF:NELF:early elongation complexArrowR-HSA-113402 (Reactome)
DSIF:NELF:early elongation complexR-HSA-112381 (Reactome)
DSIF:NELF:early elongation complexR-HSA-113409 (Reactome)
ELLArrowR-HSA-113429 (Reactome)
ELLR-HSA-112379 (Reactome)
Early elongation

complex with hyperphosphorylated

Pol II CTD		ArrowR-HSA-112381 (Reactome)
Early elongation

complex with hyperphosphorylated

Pol II CTD		R-HSA-112379 (Reactome)
Elongation complex prior to separationArrowR-HSA-113412 (Reactome)
Elongation complex prior to separationR-HSA-112396 (Reactome)
Elongation complex

with separated and uncleaved

transcript		ArrowR-HSA-112396 (Reactome)
Elongation complexArrowR-HSA-112379 (Reactome)
Elongation complexR-HSA-112385 (Reactome)
Elongin B:C complexArrowR-HSA-112435 (Reactome)
Elongin B:C complexR-HSA-112436 (Reactome)
Elongin ComplexArrowR-HSA-112436 (Reactome)
Elongin ComplexArrowR-HSA-113429 (Reactome)
Elongin ComplexR-HSA-112379 (Reactome)
FACT complexArrowR-HSA-112429 (Reactome)
FACT complexArrowR-HSA-113429 (Reactome)
FACT complexR-HSA-112379 (Reactome)
GTF2BArrowR-HSA-73946 (Reactome)
GTF2BArrowR-HSA-75856 (Reactome)
GTF2BArrowR-HSA-75869 (Reactome)
GTF2BR-HSA-109637 (Reactome)
Ligated exon containing complexR-HSA-72180 (Reactome)
Mature

Intronless transcript derived Histone

mRNA:SLBP:CBP80:CBP20		ArrowR-HSA-77586 (Reactome)
Mature intronless

transcript derived Histone pre-mRNA:CBC

complex		ArrowR-HSA-111437 (Reactome)
NELF complexArrowR-HSA-112437 (Reactome)
NELF complexArrowR-HSA-113429 (Reactome)
NELF complexR-HSA-113402 (Reactome)
NELFAR-HSA-112437 (Reactome)
NELFBR-HSA-112437 (Reactome)
NELFCDR-HSA-112437 (Reactome)
NELFER-HSA-112437 (Reactome)
NTPArrowR-HSA-113402 (Reactome)
NTPArrowR-HSA-113412 (Reactome)
NTPArrowR-HSA-113429 (Reactome)
NTPR-HSA-111264 (Reactome)
NTPR-HSA-112385 (Reactome)
NTPR-HSA-113402 (Reactome)
NTPR-HSA-113412 (Reactome)
NTPR-HSA-75850 (Reactome)
NTPR-HSA-75861 (Reactome)
NTPR-HSA-75869 (Reactome)
NTPR-HSA-75873 (Reactome)
NTPR-HSA-76576 (Reactome)
P-TEFb complexArrowR-HSA-112430 (Reactome)
P-TEFb complexArrowR-HSA-113429 (Reactome)
P-TEFb complexR-HSA-112381 (Reactome)
P-TEFb complexmim-catalysisR-HSA-112381 (Reactome)
PPiArrowR-HSA-111264 (Reactome)
PPiArrowR-HSA-75850 (Reactome)
PPiArrowR-HSA-75864 (Reactome)
PPiArrowR-HSA-75869 (Reactome)
PPiArrowR-HSA-75873 (Reactome)
PPiArrowR-HSA-76576 (Reactome)
Paused processive elongation complexArrowR-HSA-113411 (Reactome)
Paused processive elongation complexR-HSA-112392 (Reactome)
PiArrowR-HSA-75949 (Reactome)
Pol II Initiation

complex with phosphodiester-PPi

intermediate		ArrowR-HSA-75866 (Reactome)
Pol II Initiation

complex with phosphodiester-PPi

intermediate		R-HSA-75864 (Reactome)
Pol II Promoter Escape ComplexR-HSA-75856 (Reactome)
Pol II initiation complexArrowR-HSA-75861 (Reactome)
Pol II initiation complexR-HSA-75866 (Reactome)
Pol II transcription

complex containing extruded transcript

to +30		ArrowR-HSA-113430 (Reactome)
Pol II transcription

complex containing extruded transcript

to +30		R-HSA-77071 (Reactome)
Pol II transcription

complex containing

transcript to +30		ArrowR-HSA-111264 (Reactome)
Pol II transcription

complex containing

transcript to +30		R-HSA-113430 (Reactome)
Pol II transcription

complex with (ser5) phosphorylated CTD containing extruded

transcript to +30		ArrowR-HSA-77071 (Reactome)
Pol II transcription

complex with (ser5) phosphorylated CTD containing extruded

transcript to +30		R-HSA-77069 (Reactome)
Processive elongation complexArrowR-HSA-112385 (Reactome)
Processive elongation complexArrowR-HSA-112392 (Reactome)
Processive elongation complexArrowR-HSA-113413 (Reactome)
Processive elongation complexR-HSA-113411 (Reactome)
Processive elongation complexR-HSA-113412 (Reactome)
Processive elongation complexR-HSA-113414 (Reactome)
Processive elongation complexR-HSA-113429 (Reactome)
R-HSA-109636 (Reactome) Although TBP (TATA box binding factor) is necessary and sufficient for initiation of basal transcription, the other subunits of the general transcription factor TFIID, the TBP-associated factors, are required for response to transcriptional activators. TBP binds to the TATA box (a core promoter element), and bends the DNA 80 degrees toward the major groove. This conformation of TBP-TATA box provides the proper topology for the binding of the general transcription factor TFIIB.

Transcriptional activators function by affecting the kinetics of binding of TBP to the promoter DNA.

R-HSA-109637 (Reactome) The general transcription factor TFIIB is a single polypeptide of approximately 35 kDa. There is a Zn-binding domain near the N terminus of TFIIB, and the C-terminal domain encompasses two imperfect repeats; between the N and C termini is a phylogenetically conserved region. The C terminus interacts with TBP and RNA Polymerase II, whereas the N terminus interacts with factor TFIIF and RNA polymerase II. TFIIB is a sequence-specific factor, and it interacts with the BRE element within the promoter.

TFIIB interacts with the Rpb1 subunit of RNA polymerase II to define transcription strat sites. Several activators directly bind TFIIB, and stimulate transcription. The N-terminus and the C-terminus can participate in intramolecular interactions, and this can be disrupted by specific activators by causing a conformational change in TFIIB.

TFIIA also binds the preinitiation complex along with TFIIB. However, TFIIA is not required for accurate initiation, but rather functions as a coactivator of transcription.

R-HSA-109638 (Reactome) The general transcription factor TFIIF has a high affinity for the RNA Polymerase II holoenzyme. TFIIF stabilizes the preinitiation complex, and suppresses non-specific binding of RNA Pol II to DNA, and is thus critical for start site recognition.
R-HSA-109639 (Reactome) The binding of TFIIH completes the assembly of the preinitiation complex (PIC) for RNA Polymerase II transcription. Although RNA polymerase binds the TATA box on the promoter DNA, no initiation of transcription occurs until TFIIH is bound to the PIC. TFIIH is the only factor with known enzymatic activities.
R-HSA-111264 (Reactome) RNA polymerase II transcription complexes are susceptible to transcriptional stalling and arrest, when extending nascent transcripts to 30-nt. This susceptibility depends on presence on down-stream DNA, the particular DNA-sequence of the template and presence of transcription factors. Transcription factor TFIIH remains associated to the RNA pol II elongation complex until position +30. At this stage transcription elongation factor TFIIS can rescue stalled transcription elongation complexes. The transcription bubble varies between 13- and 22-nt in size.
R-HSA-111437 (Reactome) Processing is initiated once the U7 snRNP is loaded onto the pre-mRNA. The pre-mRNA HDE makes base-pairing contacts with the 5′ end of U7 snRNA. Binding of the U7 snRNP to the pre-mRNA is stabilized by interactions between a U7 snRNP protein, hZFP100 and other trans-acting factors, including the factor that catalyzes the cleavage reaction, which have yet to be defined. The cleavage occurs in the presence of EDTA as does the cleavage reaction in polyadenylation, it is likely that this reaction is catalyzed by a protein. There may well be additional proteins associated with the U7 snRNP, since the in vitro processing occurs in the absence of SLBP, it is possible that all the other factors required for processing are associated with the active form of the U7 snRNP.
R-HSA-112379 (Reactome) At the beginning of this reaction, 1 molecule of 'FACT complex', 1 molecule of 'Elongin Complex', 1 molecule of 'Early elongation complex with hyperphosphorylated Pol II CTD', 1 molecule of 'TFIIH', 1 molecule of 'RNA polymerase II elongation factor ELL', and 1 molecule of 'TFIIS protein' are present. At the end of this reaction, 1 molecule of 'Elongation complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-112381 (Reactome) Cdk-9 is the kinase subunit of P-TEFb that phosphorylates Serine 2 on the heptapeptide repeats of Pol II CTD alleviating the negative action of DSIF-NELF complex. This reaction is considered to be a rate limiting step for processive elongation. P-TEFb complex, that has a DRB-sensitive cyclin-dependent kinase activity, is composed of ~43 kDa, Cdk9 kinase (PITALRE), and either Cyclin T1, Cyclin T2a, Cyclin T2b, or Cyclin K. The exact mechanism by which P-TEFb removes the inhibition of elongation by DSIF-NELF is not yet known. P-TEFb is also capable of phosphorylating Spt5 subunit of DSIF complex.
A P-TEFb complex (which contains only the Cyclin T1) is implicated in the efficient synthesis of human immunodeficiency virus-1 (HIV-1) transcripts. Cyclin T1 subunit of the P-TEFb(Cyclin T1:Cdk9) complex interacts with HIV-1 encoded Tat protein that binds to the transactivation response (TAR) element in the nascent HIV-1 transcript (reviewed in Price,2000).
The mechanism by which DSIF, NELF and P-TEFb or TAK/P-TEFb act together in Pol II-regulated elongation is yet to be fully understood. Various biochemical evidences point to a model in which DSIF and NELF negatively regulate elongation through interactions with polymerase containing a hypophosphorylated CTD. Subsequent phosphorylation of the Pol II CTD by P-TEFb might promote elongation by inhibiting interactions of DSIF and NELF with the elongation complex.

R-HSA-112383 (Reactome) FCP1 dephosphorylates RNAP II in ternary elongation complexes as well as in solution and, therefore, is thought to function in the recycling of RNAP II during the transcription cycle. Biochemical experiments suggest that human FCP1 targets CTDs that are phosphorylated at serine 2 (CTD-serine 2) and/or CTD-serine 5. It is also observed to stimulate elongation independent of its catalytic activity. Dephosphorylation of Ser2 - phosphorylated Pol II results in hypophosphorylated form that disengages capping enzymes (CE).
R-HSA-112385 (Reactome) High-resolution structures of free, catalytically active yeast Pol II and of an elongating form reveal that Pol II elongation complex includes features like:
- RNA-DNA hybrid, an unwound template ahead of 3'-OH terminus of growing transcript and an exit groove at the base of the CTD, possibly for dynamic interaction of processing and transcriptional factors.
- a cleft or channel created by Rpb1 and Rpb2 subunits to accommodate DNA template, extending to Mg2+ ion located deep in the enzyme core
-a 50 kDa "clamp" with open confirmation in free polymerase, allowing entry of DNA strands but closed in the processive elongation phase.
The clamp is composed of portions of Rpb1,Rpb2 and Rpb3 , five loops or "switches" that change from unfolded to well-folded structures stabilizing the elongation complex, and a long "bridging helix" that emanates from Rpb1 subunit, crossing near the Mg2+ ion. The bridging helix is thought to "bend" to push on the base pair at the 3'-end of RNA-DNA hybrid like a ratchet, translocating Pol II along the DNA (Cramer et al.,2001; Gnatt et al.,2001).In addition to its dynamic biochemical potential, Pol II possess a repertoire of functions to serve as a critical platform of recruiting and coordinating the actions of a host of additional enzyme and proteins involved in various pathways.

R-HSA-112392 (Reactome) Recovery from pausing occurs spontaneously after a variable length of time as the enzyme spontaneously slides forward again. This renders the transcript's 3'-OH terminus realigned with the catalytic Mg2+ site of the enzyme. TFIIS is capable of excising the nascent transcript at 2 or 3 nucleotides upstream of the transcript's 3'-end to reinitiate processive elongation (reviewed by Shilatifard et al., 2003).
R-HSA-112395 (Reactome) At the beginning of this reaction, 1 molecule of 'Arrested processive elongation complex' is present. At the end of this reaction, 1 molecule of 'Aborted elongation complex after arrest' is present.

This reaction takes place in the 'nucleus'.

R-HSA-112396 (Reactome) At the beginning of this reaction, 1 molecule of 'Elongation complex prior to separation' is present. At the end of this reaction, 1 molecule of 'Elongation complex with separated and uncleaved transcript' is present.

This reaction takes place in the 'nucleus'.

R-HSA-112429 (Reactome) At the beginning of this reaction, 1 molecule of 'FACT 140 kDa subunit', and 1 molecule of 'FACT 80 kDa subunit' are present. At the end of this reaction, 1 molecule of 'FACT complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-112430 (Reactome) At the beginning of this reaction, 1 molecule of 'Cdk 9 protein', 1 molecule of 'Cyclin T1', and 1 molecule of 'Cyclin T2' are present. At the end of this reaction, 1 molecule of 'P-TEFb complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-112434 (Reactome) At the beginning of this reaction, 1 molecule of 'SUPT5H protein', and 1 molecule of 'SPT4H1 protein' are present. At the end of this reaction, 1 molecule of 'DSIF complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-112435 (Reactome) At the beginning of this reaction, 1 molecule of 'Elongin B protein', and 1 molecule of 'Elongin C protein' are present. At the end of this reaction, 1 molecule of 'Elongin B:C complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-112436 (Reactome) At the beginning of this reaction, 1 molecule of 'Elongin A1 protein', and 1 molecule of 'Elongin B:C complex' are present. At the end of this reaction, 1 molecule of 'Elongin Complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-112437 (Reactome) At the beginning of this reaction, 1 molecule of 'NELF-A protein', 1 molecule of 'RD protein', 1 molecule of 'NELF-B protein', and 1 molecule of 'NELF-C/D protein' are present. At the end of this reaction, 1 molecule of 'NELF complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-113402 (Reactome) NELF complex is a ~ 300 kDa multiprotein complex composed of 5 peptides (A - E): ~66,61,59,58 and 46 kDa. All these peptides are required for NELF-mediated inhibition of Pol II elongation. NELF complex has been reported to bind to the pre-formed DSIF:RNA Pol II complex that may act as a scaffold for its binding. NELF-A is suspected to be involved in Wolf-Hirschhorn syndrome.
Binding of DSIF:NELF to RNA Pol II CTD results in abortive termination of early elongation steps by the growing transcripts.
R-HSA-113407 (Reactome) DSIF is a heterodimer consisting of hSPT4 (human homolog of yeast Spt4- p14) and hSPT5 (human homolog of yeast Spt5-p160). DSIF association with Pol II may be enabled by Spt5 binding to Pol II creating a scaffold for NELF binding (Wada et al.,1998). Spt5 subunit of DSIF can be phosphorylated by P-TEFb.
R-HSA-113409 (Reactome) In the early elongation phase, shorter transcripts typically of ~30 nt in length are generated due to random termination of elongating nascent transcripts. This abortive cessation of elongation has been observed mainly in the presence of DSIF-NELF bound to Pol II complex. (Reviewed in Conaway et al.,2000; Shilatifard et al., 2003 ).
R-HSA-113411 (Reactome) Pol II pausing is believed to result from reversible backtracking of the Pol II enzyme complex by ~2 to 4 nucleotides. This leads to misaligned 3'-OH terminus that is unable to be an acceptor for the incoming NTPs in synthesis of next phosphodiester bond (reviewed by Shilatifard et al., 2003).
R-HSA-113412 (Reactome) At the beginning of this reaction, 1 molecule of 'Processive elongation complex', and 1 molecule of 'NTP' are present. At the end of this reaction, 1 molecule of 'Elongation complex prior to separation', and 1 molecule of 'NTP' are present.

This reaction takes place in the 'nucleus'.

R-HSA-113413 (Reactome) TFIIS reactivates arrested RNA Pol II directly interacting with the enzyme resulting in endonucleolytic excision of nascent transcript ~7-14 nucleotides upstream of the 3' end. This reaction is catalyzed by the catalytic site and results in the generation of a new 3'-OH terminus that could be used for re-extension from the correctly base paired site (reviewed by Shilatifard et al., 2003).
R-HSA-113414 (Reactome) RNA Pol II arrest is believed to be a result of irreversible backsliding of the enzyme by ~7-14 nucleotides. It is suggested that, arrest leads to extrusion of displaced transcripts 3'-end through the small pore near the Mg2+ ion. Pol II arrest may lead to abortive termination of elongation due to irreversible trapping of the 3'-end of the displaced transcript in the pore (reviewed by Shilatifard et al., 2003).
R-HSA-113429 (Reactome) At the beginning of this reaction, 1 molecule of 'Processive elongation complex' is present. At the end of this reaction, 1 molecule of 'DSIF complex', 1 molecule of 'FACT complex', 1 molecule of 'RNA Polymerase II holoenzyme complex (hyperphosphorylated)', 1 molecule of 'damaged DNA substrate:nascent mRNA hybrid', 1 molecule of 'Elongin Complex', 1 molecule of 'FCP1P protein', 1 molecule of 'P-TEFb complex', 1 molecule of 'NELF complex', 1 molecule of 'RNA polymerase II elongation factor ELL', 1 molecule of 'NTP', 1 molecule of 'TFIIS protein', and 1 molecule of 'TFIIF' are present.

This reaction takes place in the 'nucleus'.

R-HSA-113430 (Reactome) At the beginning of this reaction, 1 molecule of 'Pol II transcription complex containing transcript to +30' is present. At the end of this reaction, 1 molecule of 'Pol II transcription complex containing extruded transcript to +30' is present.

This reaction takes place in the 'nucleus' (Buratowski 2009).
R-HSA-72180 (Reactome) Endonucleolytic cleavage separates the pre-mRNA into an upstream fragment destined to become the mature mRNA, and a downstream fragment that is rapidly degraded. Cleavage depends on two signals in the RNA, a highly conserved hexanucleotide, AAUAAA, 10 to 30 nucleotides upstream of the cleavage site, and a poorly conserved GU- or U-rich downstream element. Additional sequences, often upstream of AAUAAA, can enhance the efficiency of the reaction. Cleavage occurs most often after a CA dinucleotide. A single gene can have more than one 3' processing site.

Cleavage is preceded by the assembly of a large processing complex, the composition of which is poorly defined. ATP, but not its hydrolysis, is required for assembly. Cleavage at the 3'-end of mRNAs depends on a number of protein factors. CPSF, a heterotetramer, binds specifically to the AAUAAA sequence. The heterotrimer CstF binds the downstream element. CF I, which appears to be composed of two subunits, one of several related larger polypeptides and a common smaller one, also binds RNA, but with unknown specificity. RNA recognition by these proteins is cooperative. Cleavage also requires CF II, composed of at least two subunits, and poly(A) polymerase, the enzyme synthesizing the poly(A) tail in the second step of the reaction. The polypeptide catalyzing the hydrolysis of the phosphodiester bond remains to be identified.

Cleavage produces a 3'-OH on the upstream fragment and a 5'-phosphate on the downstream fragment. At some unknown point after cleavage, the downstream RNA fragment, CstF, CF I and CF II are thought to be released, whereas CPSF and poly(A) polymerase remain to carry out polyadenylation.

R-HSA-73946 (Reactome) At the beginning of this reaction, 1 molecule of 'pol II transcription complex' is present. At the end of this reaction, 1 molecule of 'TFIIA', 1 molecule of 'TFIIH', 1 molecule of 'TFIIE', 1 molecule of 'TFIID', 1 molecule of 'TFIIB', 1 molecule of 'RNA Polymerase II (unphosphorylated):TFIIF complex', and 1 molecule of 'template DNA with first transcript dinucleotide, opened to +8 position' are present.

This reaction takes place in the 'nucleus'.

R-HSA-75095 (Reactome) Factor TFIIE enters the preinitiation complex after TFIIF recruits RNA Polymerase II. TFIIE is composed of two subunits of 56 kDA and 34 kDa. TFIIE facilitates the recruitment of factor TFIIH to the preinitiation complex, and it also stimulates the phosphorylation of the RNA Polymerase II CTD by TFIIH.
R-HSA-75850 (Reactome) Formation of the second phosphodiester bond creates a 3-nt product. This short transcript is still loosely associated with the RNA polymerase II initiation complex and can dissociate to yield abortive products, which are not further extended. The transcription complex still requires continued ATP-hydrolysis by TFIIH and remains sensitive to single-stranded oligo-nucleotide inhibition.

The open region (“transcription bubble�) expands concomitant with the site of RNA-extension. In this case this region spans positions -9 to +3.

R-HSA-75856 (Reactome) At the beginning of this reaction, 1 molecule of 'Pol II Promoter Escape Complex' is present. At the end of this reaction, 1 molecule of 'TFIIA', 1 molecule of 'TFIIH', 1 molecule of 'TFIIE', 1 molecule of 'TFIID', 1 molecule of 'TFIIB', 1 molecule of 'RNA Polymerase II (unphosphorylated):TFIIF complex', and 1 molecule of 'DNA containing Pol II promoter with transcript with 2 or 3 nucleotides' are present.

This reaction takes place in the 'nucleus'.

R-HSA-75861 (Reactome) At the beginning of this reaction, 1 molecule of 'pol II open pre-initiation complex', and 2 molecules of 'NTP' are present. At the end of this reaction, 1 molecule of 'Pol II initiation complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-75862 (Reactome) At the beginning of this reaction, 1 molecule of 'pol II open pre-initiation complex' is present. At the end of this reaction, 1 molecule of 'pol II closed pre-initiation complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-75864 (Reactome) At the beginning of this reaction, 1 molecule of 'Pol II Initiation complex with phosphodiester-PPi intermediate' is present. At the end of this reaction, 1 molecule of 'pyrophosphate', and 1 molecule of 'pol II transcription complex' are present.

This reaction takes place in the 'nucleus'.

R-HSA-75866 (Reactome) At the beginning of this reaction, 1 molecule of 'Pol II initiation complex' is present. At the end of this reaction, 1 molecule of 'Pol II Initiation complex with phosphodiester-PPi intermediate' is present.

This reaction takes place in the 'nucleus'.

R-HSA-75869 (Reactome) Formation of the third phosphodiester bond creates a 4-nt product. This commits the initiation complex to promoter escape. The short 4-nt transcript is still loosely associated with the RNA polymerase II initiation complex and can dissociate to yield abortive products, which are not further extended. Inhibition of ATP-hydrolysis by TFIIH does not lead to collapse of the open region any longer. The transcription complex has lost the sensitivity to single-stranded oligo-nucleotide inhibition. However, ATP-hydrolysis and TFIIH are required for efficient promoter escape. The open region ("transcription bubble") expands concomitant with the site of RNA-extension. In this case this region spans positions -9 to +4.
R-HSA-75873 (Reactome) Formation of the second phosphodiester bond creates a 3-nt product. This transcript is still loosely associated with the RNA polymerase II initiation complex and can dissociate to yield abortive products, which are not further extended. At this stage pausing by RNA polymerase II may result in repeated slippage and reextension of the nascent RNA. The transcription complex still requires continued ATP-hydrolysis by TFIIH for efficient promoter escape. Basal transcription factor TFIIE dissociates from the initiation complex before position +10.

Basal transcription factor TFIIF may reassociate and can stimulate transcription elongation at multiple stages. The open region (“transcription bubble�) expands concomitant with the site of RNA-extension, eventually reaching an open region from -9 to +9.

R-HSA-75891 (Reactome) At the beginning of this reaction, 1 molecule of 'pol II transcription complex containing 4-9 nucleotide long transcript' is present. At the end of this reaction, 1 molecule of 'template DNA:4-9 nucleotide transcript hybrid', 1 molecule of 'TFIIH', 1 molecule of 'TFIIE', and 1 molecule of 'RNA Polymerase II (unphosphorylated):TFIIF complex' are present.

This reaction takes place in the 'nucleus'.

R-HSA-75949 (Reactome) After assembly of the complete RNA polymerase II-preinitiation complex, the next step is separation of the two DNA strands. This isomerization step is known as the closed-to-open complex transition and occurs prior to the initiation of mRNA synthesis. In the RNA polymerase II system this step requires the hydrolysis of ATP or dATP into Pi and ADP or dADP (in contrast to the other RNA polymerase systems) and is catalyzed by the XPB subunit of TFIIH. The region of the promoter, which becomes single-stranded , spans from –10 to +2 relative to the transcription start site.

Negative supercoiling in the promoter region probably induces transient opening events and can alleviate requirement of TFIIE, TFIIH and ATP-hydrolysis for open complex formation. ATP is also used in this step by the cdk7-subunit of TFIIH to phosphorylate the heptad repeats of the C-terminal domain of the largest subunit of RNA polymerase II (RPB1) on serine-2

R-HSA-76576 (Reactome) Formation of phosphodiester bonds nine and ten creates RNA products, which do not dissociate from the RNA pol II initiation complex. The transcription complex has enter the productive elongation phase. TFIIH and ATP-hydrolysis are required for efficient promoter escape. The open region (“transcription bubble�) expands concomitant with the site of RNA-extension. The region upstream from the transcription start site (-9 to -3) collapses to the double-stranded state. TFIIH remains associated to the RNA pol II initiation complex.
R-HSA-77068 (Reactome) At the beginning of this reaction, 1 molecule of 'RNA Pol II with phosphorylated CTD: CE complex' is present. At the end of this reaction, 1 molecule of 'RNA Pol II with phosphorylated CTD: CE complex with activated GT' is present.

This reaction takes place in the 'nucleus'.

R-HSA-77069 (Reactome) At the beginning of this reaction, 1 molecule of 'mRNA capping enzyme', and 1 molecule of 'Pol II transcription complex with (ser5) phosphorylated CTD containing extruded transcript to +30' are present. At the end of this reaction, 1 molecule of 'RNA Pol II with phosphorylated CTD: CE complex' is present.

This reaction takes place in the 'nucleus'.

R-HSA-77071 (Reactome) Phosphorylation of serine 5 residue at the CTD of pol II largest subunit is an important step signaling the end of initiation and escape into processive elongation processes. Cdk7 protein subunit of TFIIH phosphorylates RNA Pol II CTD serine 5 residues on its heptad repeats (Buratowski 2009).
R-HSA-77073 (Reactome) The capping enzyme interacts with the Spt5 subunit of transcription elongation factor DSIF. This interaction may couple the capping reaction with promoter escape or elongation, thereby acting as a "checkpoint" to assure that capping has occurred before the polymerase proceeds to make the rest of the transcript.
R-HSA-77586 (Reactome) Processing is initiated once the SLBP (bound to the stem loop) and the U7 snRNP (bound to the HDE) are both loaded onto the pre-mRNA. The pre-mRNA HDE makes base-pairing contacts with the 5′ end of U7 snRNA. Binding of the U7 snRNP to the pre-mRNA is stabilized by interactions between a U7 snRNP protein, hZFP100 and SLBP. It should be noted that there must be other trans-acting factors, including the factor that catalyzes the cleavage reaction, which have yet to be defined. The cleavage occurs in the presence of EDTA as does the cleavage reaction in polyadenylation, it is likely that this reaction is catalyzed by a protein. There may well be additional proteins associated with the U7 snRNP, and since in some conditions in vitro processing occurs in the absence of SLBP, it is possible that all the other factors required for processing are associated with the active form of the U7 snRNP.
R-HSA-77592 (Reactome) The polypeptide catalyzing the hydrolysis of the phosphodiester bond remains to be identified. Cleavage produces a 3'-OH on the upstream fragment and a 5'-phosphate on the downstream fragment. At some unknown point after cleavage, the downstream fragment, CstF, CF I and CF II are thought to be released, whereas CPSF and poly(A) polymerase remain to carry out polyadenylation.
RNA

Pol II

(hypophosphorylated) complex bound to DSIF protein		ArrowR-HSA-113407 (Reactome)
RNA

Pol II

(hypophosphorylated) complex bound to DSIF protein		R-HSA-113402 (Reactome)
RNA

Pol II

(hypophosphorylated):capped pre-mRNA complex		ArrowR-HSA-112383 (Reactome)
RNA

Pol II

(hypophosphorylated):capped pre-mRNA complex		R-HSA-113407 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex		ArrowR-HSA-73946 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex		ArrowR-HSA-75856 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex		ArrowR-HSA-75891 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex		R-HSA-109638 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex		mim-catalysisR-HSA-111264 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex		mim-catalysisR-HSA-75850 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex		mim-catalysisR-HSA-75869 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex		mim-catalysisR-HSA-75873 (Reactome)
RNA

Polymerase II

(unphosphorylated):TFIIF complex		mim-catalysisR-HSA-76576 (Reactome)
RNA

Polymerase II holoenzyme complex

(hyperphosphorylated)		ArrowR-HSA-113429 (Reactome)
RNA Pol II with

phosphorylated CTD: CE complex with

activated GT		ArrowR-HSA-77068 (Reactome)
RNA Pol II with

phosphorylated CTD: CE complex with

activated GT		R-HSA-77073 (Reactome)
RNA Pol II with

phosphorylated CTD:

CE complex		ArrowR-HSA-77069 (Reactome)
RNA Pol II with

phosphorylated CTD:

CE complex		R-HSA-77068 (Reactome)
RNGTTR-HSA-77069 (Reactome)
RNMTR-HSA-77073 (Reactome)
SSRP1R-HSA-112429 (Reactome)
SUPT16HR-HSA-112429 (Reactome)
SUPT4H1R-HSA-112434 (Reactome)
TCEA1ArrowR-HSA-113429 (Reactome)
TCEA1R-HSA-112379 (Reactome)
TCEB1R-HSA-112435 (Reactome)
TCEB2R-HSA-112435 (Reactome)
TCEB3R-HSA-112436 (Reactome)
TFIIAArrowR-HSA-73946 (Reactome)
TFIIAArrowR-HSA-75856 (Reactome)
TFIIAArrowR-HSA-75873 (Reactome)
TFIIAR-HSA-109637 (Reactome)
TFIIDArrowR-HSA-73946 (Reactome)
TFIIDArrowR-HSA-75856 (Reactome)
TFIIDArrowR-HSA-75873 (Reactome)
TFIIDR-HSA-109636 (Reactome)
TFIIEArrowR-HSA-73946 (Reactome)
TFIIEArrowR-HSA-75856 (Reactome)
TFIIEArrowR-HSA-75873 (Reactome)
TFIIEArrowR-HSA-75891 (Reactome)
TFIIER-HSA-75095 (Reactome)
TFIIFArrowR-HSA-113429 (Reactome)
TFIIHArrowR-HSA-112383 (Reactome)
TFIIHArrowR-HSA-112385 (Reactome)
TFIIHArrowR-HSA-73946 (Reactome)
TFIIHArrowR-HSA-75856 (Reactome)
TFIIHArrowR-HSA-75891 (Reactome)
TFIIHR-HSA-109639 (Reactome)
TFIIHR-HSA-112379 (Reactome)
TFIIHR-HSA-112383 (Reactome)
TFIIHmim-catalysisR-HSA-75850 (Reactome)
TFIIHmim-catalysisR-HSA-75869 (Reactome)
TFIIHmim-catalysisR-HSA-75949 (Reactome)
TFIIHmim-catalysisR-HSA-77071 (Reactome)
U7 snRNP:ZNF473ArrowR-HSA-111437 (Reactome)
U7 snRNP:ZNF473ArrowR-HSA-77586 (Reactome)
capped

pre-mRNA:CBC:RNA Pol II (phosphorylated)

complex		R-HSA-112383 (Reactome)
damaged DNA

substrate:nascent

mRNA hybrid		ArrowR-HSA-113429 (Reactome)
downstream

intronless mRNA

fragment		ArrowR-HSA-77592 (Reactome)
intronless pre-mRNA cleavage complexR-HSA-77592 (Reactome)
mRNA 3'-end cleavage factormim-catalysisR-HSA-72180 (Reactome)
p-SUPT5HR-HSA-112434 (Reactome)
p-SUPT5HR-HSA-77073 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB complex		ArrowR-HSA-109637 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB complex		R-HSA-109638 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complex		ArrowR-HSA-109638 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complex		R-HSA-75095 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complex		ArrowR-HSA-75095 (Reactome)
pol

II

promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complex		R-HSA-109639 (Reactome)
pol II

promoter:TFIID

complex		ArrowR-HSA-109636 (Reactome)
pol II

promoter:TFIID

complex		R-HSA-109637 (Reactome)
pol II closed

pre-initiation

complex		ArrowR-HSA-109639 (Reactome)
pol II closed

pre-initiation

complex		ArrowR-HSA-75862 (Reactome)
pol II closed

pre-initiation

complex		R-HSA-75949 (Reactome)
pol II open

pre-initiation

complex		ArrowR-HSA-75949 (Reactome)
pol II open

pre-initiation

complex		R-HSA-75861 (Reactome)
pol II open

pre-initiation

complex		R-HSA-75862 (Reactome)
pol II transcription

complex containing 11 nucleotide long

transcript		ArrowR-HSA-76576 (Reactome)
pol II transcription

complex containing 11 nucleotide long

transcript		R-HSA-111264 (Reactome)
pol II transcription

complex containing 3 Nucleotide long

transcript		ArrowR-HSA-75850 (Reactome)
pol II transcription

complex containing 3 Nucleotide long

transcript		R-HSA-75869 (Reactome)
pol II transcription

complex containing 4 nucleotide long

transcript		ArrowR-HSA-75869 (Reactome)
pol II transcription

complex containing 4 nucleotide long

transcript		R-HSA-75873 (Reactome)
pol II transcription

complex containing 4-9 nucleotide long

transcript		R-HSA-75891 (Reactome)
pol II transcription

complex containing 9 nucleotide long

transcript		ArrowR-HSA-75873 (Reactome)
pol II transcription

complex containing 9 nucleotide long

transcript		R-HSA-76576 (Reactome)
pol II transcription complexArrowR-HSA-75864 (Reactome)
pol II transcription complexR-HSA-73946 (Reactome)
pol II transcription complexR-HSA-75850 (Reactome)
template DNA with

first transcript dinucleotide, opened to +8

position		ArrowR-HSA-73946 (Reactome)
template DNA:4-9

nucleotide

transcript hybrid		ArrowR-HSA-75891 (Reactome)
upstream

mRNA

fragment:CPSF:PAP:PABPN1 complex		ArrowR-HSA-77592 (Reactome)
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