RNA Polymerase II Transcription (Homo sapiens)

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9, 2042, 3, 9, 20245, 12, 20, 2223, 246, 1544172411119, 194119, 1924241, 8-10, 13...TFIIE RNA Polymerase II holoenzyme complex DSIF complex TFIID TFIIH TFIIF capped intronless pre-mRNACBC complex RNA Polymerase II holoenzyme complex TFIIF TFIIF CstFCPSFcapped intronless pre-mRNACBC complex FACT complex TFIIF NELF complex RNA Polymerase II holoenzyme complex Early elongation complex with hyperphosphorylated Pol II CTD DSIFNELFearly elongation complex RNA Polymerase II holoenzyme complex pre-EJC complex NTP Cap Binding Complex CAK NELF complex Elongation complex with separated and uncleaved transcript Cap Binding Complex mRNA 3'-end cleavage factor TFIIH CEPol II CTDSpt5 complex TFIIH CAK DSIF complex Ligated exon containing complex Pol II transcription complex with RNA Polymerase II holoenzyme complex FACT complex capped pre-mRNACBCRNA Pol II RNA Polymerase II holoenzyme complex Capped Intronless Histone pre-mRNACBP80CBP20SLBP CF II RNA Polymerase II P-TEFb complex TFIIA TFIIF Elongin BC complex NTP RNA Polymerase II holoenzyme complex CstF Elongin BC complex TFIID RNA Polymerase II holoenzyme complex CAK TFIIH TFIIH Elongation complex CAK Aborted elongation complex after arrest Processive elongation complex pol II promoterTFIID complex nucleoplasmRNA Polymerase II holoenzyme complex pol II promoterTFIID complex Elongin BC complex RNA Polymerase II holoenzyme complex CAK CstF CAK RNA Polymerase II holoenzyme complex RNA Polymerase II Pol II Initiation complex with phosphodiester-PPi intermediate Capped Intronless Histone pre-mRNACBCZFP100 Complex Elongin Complex CPSFcapped intronless pre-mRNACBC complex RNA Polymerase II holoenzyme complex Aborted early elongation complex CPSF TFIIF TFIIF RNA Polymerase II holoenzyme complex Paused processive elongation complex TFIIF TFIIH TFIIH Arrested processive elongation complex TFIIA RNA polymerase II Pol II transcription complex containing transcript to +30 pol II transcription complex containing 11 nucleotide long transcript pol II open pre-initiation complex FACT complex Magoh-Y14 complex TFIIH RNA Pol II with phosphorylated CTD CE complex with activated GT RNA Polymerase II holoenzyme complex RNA Polymerase II DSIF complex RNA Polymerase II RNA Polymerase II DSIF complex pol II promoterTFIIDTFIIATFIIB complex pol II promoterTFIID complex TFIIA RNA Polymerase II DSIF complex NELF complex RNA Polymerase II holoenzyme complex TFIIE FACT complex Cap Binding Complex DSIF complex intronless pre-mRNA cleavage complex CAK P-TEFb complex TFIIE RNA Polymerase II holoenzyme complex TFIIF CPSF TFIIH RNA Polymerase II holoenzyme complex TFIIE TFIID pol II promoterTFIID complex RNA Polymerase II holoenzyme complex NTP CF I pol II promoterTFIID complex TFIIE TFIIF TFIIH RNA Polymearse IINTPTFIIF complex NTP Elongin Complex TFIID TFIIF RNA Polymerase II FACT complex upstream mRNA fragmentCPSFPAPPABPN1 complex TFIIE TFIIE TFIID Elongin Complex TFIIF CAK TFIIA TFIIF TFIIH Elongin BC complex NELF complex TFIIF TFIIF RNA Polymerase II holoenzyme complex P-TEFb complex TFIIE pol II promoterTFIIDTFIIATFIIB complex RNA Pol II NELF complex RNA Polymerase II holoenzyme complex TFIIH RNA polymerase II P-TEFb complex CAK TFIID pol II promoterTFIIDTFIIATFIIB complex TFIID RNA Pol II Elongin Complex RNA Pol II RNA Polymerase II TFIIF pol II promoterTFIIDTFIIATFIIBPol IITFIIF complex U7 snRNPZNF473 TFIID TFIIF U7 snRNPZNF473 TFIIH Cap Binding Complex FACT complex CAK TFIID Capped Intronless Histone pre-mRNACBC complex Elongin BC complex RNA Polymerase II holoenzyme complex TFIID Cap Binding Complex 3' end cleaved, ligated exon containing complex TFIIF DSIF complex U7 snRNP-specific Sm core complex CF I TFIID Cap Binding Complex RNA Pol II RNA Polymerase II holoenzyme complex TFIIF P-TEFb complex TFIIF FACT complex pol II transcription complex containing 4 nucleotide long transcript RNA Polymerase II holoenzyme complex TFIIH CF II RNA polymerase II RNA Polymerase II holoenzyme complex TFIIF pol II transcription complex Mature intronless transcript derived Histone pre-mRNACBC complex TFIIF Pol II transcription complex containing extruded transcript to +30 CF I Cap Binding Complex CF II U7 snRNPZNF473 RNA Polymerase II holoenzyme complex CAK pol II transcription complex containing 9 nucleotide long transcript TFIIE pol II closed pre-initiation complex CAK Elongation complex prior to separation NELF complex pol II transcription complex containing 3 Nucleotide long transcript TFIIF Elongin BC complex CAK TFIIH Elongin BC complex pol II promoterTFIIDTFIIATFIIBPol IITFIIF complex TFIIA RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex NELF complex Cap Binding Complex CAK TFIIA TFIIF RNA Polymerase II holoenzyme complex CstF CPSF TFIIA TFIIH RNA Polymerase II pol II promoterTFIIDTFIIATFIIB complex NELF complex RNA Polymerase II holoenzyme complex Elongin Complex RNA Polymerase II CAK RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex TFIIH RNA Polymerase II holoenzyme complex TFIIE DSIF complex RNA polymerase II CAK Elongin Complex NTP Elongin BC complex TFIIF P-TEFb complex TFIIF RNA Polymerase II Cap Binding Complex CPSF DSIF complex CAK RNA Polymerase II TFIIF TFIIF TFIIA RNA Pol II TFIIE Cleavage and Polyadenylation Complex Elongin Complex Pol II initiation complex TFIIA RNA Polymerase II holoenzyme complex TFIIF TFIIF TFIIH RNA Pol II RNA Polymerase II holoenzyme complex TFIID RNA Polymerase II RNA Polymerase II EJC complex RNA Polymerase II pol II transcription complex containing 4-9 nucleotide long transcript Elongin Complex Pol II Promoter Escape Complex RNA Polymerase II holoenzyme complex TFIIH RNA Polymerase II holoenzyme complex TFIIE pol II promoterTFIIDTFIIATFIIBPol IITFIIFTFIIE complex CAK TFIIH CAK FACT complex Early elongation complex with hyperphosphorylated Pol II CTD RNA Pol II with phosphorylated CTD CE complex Magoh-Y14 complex RNA Pol II RNA Polymerase II holoenzyme complex TFIIA NELF complex RNA Polymerase II holoenzyme complex TFIIA P-TEFb complex TFIID Cap Binding Complex Capped Intronless Histone pre-mRNACBP80CBP20SLBPZFP100 Complex CAK CAK RNA Polymerase II Cap Binding Complex TFIIH DSIF complex Elongin BC complex CAK P-TEFb complex CAK TFIIF TFIIA TFIIH U7 snRNP-specific Sm core complex Mature Intronless transcript derived Histone mRNASLBPCBP80CBP20 TFIID pol II promoterTFIIDTFIIATFIIBPol IITFIIF complex RNA Polymerase II holoenzyme complex P-TEFb complex TFIIF DSIF complex pre-EJC complex TFIIF NELF complex CF II U7 snRNP-specific Sm core complex TFIIH RNA polymerase II TFIIA TFIIF RNA Polymerase II NELF complex RNA Polymerase II holoenzyme complex EJC complex Capped Intronless Histone pre-mRNACBC complex CF I RNA Polymerase II holoenzyme complex DSIF complex LSM10 GTF2A2 GTF2F1POLR2DATP POLR2I NTPPOLR2FCCNH POLR2E p-SUPT5HELL POLR2FCCNH SRSF5 POLR2L GTF2H1SUPT16H GTP POLR2E POLR2J GTF2E1 GTF2H1CPSF1 POLR2E GTF2A1TBP GTF2E1 TAF10 GTF2H1TCEB2 SUPT4H1 CCNH SNRPB POLR2C POLR2C POLR2J Pol II transcription complex containing extruded transcript to +30GTF2H3 PCF11 ERCC2 SSRP1CDK7 PABPN1 GTF2H2 POLR2L POLR2L SUPT16H POLR2L GTF2H4 CDK9 NTPGTF2H1POLR2L SUPT4H1NELFCD CCNT1 POLR2B POLR2J NELFAMNAT1 CDK7 NUDT21 CTP POLR2K CTDP1 MNAT1 TFIIEPOLR2FPOLR2C TFIIHGTF2H4 RBM8A NTPCPSF3 GTF2F2GTF2B SRSF3 TCEB3 NELFENTPTCEB2 SSRP1 GTF2E1 POLR2A POLR2J GTF2F1CDK7 TAF10 TAF5 POLR2J CSTF3 CDK7 p-SUPT5H POLR2B SUPT16H U2AF1 POLR2A SRSF4 GTF2A1TAF12 GTF2H4 SNRPB GTF2F2pol II transcription complex containing 11 nucleotide long transcriptPOLR2G POLR2G GTF2H3 TAF10 ERCC3 TAF10 CDK7 SUPT4H1 POLR2J GTF2H1SSRP1 POLR2H GTF2F1POLR2E TAF11 SNRPG CstFPOLR2E P-TEFb complexTAF12 Aborted early elongation complexGTF2A1POLR2K UTP TCEB2POLR2A p-SUPT5H CCNT1 GTF2F1NCBP1 POLR2FPOLR2I POLR2E NCBP2 POLR2E TAF1 SUPT4H1 POLR2K GTF2H3 GTF2F1CCNT1 TAF1 MAGOH Arrested processive elongation complexGTF2F1GTF2H2 NELFB MNAT1 p-S2,S5-POLR2A GTF2E2 POLR2FPOLR2FPOLR2K NELFE NELFCD POLR2H POLR2E GTF2F1GTF2B p-S2,S5-POLR2A GTF2E2 pol II transcription complexNELFCD CPSF1 POLR2DPOLR2G NCBP1 TAF6 TCEA1 CCNT2 CCNT2POLR2J TAF5 TCEB3POLR2DTCEB3 GTF2H2 GTF2F1TBP GTF2A2 ERCC3 POLR2I SRSF2 POLR2DTFIIDTCEB1TAF11 CPSF3 POLR2DPOLR2H POLR2I RNMT CDK7 GTF2H3 GTP POLR2A GTF2F1CCNH MNAT1 GTF2H3 TAF10 POLR2G TAF4 Mature intronless transcript derived Histone pre-mRNACBC complexPOLR2I CSTF3 NFX.1 POLR2J POLR2B ERCC3 GTF2H4 CDK9 ERCC3 TAF4B p-SUPT5H POLR2FGTF2F2POLR2DPOLR2FNELFB GTF2F2POLR2J GTF2A2 POLR2DTAF6 GTF2H3 TAF5 POLR2C TAF13 TCEB1 MNAT1 POLR2I POLR2H TAF4B GTF2H3 TAF13 NELFCD POLR2FGTF2A1POLR2I GTF2H4 POLR2FTAF4B CCNT2 POLR2G NCBP2 POLR2DPOLR2L GTF2F1GTF2F1NELFB GTF2H3 CLP1 TBP GTF2F2SUPT16H POLR2B POLR2L POLR2E TAF13 NFX.1 TCEB1 GTF2H1POLR2FPOLR2G GTF2B SUPT16HNELFCD CDK7 POLR2B POLR2H GTF2A1POLR2H CSTF1 CTP NTPPOLR2DGTF2E1 GTF2A2 POLR2K POLR2L GTF2H1NELFBPOLR2C GTF2H2 POLR2G POLR2I NCBP2 POLR2E GTF2F1mRNA 3'-end cleavage factorNELFE GTF2H2 CSTF1 TAF9 ERCC2 POLR2E GTF2H1GTF2H3 TAF9 POLR2K GTF2H3 POLR2K template DNA4-9 nucleotide transcript hybridCPSF7 GTF2H2 POLR2B CPSF7 POLR2E CCNH TAF4B POLR2DPOLR2K POLR2FPOLR2H POLR2C GTF2F1CCNT1GTF2E1 POLR2G MNAT1 POLR2A NELFCD GTF2F2CCNH POLR2J TCEA1 TAF4 POLR2L SSRP1 POLR2FPOLR2I GTF2A1POLR2DPOLR2C DNA containing Pol II promoter with transcript with 2 or 3 nucleotidesTAF13 CPSF2 CCNH GTF2E1 CPSF7 ERCC2 POLR2J CCNH CCNH GTF2F1Pol II Initiation complex with phosphodiester-PPi intermediatep-S5-POLR2A TAF4B GTF2H4 TAF4 Pol II transcription complex containing transcript to +30GTF2H4 LSM11 ATP POLR2H NELFCD PCF11 ELL POLR2FGTF2A1ZNF473 RNMTPOLR2L POLR2K POLR2FTAF6 POLR2A POLR2H RNA Pol II with phosphorylated CTD CE complex with activated GTNCBP1 POLR2J POLR2DPOLR2K POLR2H PPiPol II Promoter Escape ComplexPOLR2L POLR2E NELFANELF complexPOLR2L SRSF1 TAF10 POLR2H TAF12 GTF2H1POLR2C PABPN1 GTF2H4 SUPT4H1 TAF4 GTF2A1GTF2H3 GTF2F2TBP GTF2E2 POLR2H GTF2H3 TBP POLR2K SUPT4H1 GTF2A1SRRM1 TCEA1 CDK7 CDK9 TCEB2 TCEB3 GTF2H3 GTF2F1pol II promoterTFIIDTFIIATFIIB complexNELFB GTF2H2 POLR2FERCC3 GTF2B POLR2B TAF1 POLR2FPOLR2K GTF2F1TBP CDK9 CCNT2 PAPOLAPOLR2J POLR2DPOLR2C POLR2DTCEB3 TAF4 NCBP2 NCBP1 GTF2F2NELFCD POLR2FNUDT21 POLR2A NCBP1 TAF10 TAF12 GTF2H1ERCC2 GTF2F1GTF2F2POLR2B POLR2C ERCC2 NELFAPOLR2H NCBP2 CTDP1 p-S2,S5-POLR2A TCEB1 TAF12 TAF4B GTF2F2NCBP2 NCBP2 POLR2C CPSF7 GTF2H3 POLR2C p-SUPT5H MNAT1 GTF2F1p-SUPT5H RNPS1 MNAT1 POLR2A p-S5-POLR2A POLR2B CTDP1 NUDT21 TAF12 TAF4 pol II transcription complex containing 4-9 nucleotide long transcriptp-S2,S5-POLR2A TFIIFPOLR2I GTF2B TAF4B CCNT1 POLR2E POLR2C GTF2H4 TAF1 POLR2L GTF2A1TAF4 GTF2A1Capped Intronless Histone pre-mRNACBP80CBP20SLBPZFP100 ComplexPOLR2DPOLR2I NELFE NELFB PPiTAF9 DHX38 GTF2A2 POLR2C POLR2L POLR2L POLR2FGTF2H4 Ligated exon containing complexPOLR2B TAF11 POLR2E p-SUPT5H NELFB POLR2G POLR2K ERCC2 CF IITBP CDK7 TAF9 NCBP2 GTF2F1TCEB3 SRRM1 CCNH GTF2F2POLR2FTAF13 GTF2H4 MNAT1 CTDP1POLR2B POLR2B POLR2K POLR2J POLR2E GTF2F1POLR2DNCBP1 upstream mRNA fragmentCPSFPAPPABPN1 complexpol II transcription complex containing 3 Nucleotide long transcriptCDK7 GTF2F1POLR2B POLR2I POLR2B CTDP1 capped pre-mRNACBCRNA Pol II SRSF9 TAF6 CPSF1 POLR2K POLR2I POLR2I SNRPE Pip-S5-POLR2A TAF9 POLR2E GTF2H4 POLR2B GTF2H3 POLR2L GTF2B GTF2E1 GTF2A2 CPSF2 TAF6 TAF4 UTP POLR2B POLR2B CDK9 UPF3B POLR2K ALYREF GTP PPiPOLR2I pol II transcription complex containing 9 nucleotide long transcriptPOLR2FPOLR2FGTF2A1NTPERCC3 DSIF complexTCEB1 p-SUPT5H GTF2A2 TAF10 ERCC3 PCF11 CCNT2 LSM10 CDC40 CTDP1 LSM11 ERCC3 GTF2F2UTP GTF2E1 CDK7 CEPol II CTDSpt5 complexCSTF1 NELFB POLR2A POLR2FTAF13 TAF4 POLR2H GTF2H1GTF2F2POLR2I NELFE POLR2B GTF2A2 MNAT1 Elongin ComplexTAF1 GTF2F1CPSF3 NCBP2 TAF9 TAF12 POLR2L POLR2H NCBP2 TAF4B POLR2A TAF5 GTF2A1POLR2H 3' end cleaved, ligated exon containing complexPOLR2FPOLR2K POLR2G POLR2K RNGTT POLR2H TAF1 RNA Pol II with phosphorylated CTD CE complexPOLR2G Elongation complex with separated and uncleaved transcriptPOLR2K ZNF473 NELFAPOLR2E TCEA1POLR2K POLR2DPOLR2H CDK7 GTF2H2 RNA Pol II POLR2J POLR2G POLR2L TAF12 TCEB1 TAF4B damaged DNA substratenascent mRNA hybridMNAT1 SRSF9 GTF2A1NELFE NTPPOLR2DPOLR2K GTF2A1SNRPE TAF4 p-S5-POLR2A GTF2F2POLR2B Pol II transcription complex with CCNH CCNH GTF2H2 TAF11 POLR2C CCNT2 TAF13 POLR2C TAF13 TCEA1 GTF2F2TAF4 POLR2E POLR2H GTF2H3 CCNT1 GTF2F2CPSF2 TCEB1 POLR2I CPSF1 ERCC2 NELFB SNRPF GTF2E1 SUPT4H1 downstream intronless mRNA fragmentSRSF4 MNAT1 SNRPG GTF2H4 CDK7 TFIIHPOLR2I TAF5 POLR2J TAF13 POLR2B POLR2L POLR2C POLR2J TAF10 GTF2H4 SUPT4H1 POLR2L GTF2E2 POLR2E TAF11 TAF12 SRSF3 POLR2FTAF1 ERCC2 POLR2H POLR2DTCEB2 SUPT16H PPiGTF2H4 GTF2F1TAF5 TAF13 GTF2E2 GTF2H4 p-SUPT5H TAF6 ERCC2 SRSF6 GTF2H2 POLR2L GTF2H1Early elongation complex with hyperphosphorylated Pol II CTDPOLR2FERCC3 GTF2H3 CTDP1 POLR2H NELFAERCC2 TAF10 GTF2H1CTDP1 POLR2H GTF2B GTF2F1ELL CPSF2 MNAT1 POLR2J GTF2F2POLR2L TFIIHNCBP2 ALYREF TAF6 CDK9 POLR2G LSM10 FACT complexGTF2H4 POLR2DCLP1 TAF1 CCNH CSTF2GTF2H1POLR2B POLR2Dtemplate DNA with first transcript dinucleotide, opened to +8 positionTAF9 ERCC2 POLR2K GTF2A1PCF11 NELFASSRP1 GTF2E2 TAF13 TAF1 p-SUPT5H POLR2E SNRPG POLR2G GTF2A2 NCBP1 U2AF2 NELFANELFB TCEB2 ERCC2 SRSF7 TCEA1 ERCC3 NCBP1 GTF2H1TCEB2 pol II transcription complex containing 4 nucleotide long transcriptPABPN1 CDK9 POLR2B POLR2E GTF2F1TAF9 POLR2E CCNH SUPT16H NCBP2 GTF2H1CDK7 NCBP1 TAF5 GTF2F2POLR2K GTF2H3 TAF4 RNA Polymerase II holoenzyme complex POLR2G MNAT1 TAF4B NCBP2 NELFE POLR2J NELFCDSSRP1 TAF1 TBP POLR2C GTF2F1CCNH POLR2L CCNT1 CDK9 GTF2F2RBM8A POLR2I GTF2H1POLR2I POLR2I RNGTTSSRP1 GTF2BGTF2F2POLR2G CTDP1 POLR2C CDK9 ERCC3 SRSF1 POLR2J Capped Intronless Histone pre-mRNACBCZFP100 ComplexPOLR2DERCC2 Processive elongation complexGTF2A1TAF12 TAF4 TAF5 POLR2C GTF2E2 NUDT21 p-S2,S5-POLR2A GTF2F2POLR2B POLR2FPOLR2H TAF11 POLR2H CCNH NTPMNAT1 POLR2C TAF5 POLR2K POLR2I TAF11 CTDP1 POLR2J NELFB CCNT2 GTF2E2 POLR2L GTF2H2 POLR2A RNA Pol II POLR2E POLR2H PPiTCEA1 NELFB GTF2A1CDK7 GTF2A1DHX38 p-S5-POLR2A POLR2I TAF13 UTP TAF12 ELL NELFE TBP POLR2C ERCC2 GTF2F2POLR2B TAF5 GTF2F1NELFAPOLR2I POLR2E ELL POLR2DMNAT1 POLR2K ELLRNPS1 p-S5-POLR2A CSTF3 POLR2G SNRPE GTF2H2 GTF2H1MNAT1 ATPDSIFNELFearly elongation complexNCBP1 POLR2L SUPT4H1 POLR2I CCNH POLR2DPOLR2J POLR2G CTP Mature Intronless transcript derived Histone mRNASLBPCBP80CBP20CTDP1 ERCC2 ERCC2 LSM11 GTF2B POLR2K SUPT4H1 GTF2F1p-SUPT5H GTF2F2TAF11 TAF10 POLR2FTAF6 POLR2K CCNT1 GTF2H4 SSRP1 ZNF473 POLR2L NELFATCEB2 POLR2B POLR2G GTF2A1p-S2,S5-POLR2A NELFE GTF2B CCNT1 POLR2L p-S5-POLR2A CTP CCNH POLR2B POLR2L p-S2,S5-POLR2A SNRPD3 NELFAPOLR2E POLR2J CDK7 GTF2H2 POLR2FPOLR2FGTF2BElongin BC complexPOLR2J ERCC2 TAF6 TAF5 POLR2I TAF4B GTF2F2TFIIDNCBP2 POLR2C POLR2C TAF13 ERCC2 POLR2H NTPCCNH POLR2I pol II closed pre-initiation complexPOLR2G TAF13 CPSF3 SUPT4H1 NCBP1 POLR2A CDK7 GTF2F2TAF6 POLR2FPOLR2C TAF11 GTF2H2 TBP TAF9 CLP1 GTF2E2 POLR2DPOLR2E TCEB3 POLR2H POLR2E TBP GTF2F1GTF2H2 MNAT1 POLR2C SRSF11 TAF11 POLR2G SSRP1 POLR2DMNAT1 ATP PAPOLAPol II initiation complexTAF12 GTF2E2 ERCC2 POLR2G SRSF11 MNAT1 GTF2H2 ERCC2 POLR2DTAF10 ERCC3 UTP NELFCD CDC40 TFIIAPOLR2DPOLR2K RNGTT MNAT1 TAF1 GTF2F2SNRPF PAPOLATBP POLR2E TCEB1 p-S2,S5-POLR2A GTF2H4 GTF2A2 POLR2B CCNT1 TAF5 SUPT16H ERCC3 ERCC3 POLR2G POLR2L TAF6 POLR2H POLR2B POLR2K NELFCD U2AF1 CDK7 POLR2I GTP SRSF5 POLR2G SRSF7 DNA containing RNA Polymerase II promoterTAF6 TAF4 SUPT16H SUPT4H1 TAF9 TAF1 POLR2E TAF11 NCBP1 PAPOLACDK7 p-S5-POLR2A GTF2H4 NTPGTF2F1Elongation complexp-SUPT5H GTF2H2 ERCC3 TAF9 CTDP1 NTPGTF2H2 POLR2I GTF2F2MNAT1 TCEB3 POLR2A POLR2B GTF2H2 p-S5-POLR2A CTP TAF1 U7 snRNPZNF473CDK7 TAF10 TAF5 POLR2J TAF5 GTF2A1POLR2G POLR2H CCNH U2AF2 POLR2H CDK7 ELL GTF2E1 PABPN1 POLR2G NELFE RNGTT GTF2A1POLR2J POLR2DPOLR2L NCBP1 SLBP POLR2DTAF4B TAF12 ELL NCBP1 POLR2L ERCC3 POLR2K POLR2J POLR2J GTF2H4 ATP GTF2H1POLR2DNELFAPOLR2G TFIIHGTF2F2POLR2I PPiTCEB1 TCEB2 GTF2A2 MNAT1 ADPCCNT2 POLR2E GTF2F1MAGOH TFIIHGTF2A2 p-S2,S5-POLR2A pol II promoterTFIIDTFIIATFIIBPol IITFIIFTFIIE complexSNRPD3 GTF2F2TAF1 CCNH POLR2G CDK9POLR2J POLR2G CTDP1 CDK7 ERCC3 POLR2H GTF2E1 ERCC3 POLR2I ERCC3 GTF2E2 Cap Binding Complex GTF2H3 pol II promoterTFIIDTFIIATFIIBPol IITFIIF complexPOLR2G POLR2DGTF2F2UPF3B CSTF2NELFCD GTF2H1POLR2L SLBP GTF2H3 TFIIEPOLR2A TAF11 POLR2DGTF2H1GTF2F1ERCC3 TAF10 SRSF2 POLR2DGTF2F1TCEB2 POLR2J POLR2C TAF4B POLR2C GTF2F2TCEB3 GTF2F2GTF2H4 TAF6 POLR2J POLR2K TBP POLR2E GTF2A1SNRPB CLP1 CCNH POLR2G ERCC3 POLR2B POLR2C ATP CCNH POLR2G GTF2H2 POLR2I TAF6 CF Iintronless pre-mRNA cleavage complexElongation complex prior to separationGTF2H3 SNRPF GTF2F2POLR2H CCNT2 GTF2H2 GTF2A1p-SUPT5H POLR2J POLR2A POLR2L Paused processive elongation complexSUPT4H1 POLR2G POLR2C POLR2J POLR2B TCEB1 POLR2A POLR2I POLR2K GTF2H2 ERCC2 GTF2F2ERCC3 POLR2C POLR2I POLR2C GTP TAF11 POLR2L Aborted elongation complex after arrestPOLR2C CDK7 GTF2H1GTF2A1GTF2B pol II promoterTFIID complexGTF2F1ERCC2 p-SUPT5H GTF2E1 GTF2H1POLR2G POLR2E TAF12 TAF11 POLR2C CCNT2 GTF2E2 GTF2H3 POLR2B GTF2H2 TAF9 POLR2J TAF9 pol II open pre-initiation complexPOLR2E TFIIATCEA1 ERCC3 POLR2K NELFAPOLR2H POLR2FGTF2A2 GTF2H4 GTF2A1ERCC2 NELFE SNRPD3 POLR2B TBP CSTF2POLR2B NELFE TAF4B TAF9 POLR2FPOLR2H POLR2FGTF2H3 RNA Polymerase II SRSF6 POLR2K 18217


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  15. Sims RJ, Belotserkovskaya R, Reinberg D.; ''Elongation by RNA polymerase II: the short and long of it.''; PubMed Europe PMC Scholia
  16. Pal M, McKean D, Luse DS.; ''Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence.''; PubMed Europe PMC Scholia
  17. Holstege FC, Fiedler U, Timmers HT.; ''Three transitions in the RNA polymerase II transcription complex during initiation.''; PubMed Europe PMC Scholia
  18. Kadonaga JT.; ''Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors.''; PubMed Europe PMC Scholia
  19. Dvir A, Tan S, Conaway JW, Conaway RC.; ''Promoter escape by RNA polymerase II. Formation of an escape-competent transcriptional intermediate is a prerequisite for exit of polymerase from the promoter.''; PubMed Europe PMC Scholia
  20. Jawdekar GW, Henry RW.; ''Transcriptional regulation of human small nuclear RNA genes.''; PubMed Europe PMC Scholia
  21. Tirode F, Busso D, Coin F, Egly JM.; ''Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7.''; PubMed Europe PMC Scholia
  22. Yoh SM, Cho H, Pickle L, Evans RM, Jones KA.; ''The Spt6 SH2 domain binds Ser2-P RNAPII to direct Iws1-dependent mRNA splicing and export.''; PubMed Europe PMC Scholia
  23. Wahle E, Rüegsegger U.; ''3'-End processing of pre-mRNA in eukaryotes.''; PubMed Europe PMC Scholia
  24. Van Arsdell SW, Weiner AM.; ''Human genes for U2 small nuclear RNA are tandemly repeated.''; PubMed Europe PMC Scholia
  25. Bertolotti A, Melot T, Acker J, Vigneron M, Delattre O, Tora L.; ''EWS, but not EWS-FLI-1, is associated with both TFIID and RNA polymerase II: interactions between two members of the TET family, EWS and hTAFII68, and subunits of TFIID and RNA polymerase II complexes.''; PubMed Europe PMC Scholia
  26. Duan DR, Pause A, Burgess WH, Aso T, Chen DY, Garrett KP, Conaway RC, Conaway JW, Linehan WM, Klausner RD.; ''Inhibition of transcription elongation by the VHL tumor suppressor protein.''; PubMed Europe PMC Scholia
  27. Maston GA, Evans SK, Green MR.; ''Transcriptional regulatory elements in the human genome.''; PubMed Europe PMC Scholia
  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

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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 complexComplexREACT_3092 (Reactome)
ADPMetaboliteCHEBI:16761 (ChEBI)
ALYREF ProteinQ86V81 (Uniprot-TrEMBL)
ATP MetaboliteCHEBI:15422 (ChEBI)
ATPMetaboliteCHEBI:15422 (ChEBI)
Aborted early elongation complexComplexREACT_3362 (Reactome)
Aborted elongation complex after arrestComplexREACT_6654 (Reactome)
Arrested processive elongation complexComplexREACT_4675 (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 complex		ComplexREACT_2332 (Reactome) Spt5 reacts with Guanyl Transferase (GT) of the capping enzyme (CE).
CF IIComplexREACT_3772 (Reactome)
CF IComplexREACT_4896 (Reactome)
CLP1 ProteinQ92989 (Uniprot-TrEMBL)
CPSF1 ProteinQ10570 (Uniprot-TrEMBL)
CPSF2 ProteinQ9P2I0 (Uniprot-TrEMBL)
CPSF3 ProteinQ9UKF6 (Uniprot-TrEMBL)
CPSF7 ProteinQ8N684 (Uniprot-TrEMBL)
CSTF1 ProteinQ05048 (Uniprot-TrEMBL)
CSTF2ProteinP33240 (Uniprot-TrEMBL)
CSTF3 ProteinQ12996 (Uniprot-TrEMBL)
CTDP1 ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTDP1ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTP MetaboliteCHEBI:17677 (ChEBI)
Cap Binding Complex ComplexREACT_3884 (Reactome)
Capped Intronless Histone pre-mRNA

CBC

ZFP100 Complex		ComplexREACT_5338 (Reactome)
Capped Intronless Histone pre-mRNA

CBP80 CBP20 SLBP

ZFP100 Complex		ComplexREACT_3667 (Reactome)
CstFComplexREACT_3503 (Reactome)
DHX38 ProteinQ92620 (Uniprot-TrEMBL)
DNA containing Pol II promoter with transcript with 2 or 3 nucleotidesREACT_3936 (Reactome)
DNA containing RNA Polymerase II promoterREACT_2835 (Reactome)
DSIF

NELF

early elongation complex		ComplexREACT_4575 (Reactome)
DSIF complexComplexREACT_2797 (Reactome)
ELL ProteinP55199 (Uniprot-TrEMBL)
ELLProteinP55199 (Uniprot-TrEMBL)
ERCC2 ProteinP18074 (Uniprot-TrEMBL)
ERCC3 ProteinP19447 (Uniprot-TrEMBL)
Early elongation complex with hyperphosphorylated Pol II CTDComplexREACT_2481 (Reactome)
Elongation complex prior to separationComplexREACT_5853 (Reactome)
Elongation complex with separated and uncleaved transcriptComplexREACT_5512 (Reactome)
Elongation complexComplexREACT_3511 (Reactome)
Elongin B C complexComplexREACT_2434 (Reactome)
Elongin ComplexComplexREACT_5616 (Reactome)
FACT complexComplexREACT_4314 (Reactome)
GTF2A1ProteinP52655 (Uniprot-TrEMBL)
GTF2A2 ProteinP52657 (Uniprot-TrEMBL)
GTF2B ProteinQ00403 (Uniprot-TrEMBL)
GTF2BProteinQ00403 (Uniprot-TrEMBL)
GTF2E1 ProteinP29083 (Uniprot-TrEMBL)
GTF2E2 ProteinP29084 (Uniprot-TrEMBL)
GTF2F1ProteinP35269 (Uniprot-TrEMBL)
GTF2F2ProteinP13984 (Uniprot-TrEMBL)
GTF2H1ProteinP32780 (Uniprot-TrEMBL)
GTF2H2 ProteinQ13888 (Uniprot-TrEMBL)
GTF2H3 ProteinQ13889 (Uniprot-TrEMBL)
GTF2H4 ProteinQ92759 (Uniprot-TrEMBL)
GTP MetaboliteCHEBI:15996 (ChEBI)
LSM10 ProteinQ969L4 (Uniprot-TrEMBL)
LSM11 ProteinP83369 (Uniprot-TrEMBL)
Ligated exon containing complexComplexREACT_5472 (Reactome)
MAGOH ProteinP61326 (Uniprot-TrEMBL)
MNAT1 ProteinP51948 (Uniprot-TrEMBL)
Mature Intronless transcript derived Histone mRNA

SLBP CBP80

CBP20		ComplexREACT_3802 (Reactome)
Mature intronless transcript derived Histone pre-mRNA CBC complexComplexREACT_5592 (Reactome)
NCBP1 ProteinQ09161 (Uniprot-TrEMBL)
NCBP2 ProteinP52298 (Uniprot-TrEMBL)
NELF complexComplexREACT_2737 (Reactome)
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)
NTPMetaboliteREACT_4491 (Reactome)
NUDT21 ProteinO43809 (Uniprot-TrEMBL)
P-TEFb complexComplexREACT_3433 (Reactome)
PABPN1 ProteinQ86U42 (Uniprot-TrEMBL)
PAPOLAProteinP51003 (Uniprot-TrEMBL)
PCF11 ProteinO94913 (Uniprot-TrEMBL)
POLR2A ProteinP24928 (Uniprot-TrEMBL)
POLR2B ProteinP30876 (Uniprot-TrEMBL)
POLR2C ProteinP19387 (Uniprot-TrEMBL)
POLR2DProteinO15514 (Uniprot-TrEMBL)
POLR2E ProteinP19388 (Uniprot-TrEMBL)
POLR2FProteinP61218 (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 complexComplexREACT_3066 (Reactome)
PiMetaboliteCHEBI:18367 (ChEBI)
Pol II Initiation complex with phosphodiester-PPi intermediateComplexREACT_2410 (Reactome)
Pol II Promoter Escape ComplexComplexREACT_3851 (Reactome)
Pol II initiation complexComplexREACT_5487 (Reactome)
Pol II transcription complex containing extruded transcript to +30ComplexREACT_4335 (Reactome)
Pol II transcription complex containing transcript to +30ComplexREACT_4399 (Reactome)
Pol II transcription complex with ComplexREACT_2595 (Reactome)
Processive elongation complexComplexREACT_3018 (Reactome)
RBM8A ProteinQ9Y5S9 (Uniprot-TrEMBL)
RNA Pol II ComplexREACT_4417 (Reactome)
RNA Pol II ComplexREACT_5658 (Reactome)
RNA Pol II with phosphorylated CTD CE complex with activated GTComplexREACT_3171 (Reactome)
RNA Pol II with phosphorylated CTD CE complexComplexREACT_2371 (Reactome)
RNA Polymerase II ComplexREACT_2692 (Reactome)
RNA Polymerase II holoenzyme complex ComplexREACT_4889 (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)
TAF4 ProteinO00268 (Uniprot-TrEMBL)
TAF4B ProteinQ92750 (Uniprot-TrEMBL)
TAF5 ProteinQ15542 (Uniprot-TrEMBL)
TAF6 ProteinP49848 (Uniprot-TrEMBL)
TAF9 ProteinQ16594 (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)
TFIIAComplexREACT_5743 (Reactome)
TFIIDComplexREACT_5886 (Reactome)
TFIIEComplexREACT_2368 (Reactome)
TFIIFComplexREACT_4708 (Reactome)
TFIIHComplexREACT_3832 (Reactome)
U2AF1 ProteinQ01081 (Uniprot-TrEMBL)
U2AF2 ProteinP26368 (Uniprot-TrEMBL)
U7 snRNP ZNF473ComplexREACT_5001 (Reactome)
UPF3B ProteinQ9BZI7 (Uniprot-TrEMBL)
UTP MetaboliteCHEBI:15713 (ChEBI)
ZNF473 ProteinQ8WTR7 (Uniprot-TrEMBL)
capped pre-mRNA

CBC

RNA Pol II 		ComplexREACT_3243 (Reactome)
damaged DNA substrate nascent mRNA hybridREACT_3022 (Reactome)
downstream intronless mRNA fragmentREACT_3064 (Reactome)
intronless pre-mRNA cleavage complexComplexREACT_3895 (Reactome)
mRNA 3'-end cleavage factorComplexREACT_2642 (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 closed pre-initiation complexComplexREACT_5734 (Reactome)
pol II open pre-initiation complexComplexREACT_4930 (Reactome)
pol II promoter

TFIID TFIIA TFIIB Pol II TFIIF

TFIIE complex		ComplexREACT_4404 (Reactome)
pol II promoter

TFIID TFIIA TFIIB Pol II

TFIIF complex		ComplexREACT_2469 (Reactome)
pol II promoter

TFIID TFIIA

TFIIB complex		ComplexREACT_2339 (Reactome)
pol II promoter TFIID complexComplexREACT_5906 (Reactome)
pol II transcription complex containing 11 nucleotide long transcriptComplexREACT_3183 (Reactome)
pol II transcription complex containing 3 Nucleotide long transcriptComplexREACT_3251 (Reactome)
pol II transcription complex containing 4 nucleotide long transcriptComplexREACT_4148 (Reactome)
pol II transcription complex containing 4-9 nucleotide long transcriptComplexREACT_3928 (Reactome)
pol II transcription complex containing 9 nucleotide long transcriptComplexREACT_5212 (Reactome)
pol II transcription complexComplexREACT_2954 (Reactome)
template DNA 4-9 nucleotide transcript hybridREACT_3607 (Reactome)
template DNA with first transcript dinucleotide, opened to +8 positionREACT_3318 (Reactome)
upstream mRNA fragment

CPSF PAP

PABPN1 complex		ComplexREACT_3436 (Reactome)

Annotated Interactions

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SourceTargetTypeDatabase referenceComment
3' end cleaved, ligated exon containing complexArrowREACT_1914 (Reactome)
ADPArrowREACT_1844 (Reactome)
ATPREACT_1844 (Reactome)
CCNT1REACT_307 (Reactome)
CCNT2REACT_307 (Reactome)
CDK9REACT_307 (Reactome)
CF IArrowREACT_1914 (Reactome)
CF IArrowREACT_460 (Reactome)
CF IIArrowREACT_1914 (Reactome)
CF IIArrowREACT_460 (Reactome)
CTDP1ArrowREACT_1138 (Reactome)
CTDP1REACT_1251 (Reactome)
Cap Binding Complex ArrowREACT_2066 (Reactome)
CstFArrowREACT_1914 (Reactome)
CstFArrowREACT_460 (Reactome)
DNA containing Pol II promoter with transcript with 2 or 3 nucleotidesArrowREACT_543 (Reactome)
DNA containing RNA Polymerase II promoterREACT_745 (Reactome)
DSIF

NELF

early elongation complex		ArrowREACT_981 (Reactome)
DSIF

NELF

early elongation complex		REACT_2066 (Reactome)
DSIF complexArrowREACT_1138 (Reactome)
DSIF complexREACT_802 (Reactome)
ELLArrowREACT_1138 (Reactome)
ELLREACT_949 (Reactome)
Early elongation complex with hyperphosphorylated Pol II CTDArrowREACT_2066 (Reactome)
Early elongation complex with hyperphosphorylated Pol II CTDREACT_949 (Reactome)
Elongation complex prior to separationArrowREACT_2053 (Reactome)
Elongation complexREACT_751 (Reactome)
Elongin B C complexREACT_51 (Reactome)
Elongin ComplexArrowREACT_1138 (Reactome)
Elongin ComplexREACT_949 (Reactome)
FACT complexArrowREACT_1138 (Reactome)
FACT complexREACT_949 (Reactome)
GTF2BArrowREACT_1817 (Reactome)
GTF2BArrowREACT_543 (Reactome)
GTF2BArrowREACT_653 (Reactome)
GTF2BREACT_266 (Reactome)
Mature Intronless transcript derived Histone mRNA

SLBP CBP80

CBP20		ArrowREACT_888 (Reactome)
Mature intronless transcript derived Histone pre-mRNA CBC complexArrowREACT_1222 (Reactome)
NELF complexArrowREACT_1138 (Reactome)
NELF complexREACT_981 (Reactome)
NELFAREACT_168 (Reactome)
NELFBREACT_168 (Reactome)
NELFCDREACT_168 (Reactome)
NELFEREACT_168 (Reactome)
NTPArrowREACT_1138 (Reactome)
NTPArrowREACT_2053 (Reactome)
NTPArrowREACT_981 (Reactome)
NTPREACT_1082 (Reactome)
NTPREACT_1160 (Reactome)
NTPREACT_1817 (Reactome)
NTPREACT_2053 (Reactome)
NTPREACT_209 (Reactome)
NTPREACT_40 (Reactome)
NTPREACT_581 (Reactome)
NTPREACT_751 (Reactome)
NTPREACT_981 (Reactome)
P-TEFb complexArrowREACT_1138 (Reactome)
P-TEFb complexREACT_2066 (Reactome)
PPiArrowREACT_1055 (Reactome)
PPiArrowREACT_1082 (Reactome)
PPiArrowREACT_1817 (Reactome)
PPiArrowREACT_209 (Reactome)
PPiArrowREACT_40 (Reactome)
PPiArrowREACT_581 (Reactome)
PiArrowREACT_1844 (Reactome)
Pol II transcription complex containing transcript to +30ArrowREACT_209 (Reactome)
Pol II transcription complex with REACT_2233 (Reactome)
Processive elongation complexArrowREACT_751 (Reactome)
Processive elongation complexREACT_2053 (Reactome)
REACT_1055 (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'.

REACT_1082 (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.
REACT_1094 (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).
REACT_1138 (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'.

REACT_1160 (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'.

REACT_1185 (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.
REACT_1222 (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.
REACT_1251 (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).
REACT_1467 (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'.

REACT_1567 (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'.

REACT_1635 (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'.

REACT_1638 (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).
REACT_1645 (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).
REACT_1684 (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.
REACT_168 (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'.

REACT_1702 (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'.

REACT_1793 (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'.

REACT_1817 (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.
REACT_1821 (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.
REACT_1844 (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

REACT_1914 (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.

REACT_2030 (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'.

REACT_2053 (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'.

REACT_2066 (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.

REACT_209 (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.
REACT_2233 (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'.

REACT_234 (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).
REACT_266 (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.

REACT_294 (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'.

REACT_307 (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'.

REACT_40 (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.

REACT_423 (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.
REACT_460 (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.
REACT_51 (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'.

REACT_543 (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'.

REACT_581 (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.

REACT_632 (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.
REACT_6355 (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'.

REACT_653 (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'.

REACT_745 (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.

REACT_751 (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.

REACT_802 (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.
REACT_888 (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.
REACT_893 (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'.

REACT_936 (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'.

REACT_949 (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'.

REACT_981 (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.
REACT_989 (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 ).
RNA Pol II ArrowREACT_1251 (Reactome)
RNA Pol II REACT_802 (Reactome)
RNA Pol II REACT_981 (Reactome)
RNA Pol II with phosphorylated CTD CE complex with activated GTREACT_423 (Reactome)
RNA Polymerase II ArrowREACT_1793 (Reactome)
RNA Polymerase II ArrowREACT_543 (Reactome)
RNA Polymerase II ArrowREACT_653 (Reactome)
RNA Polymerase II REACT_1082 (Reactome)
RNA Polymerase II REACT_1684 (Reactome)
RNA Polymerase II REACT_1817 (Reactome)
RNA Polymerase II REACT_209 (Reactome)
RNA Polymerase II REACT_40 (Reactome)
RNA Polymerase II REACT_581 (Reactome)
RNA Polymerase II holoenzyme complex ArrowREACT_1138 (Reactome)
RNGTTREACT_2233 (Reactome)
RNMTREACT_423 (Reactome)
SSRP1REACT_294 (Reactome)
SUPT16HREACT_294 (Reactome)
SUPT4H1REACT_1635 (Reactome)
TCEA1ArrowREACT_1138 (Reactome)
TCEA1REACT_949 (Reactome)
TCEB1REACT_936 (Reactome)
TCEB2REACT_936 (Reactome)
TCEB3REACT_51 (Reactome)
TFIIAArrowREACT_543 (Reactome)
TFIIAArrowREACT_581 (Reactome)
TFIIAArrowREACT_653 (Reactome)
TFIIAREACT_266 (Reactome)
TFIIDArrowREACT_543 (Reactome)
TFIIDArrowREACT_581 (Reactome)
TFIIDArrowREACT_653 (Reactome)
TFIIDREACT_745 (Reactome)
TFIIEArrowREACT_1793 (Reactome)
TFIIEArrowREACT_543 (Reactome)
TFIIEArrowREACT_581 (Reactome)
TFIIEArrowREACT_653 (Reactome)
TFIIEREACT_1821 (Reactome)
TFIIFArrowREACT_1138 (Reactome)
TFIIHArrowREACT_1251 (Reactome)
TFIIHArrowREACT_1793 (Reactome)
TFIIHArrowREACT_543 (Reactome)
TFIIHArrowREACT_653 (Reactome)
TFIIHArrowREACT_751 (Reactome)
TFIIHREACT_1185 (Reactome)
TFIIHREACT_1251 (Reactome)
TFIIHREACT_1817 (Reactome)
TFIIHREACT_1844 (Reactome)
TFIIHREACT_40 (Reactome)
TFIIHREACT_632 (Reactome)
TFIIHREACT_949 (Reactome)
U7 snRNP ZNF473ArrowREACT_1222 (Reactome)
U7 snRNP ZNF473ArrowREACT_888 (Reactome)
capped pre-mRNA

CBC

RNA Pol II 		REACT_1251 (Reactome)
damaged DNA substrate nascent mRNA hybridArrowREACT_1138 (Reactome)
downstream intronless mRNA fragmentArrowREACT_460 (Reactome)
mRNA 3'-end cleavage factorREACT_1914 (Reactome)
p-SUPT5HREACT_1635 (Reactome)
p-SUPT5HREACT_423 (Reactome)
pol II closed pre-initiation complexREACT_1844 (Reactome)
pol II open pre-initiation complexArrowREACT_1844 (Reactome)
pol II open pre-initiation complexREACT_1160 (Reactome)
pol II promoter

TFIID TFIIA TFIIB Pol II TFIIF

TFIIE complex		REACT_632 (Reactome)
pol II promoter

TFIID TFIIA TFIIB Pol II

TFIIF complex		REACT_1821 (Reactome)
pol II promoter

TFIID TFIIA

TFIIB complex		REACT_1684 (Reactome)
pol II promoter TFIID complexREACT_266 (Reactome)
pol II transcription complex containing 11 nucleotide long transcriptArrowREACT_1082 (Reactome)
pol II transcription complex containing 11 nucleotide long transcriptREACT_209 (Reactome)
pol II transcription complex containing 3 Nucleotide long transcriptArrowREACT_40 (Reactome)
pol II transcription complex containing 3 Nucleotide long transcriptREACT_1817 (Reactome)
pol II transcription complex containing 4 nucleotide long transcriptArrowREACT_1817 (Reactome)
pol II transcription complex containing 4 nucleotide long transcriptREACT_581 (Reactome)
pol II transcription complex containing 9 nucleotide long transcriptArrowREACT_581 (Reactome)
pol II transcription complex containing 9 nucleotide long transcriptREACT_1082 (Reactome)
pol II transcription complexArrowREACT_1055 (Reactome)
pol II transcription complexREACT_40 (Reactome)
template DNA 4-9 nucleotide transcript hybridArrowREACT_1793 (Reactome)
template DNA with first transcript dinucleotide, opened to +8 positionArrowREACT_653 (Reactome)
upstream mRNA fragment

CPSF PAP

PABPN1 complex		ArrowREACT_460 (Reactome)
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