RNA Polymerase II Transcription (Homo sapiens)

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8, 1610183, 2042420, 221843, 12, 23, 242, 7, 11, 14, 15, 17...20, 22182, 1918223, 9, 13, 202pol II promoterTFIID complex Elongin Complex RNA Polymerase II holoenzyme complex RNA Polymerase II TFIID Elongin BC complex CPSF TFIIE TFIID capped intronless pre-mRNACBC complex DSIF complex TFIIH Ligated exon containing complex TFIIE P-TEFb complex RNA Polymerase II holoenzyme complex capped pre-mRNACBCRNA Pol II CF I TFIIH RNA Pol II RNA polymerase II Elongation complex prior to separation FACT complex RNA Polymerase II CstFCPSFcapped intronless pre-mRNACBC complex TFIIH TFIIH RNA Polymerase II holoenzyme complex TFIIH Cap Binding Complex CstF RNA Polymerase II holoenzyme complex NELF complex DSIF complex RNA Polymerase II holoenzyme complex FACT complex U7 snRNP-specific Sm core complex CstF RNA Polymerase II Elongin Complex TFIIE Elongin BC complex NTP RNA Polymerase II holoenzyme complex pol II promoterTFIID complex CPSF RNA Polymerase II holoenzyme complex RNA Polymerase II pol II transcription complex containing 11 nucleotide long transcript TFIIF TFIIF pol II promoterTFIIDTFIIATFIIB complex RNA Polymerase II holoenzyme complex RNA polymerase II Elongin BC complex FACT complex RNA Polymerase II holoenzyme complex pol II promoterTFIIDTFIIATFIIBPol IITFIIF complex RNA Polymerase II holoenzyme complex Arrested processive elongation complex DSIFNELFearly elongation complex pol II transcription complex pre-EJC complex TFIIE CAK pol II promoterTFIIDTFIIATFIIBPol IITFIIFTFIIE complex TFIIH Cap Binding Complex P-TEFb complex CF II NTP RNA Polymerase II holoenzyme complex upstream mRNA fragmentCPSFPAPPABPN1 complex Elongin BC complex Elongin BC complex TFIID TFIIE FACT complex RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex FACT complex CAK CAK TFIIH TFIIH TFIIH DSIF complex Cap Binding Complex TFIIE RNA Polymerase II holoenzyme complex CAK pol II promoterTFIIDTFIIATFIIB complex TFIIH RNA Polymearse IINTPTFIIF complex TFIID Cap Binding Complex RNA Polymerase II RNA Polymerase II holoenzyme complex CAK CAK Elongation complex Elongation complex with separated and uncleaved transcript CAK pol II promoterTFIIDTFIIATFIIBPol IITFIIF complex CAK FACT complex TFIIF CPSF TFIIF Cleavage and Polyadenylation Complex RNA Polymerase II NELF complex Cap Binding Complex EJC complex CAK RNA Polymerase II holoenzyme complex TFIIF TFIID pol II promoterTFIID complex NELF complex RNA Pol II CstF RNA Polymerase II holoenzyme complex TFIIE CAK RNA Polymerase II TFIIF RNA Polymerase II holoenzyme complex P-TEFb complex Elongin BC complex RNA Pol II DSIF complex Capped Intronless Histone pre-mRNACBC complex RNA Polymerase II RNA Polymerase II pol II transcription complex containing 4 nucleotide long transcript P-TEFb complex TFIIH TFIIF TFIIA RNA Polymerase II TFIIF TFIIF RNA Polymerase II holoenzyme complex DSIF complex TFIIH Elongin Complex Paused processive elongation complex RNA Polymerase II TFIIF Elongin BC complex NELF complex TFIIF RNA polymerase II DSIF complex Pol II transcription complex containing extruded transcript to +30 TFIIF RNA Polymerase II TFIIF DSIF complex TFIIH NELF complex TFIIH TFIIH TFIIA Mature intronless transcript derived Histone pre-mRNACBC complex TFIIF Cap Binding Complex U7 snRNP-specific Sm core complex RNA Polymerase II holoenzyme complex CF I DSIF complex TFIIA RNA Pol II with phosphorylated CTD CE complex with activated GT pol II promoterTFIIDTFIIATFIIB complex pol II transcription complex containing 4-9 nucleotide long transcript TFIIF Elongin Complex RNA Polymerase II DSIF complex pre-EJC complex TFIID Cap Binding Complex Cap Binding Complex Magoh-Y14 complex pol II transcription complex containing 3 Nucleotide long transcript RNA Polymerase II holoenzyme complex TFIIF NELF complex TFIIH TFIIF pol II open pre-initiation complex DSIF complex TFIIA TFIIH TFIID Capped Intronless Histone pre-mRNACBP80CBP20SLBP RNA Polymerase II holoenzyme complex TFIIF Cap Binding Complex TFIIA RNA Polymerase II holoenzyme complex Elongin BC complex TFIIH intronless pre-mRNA cleavage complex TFIIF CPSFcapped intronless pre-mRNACBC complex U7 snRNP-specific Sm core complex Elongin Complex TFIIF TFIIH RNA Polymerase II TFIID pol II promoterTFIID complex FACT complex RNA Pol II TFIIA RNA Polymerase II CAK TFIIA TFIIE NTP TFIIA TFIIE RNA Polymerase II holoenzyme complex TFIIE RNA Polymerase II holoenzyme complex Magoh-Y14 complex TFIIF TFIIA TFIIF Elongin Complex CF I Cap Binding Complex CAK CAK TFIIH RNA Polymerase II Aborted early elongation complex RNA Pol II with phosphorylated CTD CE complex RNA Polymerase II holoenzyme complex CAK RNA Polymerase II holoenzyme complex Pol II transcription complex containing transcript to +30 FACT complex RNA Polymerase II holoenzyme complex NELF complex RNA Polymerase II holoenzyme complex RNA Polymerase II holoenzyme complex TFIIH Pol II Initiation complex with phosphodiester-PPi intermediate P-TEFb complex CPSF NTP TFIIH nucleoplasmpol II closed pre-initiation complex CAK Early elongation complex with hyperphosphorylated Pol II CTD CF I TFIIF CAK TFIID DSIF complex RNA Pol II RNA Polymerase II holoenzyme complex NELF complex RNA Polymerase II holoenzyme complex CF II P-TEFb complex RNA Polymerase II holoenzyme complex CAK NELF complex pol II promoterTFIIDTFIIATFIIB complex RNA polymerase II TFIIF NELF complex RNA Pol II pol II transcription complex containing 9 nucleotide long transcript TFIID TFIID mRNA 3'-end cleavage factor CAK TFIIE P-TEFb complex TFIIA TFIIA Processive elongation complex Aborted elongation complex after arrest TFIIA TFIID TFIIF TFIIF RNA Polymerase II holoenzyme complex Early elongation complex with hyperphosphorylated Pol II CTD pol II promoterTFIID complex P-TEFb complex RNA Polymerase II holoenzyme complex CF II TFIIF CAK pol II promoterTFIIDTFIIATFIIBPol IITFIIF complex Elongin BC complex NELF complex TFIIE TFIIF TFIIF U7 snRNPZNF473 U7 snRNPZNF473 TFIIF Pol II initiation complex CAK TFIIF TFIIF Cap Binding Complex NTP RNA polymerase II RNA Polymerase II holoenzyme complex CEPol II CTDSpt5 complex TFIIF CAK RNA Polymerase II holoenzyme complex Capped Intronless Histone pre-mRNACBC complex U7 snRNPZNF473 TFIID TFIIA Elongin Complex TFIIF RNA Polymerase II RNA Pol II 3' end cleaved, ligated exon containing complex Pol II Promoter Escape Complex RNA Polymerase II holoenzyme complex EJC complex TFIID Capped Intronless Histone pre-mRNACBCZFP100 Complex RNA Polymerase II holoenzyme complex CAK CAK DSIF complex TFIIH Elongin Complex P-TEFb complex CF II Mature Intronless transcript derived Histone mRNASLBPCBP80CBP20 Capped Intronless Histone pre-mRNACBP80CBP20SLBPZFP100 Complex Pol II transcription complex with RNA Polymerase II holoenzyme complex SNRPB TAF4 ATP POLR2K Elongation complex prior to separationPOLR2C POLR2J CDK7 GTF2H3 GTF2F2NELFCD POLR2G GTF2H3 U2AF1 GTF2F1pol II open pre-initiation complexTCEB1 GTF2F2GTF2F2POLR2G TAF4B NCBP2 CSTF2POLR2H TAF4B CDK7 MNAT1 GTF2E1 CCNH MNAT1 SUPT16H GTF2H3 SNRPG p-S2,S5-POLR2A POLR2FPOLR2G POLR2B p-SUPT5H CSTF3 GTF2H4 NELFAERCC3 CPSF2 PiCCNH RNMTELL CCNH POLR2I POLR2J CCNH POLR2A GTF2E2 TCEB1 CCNT1 CTP POLR2H POLR2G SUPT4H1 GTF2H2 ERCC3 CPSF7 NTPGTF2F1NELFE GTF2H2 POLR2A POLR2G p-S5-POLR2A ERCC2 POLR2J CSTF3 POLR2I CPSF7 POLR2I TAF13 CDC40 CTDP1 CCNT1GTF2F2NELFETCEB2 CCNH POLR2DPOLR2DMNAT1 ERCC3 GTF2B TAF12 POLR2DNCBP2 ERCC3 POLR2B POLR2H ELL SRRM1 POLR2DSRSF5 TAF5 TAF6 Pol II transcription complex containing transcript to +30SNRPG GTF2B POLR2B POLR2E POLR2K GTF2A1pol II promoterTFIID complexGTF2H1GTF2E1 ERCC3 POLR2I POLR2G GTF2B TCEB2 POLR2L GTF2E2 GTF2F2TAF9 Capped Intronless Histone pre-mRNACBCZFP100 ComplexCF IIGTF2F2Cap Binding Complex TAF6 POLR2FPOLR2I CCNT2 POLR2J SSRP1POLR2DATP CTP GTF2A2 CSTF1 POLR2G POLR2C POLR2H NELFB GTF2F2TBP SUPT4H1 CDK9 GTF2F1DNA containing Pol II promoter with transcript with 2 or 3 nucleotidesCTDP1 GTF2F1TBP CPSF7 POLR2FCTDP1 NTPPOLR2J GTF2H2 GTF2F2ERCC2 POLR2G GTF2A1GTF2F1SSRP1 CCNT1 POLR2L GTF2F2MNAT1 POLR2A TCEB3 ERCC2 POLR2B POLR2FPAPOLAPOLR2L POLR2E NELFCD GTF2E2 TCEB1 GTP Paused processive elongation complexPOLR2G TAF12 POLR2J POLR2K CDK7 SUPT4H1POLR2I GTF2A1TAF4 GTF2H1POLR2C SRSF3 POLR2K TAF13 TCEB2 TAF9 PAPOLAPOLR2L POLR2L POLR2C POLR2B ERCC3 TFIIDPOLR2I POLR2DPOLR2I GTF2H3 GTF2H2 TFIIHGTF2E1 POLR2K TAF11 pol II transcription complex containing 4-9 nucleotide long transcriptPOLR2C CPSF7 MAGOH POLR2G POLR2C GTF2H1TAF4B UTP GTF2H1TAF1 GTF2F1POLR2G GTF2B POLR2L GTF2E1 p-SUPT5H POLR2B POLR2DTAF4 POLR2K GTF2A1pol II closed pre-initiation complexTAF12 p-S2,S5-POLR2A TAF10 TCEA1 GTF2H2 POLR2C POLR2L TAF1 ATPTAF10 CTDP1 NTPTAF4B POLR2E pol II transcription complex containing 9 nucleotide long transcriptCDK7 TAF1 GTP POLR2K NCBP1 POLR2L damaged DNA substratenascent mRNA hybridPOLR2FCCNH p-SUPT5H pol II transcription complex containing 3 Nucleotide long transcriptCSTF2GTF2A1ERCC2 ELL POLR2H TCEA1 POLR2H TAF10 MAGOH NELFAPOLR2A POLR2G POLR2E TAF13 NELFBCCNT1 ERCC3 POLR2H POLR2L TAF5 POLR2L CPSF2 POLR2J CDK9 POLR2L POLR2J TAF4 GTF2F1TCEA1 POLR2J TCEB3POLR2FNTPPOLR2E POLR2E GTF2F2POLR2H POLR2A PCF11 POLR2J NTPPABPN1 CCNH GTF2H4 GTF2F2TCEB2POLR2A GTF2A2 TFIIFProcessive elongation complexGTF2F1POLR2I CLP1 POLR2J POLR2H SRSF2 POLR2H GTF2H3 TAF1 POLR2K CCNT2 POLR2G NCBP2 p-S2,S5-POLR2A GTF2A2 GTF2F1MNAT1 POLR2E GTF2H2 POLR2DCTDP1 CCNH GTF2H3 POLR2G TCEB1 TAF11 CCNH TCEB2 RNA Pol II POLR2C POLR2I POLR2L POLR2FElongin BC complexTAF10 NUDT21 GTF2H3 GTF2A1CSTF1 GTF2H4 POLR2G GTF2H3 GTF2H3 MNAT1 GTF2B POLR2DTAF1 pol II transcription complex containing 11 nucleotide long transcriptTAF11 POLR2B capped pre-mRNACBCRNA Pol II SNRPD3 Aborted early elongation complexSUPT16H CCNT1 upstream mRNA fragmentCPSFPAPPABPN1 complexNELFCD GTF2A1POLR2J SNRPE p-S5-POLR2A CCNT1 SSRP1 POLR2G TFIIAPOLR2DPOLR2L ERCC2 SLBP POLR2G POLR2K GTF2F2POLR2L POLR2I POLR2B GTF2F1GTF2F2DSIFNELFearly elongation complexNELFE TCEA1 SRSF7 GTF2E1 NCBP2 TAF6 POLR2A POLR2FPCF11 CDK7 SSRP1 TAF11 POLR2J NTPPOLR2B CDK7 TAF4 POLR2L POLR2A CDK7 GTF2F1POLR2I TAF4B RBM8A TCEB1 ERCC3 NELFE NELFB CTDP1 PPiTAF4B TAF13 p-SUPT5H PPiGTF2A1GTF2H1RNA Polymerase II POLR2C TBP CDK7 SSRP1 POLR2I CDK7 UTP NELFCD CPSF1 POLR2DPOLR2K POLR2FPOLR2K Elongation complexTAF11 CLP1 NELFCD POLR2B CCNT1 GTF2E1 SRSF1 POLR2DSRSF4 GTF2E1 TAF6 POLR2B GTF2H4 POLR2I NELF complexPOLR2C POLR2FGTF2H4 SUPT4H1 POLR2L NCBP1 TCEA1TCEB3 NELFATAF6 TAF1 TAF5 NELFB POLR2FPABPN1 template DNA4-9 nucleotide transcript hybridPOLR2FSUPT16H GTF2H2 CTDP1 POLR2B CstFSUPT4H1 GTF2H2 POLR2DPOLR2DPOLR2H NELFE PAPOLATAF6 TAF11 POLR2B NELFAPOLR2E TAF13 TAF1 NELFB GTF2F2POLR2FCCNH TBP pol II transcription complexTAF4B TAF11 POLR2J SNRPB POLR2K POLR2C POLR2I SUPT4H1 POLR2J CCNH CPSF1 TAF4 p-S2,S5-POLR2A CCNH GTF2A1TFIIHpol II transcription complex containing 4 nucleotide long transcriptCPSF2 POLR2C TAF9 GTF2F2POLR2B p-SUPT5H POLR2E GTF2F1GTF2H4 NCBP2 GTF2A1ERCC3 CCNH DNA containing RNA Polymerase II promoterSNRPD3 CTDP1 RBM8A GTF2H3 ERCC2 PPiTAF10 GTF2F2GTF2H2 p-S5-POLR2A POLR2H POLR2H GTF2F1POLR2DPOLR2H GTF2A2 POLR2K NELFB PAPOLAPOLR2B ERCC3 CDK7 POLR2H POLR2C POLR2C NELFE POLR2J DHX38 GTF2A1NCBP1 SSRP1 POLR2C POLR2E LSM11 GTF2A1POLR2DGTF2A1POLR2H GTF2A2 POLR2H Pol II transcription complex with GTF2E2 TAF13 MNAT1 TAF4 UPF3B GTF2A1TAF11 CPSF1 POLR2H p-SUPT5H POLR2C UTP ALYREF GTF2F1CSTF1 p-SUPT5H POLR2I POLR2C POLR2B RNGTT GTF2A1POLR2I GTF2F1GTF2H1CCNH ATP POLR2B GTF2E1 GTF2H1SRSF1 NCBP1 SLBP NFX.1 NELFCD Mature intronless transcript derived Histone pre-mRNACBC complexGTF2H1CCNH POLR2J MNAT1 ERCC3 POLR2J TAF4B CLP1 P-TEFb complexPOLR2DRNGTT TAF10 TAF11 POLR2L POLR2J POLR2B POLR2E CCNT2 POLR2H TAF13 GTF2H2 TFIIDELLTBP GTF2A2 NFX.1 SNRPE GTF2A2 TAF6 CCNH SUPT16H SRSF2 TAF1 POLR2DTAF12 TAF4B POLR2L SRSF11 POLR2G GTF2F1POLR2E GTF2F1POLR2I NCBP2 TBP ERCC2 POLR2K POLR2FGTF2F2NCBP2 NTPPOLR2H TCEB2 GTF2F1POLR2K POLR2L ERCC3 GTF2A1POLR2B POLR2G POLR2E GTF2A1TAF6 NELFATAF1 p-SUPT5HGTF2H2 SRSF6 TAF4B CCNT2 Elongation complex with separated and uncleaved transcriptPOLR2L GTF2F2POLR2A LSM11 TAF11 POLR2DPOLR2B POLR2H ERCC2 GTF2H3 GTF2H3 Pol II Promoter Escape ComplexTAF9 POLR2FGTF2F2TAF10 POLR2FTAF10 TCEB1 RNGTT TAF11 GTF2F2SUPT16H TFIIHGTF2F2DSIF complexNCBP2 NELFAPOLR2C PABPN1 GTF2H4 p-SUPT5H ZNF473 MNAT1 CDK9 CPSF3 SRSF3 GTF2H2 NCBP2 CCNH ERCC3 ERCC2 POLR2C TAF12 POLR2DTAF10 POLR2H TCEA1 p-S5-POLR2A POLR2G GTF2E1 POLR2I CDK9 Pol II initiation complexGTF2A2 POLR2H TAF9 TAF6 CDC40 GTF2E1 TBP GTF2H4 POLR2L POLR2K NELFB ELL POLR2I CCNH MNAT1 TAF12 TAF10 ERCC2 POLR2I NCBP1 GTF2E2 GTF2H4 U2AF2 PPiRNA Pol II with phosphorylated CTD CE complex with activated GTPOLR2I POLR2FPOLR2G GTF2H1PPiNELFE CDK9 SUPT4H1 GTF2H4 GTF2B POLR2B NELFE POLR2L TAF13 POLR2I NELFCD CSTF3 GTF2H2 POLR2G POLR2B POLR2J ERCC2 NELFANUDT21 GTF2A1POLR2J POLR2E NCBP1 Elongin ComplexGTF2BPOLR2L NCBP1 TBP GTF2H3 CPSF3 POLR2B POLR2C POLR2L POLR2I GTF2A2 GTF2H4 GTF2F1TAF5 SRSF7 SUPT4H1 TCEB2 ERCC2 TAF10 TBP Arrested processive elongation complexGTF2F2Mature Intronless transcript derived Histone mRNASLBPCBP80CBP20POLR2E POLR2B POLR2B PABPN1 SUPT4H1 p-SUPT5H GTF2F1GTF2H4 SRSF6 TCEB1 GTF2H1SNRPE TFIIHNELFB POLR2B NCBP2 Early elongation complex with hyperphosphorylated Pol II CTDPOLR2C POLR2H CTDP1 GTF2A2 GTF2F2GTF2H3 ELL POLR2A MNAT1 ERCC3 template DNA with first transcript dinucleotide, opened to +8 positionTAF12 POLR2I SSRP1 p-S5-POLR2A TAF11 POLR2B POLR2E GTF2H2 TAF1 CPSF3 CCNT2 POLR2G CCNT2TCEB2 TBP GTF2A1POLR2FCEPol II CTDSpt5 complexGTF2H3 CDK7 NELFB NELFE CCNH mRNA 3'-end cleavage factorPOLR2C MNAT1 POLR2E POLR2C MNAT1 TCEB2 MNAT1 ERCC2 POLR2K POLR2FUTP GTF2H1SRSF9 POLR2G SNRPF POLR2K GTF2H4 POLR2FGTF2E1 TAF6 TAF11 TAF12 p-S2,S5-POLR2A ERCC2 intronless pre-mRNA cleavage complexTCEB3 NELFAPOLR2H CDK7 POLR2L TAF9 SUPT16H GTF2H3 POLR2J GTF2H2 p-S2,S5-POLR2A TAF12 GTF2F1POLR2C TAF9 NELFE POLR2G p-SUPT5H GTP ERCC2 GTF2F1GTF2F1POLR2DPOLR2FPOLR2H CDK9 CDK7 TCEB1 p-SUPT5H POLR2J ERCC3 TAF4 UPF3B NCBP1 POLR2E TAF10 NTPTAF6 ERCC2 CCNT2 GTF2A1POLR2FGTF2H4 POLR2H TAF12 MNAT1 SUPT4H1 POLR2E GTF2F2NELFCD POLR2L GTF2H2 SSRP1 GTF2F2CF INCBP1 3' end cleaved, ligated exon containing complexPOLR2K LSM11 POLR2J TAF4 GTF2H2 GTF2A1POLR2FPOLR2J GTF2A1p-SUPT5H POLR2E GTF2H3 POLR2K POLR2DPOLR2K SUPT4H1 U7 snRNPZNF473NELFE GTF2H4 GTF2H4 NCBP1 TAF13 GTF2F1CDK9 POLR2I ATP pol II promoterTFIIDTFIIATFIIBPol IITFIIFTFIIE complexTAF9 GTF2B POLR2G GTF2A1GTF2F1CTP POLR2A TCEB2 NCBP2 CCNT1 CDK9NELFB POLR2H POLR2E TAF4B TCEB3 FACT complexPOLR2A NCBP2 TAF5 NCBP1 NCBP2 GTF2H3 POLR2C GTF2F1TCEB3 LSM10 Aborted elongation complex after arrestPOLR2H POLR2G ERCC3 TAF5 POLR2G POLR2G GTF2A2 SUPT16HPOLR2DGTF2H4 TAF5 TAF12 POLR2E TAF1 ERCC2 TAF13 POLR2I p-S2,S5-POLR2A POLR2FTAF10 GTF2H4 SUPT16H GTP GTF2H3 POLR2C TAF13 POLR2E TAF10 NCBP1 CDK9 POLR2DERCC3 MNAT1 GTF2E2 CDK7 p-S2,S5-POLR2A TAF9 CDK7 TAF4B CCNH downstream intronless mRNA fragmentERCC2 POLR2K GTF2F2CTDP1 NCBP2 GTF2F2Pol II Initiation complex with phosphodiester-PPi intermediatePOLR2FRNA Pol II with phosphorylated CTD CE complexGTF2H2 POLR2FSRSF9 TAF9 POLR2E TCEB3 POLR2L GTF2H2 NTPCLP1 UTP TAF6 ERCC2 GTF2H4 POLR2K DHX38 GTF2H2 POLR2A GTF2H4 POLR2K GTF2BGTF2H1POLR2B CCNT1 CPSF2 pol II promoterTFIIDTFIIATFIIB complexPOLR2K GTF2F1MNAT1 GTF2H2 TBP POLR2B ZNF473 RNPS1 CDK7 POLR2H NELFANELFATAF4B POLR2I POLR2H CTP TAF12 ELL GTF2H1GTF2H1POLR2E GTF2E2 GTF2E2 SUPT16H POLR2C GTF2F1CCNT1 CPSF3 ERCC3 POLR2C NTPU2AF1 POLR2E SRSF5 GTF2E2 TAF11 ELL POLR2I GTF2A1TBP GTF2F2TAF9 POLR2J Capped Intronless Histone pre-mRNACBP80CBP20SLBPZFP100 ComplexERCC3 POLR2DPOLR2I POLR2I MNAT1 POLR2J POLR2J POLR2J GTF2H1TAF4 TCEB1 POLR2J CDK7 POLR2C ERCC2 GTF2H2 CTDP1 POLR2DPOLR2H CDK7 NCBP1 GTF2F1TBP SNRPF ERCC3 TFIIATAF12 POLR2DTAF12 TAF5 POLR2K POLR2L GTF2H3 RNPS1 POLR2L ERCC3 NELFCD MNAT1 SRRM1 POLR2E CCNT2 RNMT TAF4B POLR2DPOLR2K RNA Pol II TCEA1 SNRPD3 SNRPF POLR2K TAF1 TAF6 NELFCD PCF11 GTF2E1 GTF2H1GTF2F1POLR2DPOLR2G TCEB1POLR2A TAF4 POLR2K SUPT4H1 POLR2K ERCC2 CDK7 POLR2C POLR2J NELFANELFB TAF4 GTF2H2 GTF2A2 GTP GTF2F2CDK7 CSTF2ERCC2 Pol II transcription complex containing extruded transcript to +30TCEB3 TAF13 LSM10 ERCC2 TBP GTF2H3 POLR2K GTF2F2POLR2G POLR2E NELFE ERCC3 GTF2H1POLR2L MNAT1 GTF2H1POLR2C GTF2H1POLR2I GTF2F1p-S5-POLR2A TAF13 POLR2E POLR2K GTF2B ALYREF NUDT21 p-SUPT5H POLR2A GTF2A1SNRPB RNGTTTAF5 POLR2DTAF9 POLR2L MNAT1 CDK7 GTF2H1GTF2B SRSF11 POLR2L TFIIHNELFB POLR2DPOLR2FTAF1 p-S2,S5-POLR2A TAF4 CTDP1 NELFAPOLR2I GTF2E2 POLR2G SSRP1 CDK7 GTF2F2TAF5 SNRPG SRSF4 GTF2H3 POLR2E GTF2H1POLR2C p-S5-POLR2A Ligated exon containing complexGTF2H3 POLR2K CTDP1POLR2E GTF2E2 NUDT21 CPSF1 POLR2Fp-S5-POLR2A ZNF473 POLR2J GTF2F1NELFCD TAF5 TAF5 ATP POLR2G POLR2DCCNH POLR2FCDK9 POLR2K POLR2FPOLR2G TAF4 POLR2C NELFCDPOLR2DPOLR2E GTF2F1POLR2J GTF2H4 CTP GTF2H1POLR2FPOLR2E p-S5-POLR2A NCBP1 TAF9 TCEA1 POLR2B POLR2FERCC3 POLR2B GTF2E2 POLR2A TAF13 POLR2I GTF2H4 TCEB3 MNAT1 POLR2B POLR2E GTF2F2TAF6 TAF9 POLR2FRNA Polymerase II holoenzyme complex MNAT1 NTPPOLR2C POLR2J CCNH POLR2DGTF2A2 GTF2B GTF2F2TFIIEPOLR2FGTF2H1GTF2F1SUPT4H1 TAF5 POLR2L pol II promoterTFIIDTFIIATFIIBPol IITFIIF complexPOLR2B ADPTAF5 GTF2H4 CCNT2 LSM10 POLR2H GTF2A1PCF11 POLR2H CCNT2 TAF1 CCNH CDK7 POLR2L TFIIEPPiPOLR2B U2AF2 GTF2F2651


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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)
CTDP1mim-catalysisREACT_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)
P-TEFb complexmim-catalysisREACT_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_1684 (Reactome)
RNA Polymerase II holoenzyme complex ArrowREACT_1138 (Reactome)
RNA Polymerase II mim-catalysisREACT_1082 (Reactome)
RNA Polymerase II mim-catalysisREACT_1817 (Reactome)
RNA Polymerase II mim-catalysisREACT_209 (Reactome)
RNA Polymerase II mim-catalysisREACT_40 (Reactome)
RNA Polymerase II mim-catalysisREACT_581 (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_1251 (Reactome)
TFIIHREACT_632 (Reactome)
TFIIHREACT_949 (Reactome)
TFIIHmim-catalysisREACT_1185 (Reactome)
TFIIHmim-catalysisREACT_1817 (Reactome)
TFIIHmim-catalysisREACT_1844 (Reactome)
TFIIHmim-catalysisREACT_40 (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 factormim-catalysisREACT_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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