RNA Polymerase II Transcription (Homo sapiens)

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4115, 19, 27, 28, 40...35693519, 639, 653531, 7312, 50, 5744, 4819, 49, 64, 7014, 20, 56, 818, 614067, 70, 76, 80142914401419, 632919404039193191414301419, 701437, 474114714116, 4012, 50, 57nucleoplasmTCEB1 SUPT16H POLR2E GTF2E2 polIIpromoter:TFIID:TFIIA:TFIIB complexPOLR2J CTDP1 GTF2A1(1-274) TAF4B ERCC3 TAF12 TAF5 Pol II PromoterEscape ComplexPOLR2G ATP NELFA ELL MLLT3 CTR9 RNAPolII(hypophosphorylated) complex bound to DSIF proteinGTF2H5 POLR2G CSTF3 POLR2J POLR2J TBP TAF2 NELFB MNAT1 ERCC3 UTP SNRPE TAF5 POLR2I POLR2F POLR2B GTF2F2 template DNA:9 nucleotide transcript hybrid TAF9 TAF6 template:capped transcript hybrid TAF9 GTF2H2 TAF2 PAPOLA PAF1CPOLR2F GTF2Bp-SUPT5HSARNP CTDP1 POLR2G TAF3 TAF11 POLR2E ERCC3 Intronless Histone pre-mRNA GTF2H5 POLR2D GTF2A2 U2AF1 POLR2C GTF2H4 RNGTT THOC2 TCEB3CL2 TCEB3CL2 MNAT1 SSRP1 GTF2H4 GTF2H3 TAF11 template DNA:30 nt transcript hybrid GTF2A2 GTF2F1 UTP TAF4 POLR2G NELFB TAF1L TCEB3 GTF2H3 WDR61 POLR2I POLR2H TAF11 GTF2F1 ELL SNRPD3 POLR2B TAF4B SUPT4H1 GTF2H2 GTF2E1 CPSF2 ERCC2 SNRPE TAF7L TAF2 CTP TFIIHTAF9B ATP GTF2H3 template DNA:30 nt transcript hybrid TFIIAp-SUPT5H CPSF4 GTF2H2 FACT complexSUPT6H EIF4A3 UTP GTF2H4 PPiPOLR2L GTF2H1 PABPN1 ELL FYTTD1 POLR2D GTF2A2 Intronless Histone pre-mRNA TAF12 TCEB2 GTF2H3 POLR2B ERCC3 CCNT2 TAF1 CCNT2 POLR2J LSM10 TCEB1Pol II transcriptioncomplex with (ser5)phosphorylated CTDcontaining extrudedtranscript to +30POLR2C GTF2H2 PCF11 TAF5 EAF2 POLR2G capped pre-mRNA TAF1L POLR2C NELFB POLR2L POLR2G POLR2D ZNF473 TBP GTF2H4 TAF7 POLR2K p-SUPT5H TCEB3C TAF7 TAF4 TCEB3CL2 NELFCD GTF2A2 TAF9B POLR2E GTF2H2 GTF2H1 TAF6 POLR2H POLR2D ERCC2 GTF2E2 GTF2F1 DNA containing PolII promoter withtranscript with 2or 3 nucleotidesGTF2F2 SUPT16H TCEB3B TAF4B CCNH TCEB3B GTF2H2 GTF2F1 POLR2I UTP POLR2F GTF2H1 POLR2E POLR2C TAF6 PPiGTF2F2 TCEB3CL POLR2J TCEB2 LSM11 CDK7 CPSF7 CDK7 POLR2I POLR2D SUPT6H GTF2H2 POLR2A POLR2K SRSF4 TCEB3 TCEB3CL TBP P-TEFb complexPOLR2C NUDT21 TAF4 POLR2D GTF2E2 CTDP1 NCBP2 Open DNA -10 to +2 containing RNA Polymerase II promoter POLR2C GTF2H3 POLR2B U2AF1L4 CDK7 pol II transcriptioncomplex containing3 Nucleotide longtranscriptCCNK GTF2F2 ERCC2 TAF9 SUPT6H damaged DNAsubstrate:nascentmRNA hybridCPSF2 upstreammRNAfragment:CPSF:PAP:PABPN1 complexSUPT16HPOLR2H POLR2I POLR2L POLR2H CCNT1,CCNT2,CCNKPAPOLA DNA containing RNA Polymerase II promoter POLR2D TCEA1 GTF2H5 RNGTTATP POLR2K TCEB1 TBP POLR2E NTPPOLR2D GTF2H4 AFF4 IWS1GTF2F2 RNMT POLR2I CCNT2 TAF13 CCNH POLR2L GTP TBP Elongin ComplexPAF1 TAF4B Elongin B:C complexNCBP1 CCNT1 TAF1 TCEB3B pol II transcriptioncomplexPOLR2A POLR2I POLR2D CSTF2 TCEA1 POLR2E CDC73 TAF1L TAF7 WDR33 TAF5 GTF2H5 p-SUPT5H ERCC3 POLR2J MNAT1 POLR2J TCEB3C TAF10 GTF2F1 pol II closedpre-initiationcomplexPOLR2G TCEA1 SSRP1 POLR2I TBP POLR2B SUPT6H TAF1L POLR2B TAF10 RTF1 NCBP2 NCBP2 SUPT4H1 POLR2C GTF2H2 Elongation complexprior to separationSUPT4H1 ERCC3 MNAT1 IWS1 POLR2J PPiTAF12 Cap Binding Complex(CBC)GTF2F2 GTF2A1(1-274) WDR61 template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end GTF2H4 GTF2F1 POLR2I NCBP2 POLR2K TAF13 POLR2F ATP POLR2G NELFE GTF2H5 GTF2H4 TAF6 GTF2H5 ATP CCNK PAF1 POLR2C EAF2 TCEB3 ALYREF TFIIEUTP TAF1 CLP1 POLR2K SYMPK NELFE SSRP1 POLR2B TAF9B MNAT1 p-S5-POLR2A EAF1 CF ICDK7 GTF2A1(1-274) p-SUPT5H TAF4 TAF6 NELFB TAF9 POLR2B upstream intronless mRNA fragment POLR2C POLR2J CASC3 CDK9 POLR2C GTF2E1 TAF1 TAF7 PAF1 GTP TAF9 CSTF3 POLR2K POLR2L POLR2A CF I - 72 kDa subunit p-S2,S5-POLR2A RNPS1 CDK7 MNAT1 TAF5 CTDP1 POLR2E TCEB3B NELFA CTDP1 GTF2H2 TCEB3CL p-S5-POLR2A THOC6 CCNT1 CDK9TAF9B TCEB2 AFF4 SRRM1 CLP1 ZNF473 TAF3 CCNH MNAT1 ATP CTR9 SRSF11 TAF11 POLR2C POLR2I CTP POLR2L POLR2B POLR2F CstFPCF11 GTF2F2 downstreamintronless mRNAfragmentMAGOHB POLR2A CCNT2 CDK9 GTF2H1 POLR2L p-S5-POLR2A PAPOLA Mature Intronless transcript derived Histone mRNA UPF3B TAF2 CSTF2T NCBP1 POLR2L GTF2B POLR2I POLR2C CCNH POLR2C Pol II initiationcomplexTAF3 POLR2H POLR2K POLR2L POLR2L CSTF3 NCBP1 TCEB3B GTF2H5 LSM11 capped pre-mRNA LEO1 NELFE Pol II transcriptioncomplex containingextruded transcriptto +30SNRPB DSIF:NELF:earlyelongation complexPOLDIP3 SUPT4H1 GTF2H1 POLR2H TAF2 POLR2G POLR2B TAF9B TAF1 GTF2H5 ERCC3 POLR2L DNA containing RNAPolymerase IIpromoterGTF2H1 SUPT4H1 GTF2H1 TAF13 U2AF2 POLR2L POLR2F RTF1 SRSF1 SUPT6H CCNH POLR2H CTDP1 CCNK CHTOP GTF2H3 ERCC2 GTF2H2 POLR2J TAF9 CTP CCNH EAF1 TAF2 POLR2F POLR2I POLR2F SUPT4H1 MNAT1 TAF11 DNA containing RNA Polymerase II promoter GTF2H2 TCEB3B TAF11 ATP GTF2A2 NELFCD TAF7L GTF2H3 POLR2F CCNT1 RTF1 CCNK GTF2A1(1-274) TAF4 POLR2I GTF2H2 GTF2F2 GTF2H2 POLR2F POLR2F GTF2F1 SUPT4H1 POLR2D MNAT1 CTP ELL PAF1 POLR2J SUPT6H GTF2F2 U7 snRNA TAF7 MLLT1 CDK9 Capped IntronlessHistonepre-mRNA:CBC:ZFP100ComplexCTP POLR2J SRSF6 GTP POLR2J GTF2H5 POLR2D SYMPK GTF2H2 MLLT3TAF4 POLR2D CCNK POLR2B POLR2E TAF1 TCEB2 CSTF2 Elongating transcript in processive Pol II mediated elongation CCNH GTF2E2 POLR2I SYMPK SRSF3 POLR2I TAF4B mRNA 3'-end cleavagefactorPOLR2D CASC3 TCEB1 ERCC2 POLR2E POLR2F GTF2F1 EAF2TAF5 TAF11 template DNA:3 nucleotide transcript hybrid GTF2H5 EAF2 p-SUPT5H TCEB3CL2 PABPN1 POLR2E TAF10 ATP CPSF3 MNAT1 GTF2F1 GTF2A1(275-376) GTF2B TAF1 template DNA withfirst transcriptdinucleotide,opened to +8positionGTF2H4 SUPT16H CCNH CPSF1 POLR2D TAF7 SUPT4H1 TAF1L GTF2E1 CPSF7 TAF13 ZC3H11A GTF2A1(275-376) CDC73 MLLT3 TAF12 NCBP2 POLR2L POLR2B ERCC2 SRSF1 GTF2A1(1-274) PCF11 RNA polymerase IItranscribes snRNAgenesPOLR2J RTF1 POLR2I NCBP2 GTF2F1 TAF1 CTP ELL TAF3 CDK7 CDC73 GTF2F1 GTF2A2 template DNA:4-9 nucleotide transcript hybrid POLR2K CDK9 TAF10 TAF9 RTF1 GTF2A1(1-274) CPSF2 NELF complexIWS1 NELFE NTPcapped pre-mRNA TAF10 POLR2F GTF2A1(1-274) GTF2A1(275-376) CPSF4 TCEB3B Paused processiveelongation complexRNGTT GTP CCNT1 GTF2F1 CTR9 POLR2H TAF1L GTF2H4 CCNH GTF2H5 TAF5 TAF4B NELFE THOC2 POLR2G SSRP1POLR2H EAF2 POLR2I SUPT4H1 TAF6 ERCC2 Early elongationcomplex withhyperphosphorylatedPol II CTDTCEB3 WDR61 CDK7 GTF2H2 POLR2J CDC40 SNRPF MNAT1 POLR2E GTF2B POLR2E SRSF2 CTP CTR9 CTDP1 NELFCD POLR2K template DNA:30 nt transcript hybrid GTF2E2 ERCC3 U7 snRNA FIP1L1 GTF2H3 POLR2D POLR2J POLR2H TAF10 GTF2F1 SSRP1 GTF2H3 POLR2B TCEB2 CHTOP POLR2E TAF11 ERCC2 GTF2A1(1-274) POLR2F WDR61 POLR2B NELFCD MLLT3 POLR2L GTF2H5 CCNK LUZP4 TAF9 CF I - 72 kDa subunit POLR2L POLR2D POLR2B p-S5-POLR2A MLLT3 GTF2F2 POLR2J CPSF1 POLR2C GTF2F1 POLR2K GTF2H3 CTDP1 GTF2H3 POLR2B TAF6 Elongating transcript in processive Pol II mediated elongation POLR2G POLR2E CCNT1 NELFA GTF2B TBP POLR2D POLR2G POLR2D TAF7 GTF2F1 POLR2G GTF2H3 CCNH TAF1L GTF2H5 TAF7L SNRPE CF I - 72 kDa subunit SSRP1 MLLT1 POLR2J GTF2F1 capped pre-mRNA NELFA TAF1 CF I - 68 kDa subunit NELFB TCEB3 PAF1 THOC5 POLR2B POLR2G GTP ERCC3 TCEB3CL NCBP2 TBP POLR2A GTP CCNH CCNH UTP NELFA Elongation complexwith separated anduncleavedtranscriptPOLR2I pol II transcriptioncomplex containing9 nucleotide longtranscriptPOLR2H GTF2A1(275-376) POLR2D CTP GTP TAF3 LEO1 CDK9 TAF2 POLR2G NCBP1 TCEB1 POLR2C TAF12 ERCC2 ERCC2 POLR2G p-S2,S5-POLR2A AFF4 CTP LEO1 GTF2F2 CCNH TAF7 EAF1 Elongation complexCPSF7 SRSF6 GTF2A1(275-376) POLR2E POLDIP3 TFIIFPOLR2E EAF1 TCEB3C NUDT21 TCEB3B NELFCD POLR2B TAF11 NELFCDERCC2 MLLT3 POLR2K POLR2D SUPT4H1TAF2 POLR2J NELFA TCEB3 CCNH GTF2E1 GTF2H1 CCNK NTPhTra2 TAF7L GTF2H1 TAF2 IWS1 ERCC2 TCEB3C CTP POLR2H CDK7 RNAPolII(hypophosphorylated):capped pre-mRNA complexMLLT1 GTF2H3 MLLT1 ERCC3 U2AF2 TAF10 POLR2C GTF2H2 TAF12 ERCC2 SRSF9 TAF1 NUDT21 RNAPolymeraseIIholoenzymecomplex(hyperphosphorylated)CDK7 GTF2H1 TFIIHGTF2H1 POLR2C POLR2D TAF3 GTF2H4 NUDT21 GTF2A1(275-376) ERCC3 GTF2BNELFB pol II transcriptioncomplex containing4 nucleotide longtranscriptPOLR2I NELFE p-S2,S5-POLR2A POLR2C polIIpromoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complexGTP CPSF1 ATP TAF10 MNAT1 GTF2H1 SUPT16H GTF2F1 POLR2E TAF7L TBP WDR61 LUZP4 TAF9B POLR2B ERCC2 TAF7L SUPT16H POLR2I p-S2,S5-POLR2A NCBP2 GTF2E1 POLR2G POLR2I GTF2H5 POLR2J GTP GTF2H3 CCNT2 NCBP1 SNRPD3 TAF10 LEO1 POLR2K POLR2J GTF2H4 LSM10 POLR2C CCNH POLR2H POLR2L TAF7 EAF2 Aborted earlyelongation complexCDC73 GTF2F1 CDK7 POLR2K LEO1 POLR2G GTF2A2 TAF7L ATP DNA containing RNA Polymerase II promoter GTF2A1(1-274) POLR2D POLR2B GTF2H1 TFIIHTAF12 POLR2F MNAT1 POLR2L TCEB3C CappedIntronlessHistonepre-mRNA:CBP80:CBP20:SLBP:ZFP100 ComplexGTF2F1 TAF5 POLR2D TCEB3CL NCBP1 TAF9 GTF2F2 TAF9 U7 snRNA CCNT2 UTP THOC7 POLR2F TAF11 POLR2G ERCC2 POLR2E CLP1 TCEB3CL2 GTF2H2 POLR2H POLR2D POLR2H TAF12 p-SUPT5H GTF2H1 GTF2F1 TCEA1 TAF4B WDR61 NTPSNRPF GTF2H1 hSLU7 TAF4 POLR2D CPSF3 POLR2F GTF2F2 UTP POLR2H IWS1 GTF2H5 GTF2A2 POLR2F TAF9B mRNA with spliced exons TAF11 GTF2F1 POLR2E POLR2L UTP SLBP MLLT1 TAF7L POLR2J TAF6 POLR2I SRSF7 TAF2 POLR2J GTF2A1(275-376) GTF2H5 POLR2K POLR2E POLR2F TCEB3CL2 ATP TCEB3 TCEB2 GTF2F1 CF I - 68 kDa subunit EAF1 CCNT1 POLR2D NELFCD Mature Intronless transcript derived Histone mRNA POLR2B CPSF4 POLR2H FIP1L1 ERCC3 SLBP TAF13 Elongin Ap-S2,S5-POLR2A MLLT1 MNAT1 TAF5 ATP GTP TFIIHGTF2E1 TAF4B GTF2F2 TAF9B EAF1 template DNA:11 nucleotide transcript hybrid TAF4B TAF11 TAF7L Pol II Initiationcomplex withphosphodiester-PPiintermediateTAF1 Capped intronless pre-mRNA TBP POLR2K CCNH THOC6 GTF2B DNA containing RNA Polymerase II promoter TAF1L CTDP1 GTF2H3 TAF4 NELFA RNA Pol II withphosphorylated CTD:CE complex withactivated GTNCBP1 AFF4 POLR2K TAF3 TFIIAGTF2E1 POLR2F UTP GTF2F2 TAF2 GTF2H4 CDK9 CPSF1 Elongating transcript prior to separation POLR2H CCNT2 POLR2L AFF4 TAF3 TAF5 POLR2B p-S5-POLR2A p-S5-POLR2A POLR2K GTF2E2 POLR2E ATP CDK7 TAF12 POLR2K TAF7 POLR2I EAF1 GTF2F2 TAF12 TCEB3 POLR2H POLR2L NTPGTF2F2 GTF2A1(1-274) ERCC3 UPF3B NTPCDK7 TCEB3CL2 NELFCD TAF6 ERCC2 GTF2A1(275-376) TAF3 SRSF7 POLR2D NCBP2 POLR2L SRSF5 RNAPolymeraseII(unphosphorylated):TFIIF complexCLP1 SUPT16H NCBP1 CCNH CPSF2 DDX39B TAF9B GTF2H5 POLR2H NTPPOLR2H GTF2A1(275-376) POLR2E POLR2C NELFCD SRSF9 Elongating transcript in processive Pol II mediated elongation CSTF1 CPSF4 POLR2L TCEB3 POLR2H TAF7 POLR2E ALYREF POLR2A TAF5 RNMTpol II transcriptioncomplex containing11 nucleotide longtranscriptMNAT1 POLR2I TAF4 ERCC2 GTF2A1(275-376) p-S5-POLR2A GTF2E1 POLR2I p-S2,S5-POLR2A POLR2G NCBP2 CDK7 TAF1L CCNT2 PAF1 CCNT2 TCEB3C POLR2J pol IIpromoter:TFIIDcomplexDNA containing RNA Polymerase II promoter GTF2F1 POLR2E TAF1 IWS1 POLR2B TAF13 GTF2H4 GTF2A2 CDK7 CCNH NELFA GTF2B ERCC3 TAF13 POLR2G TCEB3CL hSLU7 AFF4 Processiveelongation complexGTF2H1 LEO1 SRSF4 SYMPK NELFE MNAT1 TBP THOC1 CF I - 72 kDa subunit ATP TAF4B GTF2H1 SplicedmRNA:CBC:EJC:TREXPOLR2L p-S5-POLR2A DNA containing Pol II promoter with transcript with 2 or 3 nucleotides TCEB3C SRSF5 POLR2H NCBP1 POLR2J TAF11 POLR2A PABPN1 Template DNA hybrid with phosphodiester-PPi intermediate MLLT1 POLR2A CTDP1POLR2F TCEB2 NELFCD PABPN1 ELL CCNK GTF2F2 POLR2C GTF2H4 PPiPOLR2K cappedpre-mRNA:CBC:RNAPol II(phosphorylated)complexGTF2F1 PPiPOLR2L GTF2F2 TAF1L CDC73 SNRPB POLR2C UTP FYTTD1 CDK9 POLR2A POLR2D DHX38 AFF4 template DNA:4 nucleotide transcript hybrid WDR33 CCNT1 POLR2H SRSF3 pol II transcriptioncomplex containing4-9 nucleotide longtranscriptPOLR2A AFF4POLR2L WDR61 p-SUPT5H ADPTAF13 LEO1 POLR2A GTP TAF9B RNGTT SARNP POLR2C POLR2K GTF2F2 POLR2A POLR2E GTF2B template DNA:30 nt transcript hybrid CTP POLR2K GTF2A1(1-274) POLR2G ERCC3 TAF1 TAF2 TAF3 GTF2A1(275-376) POLR2C p-SUPT5H LEO1 CTDP1 Aborted elongationcomplex afterarrestSRRM1 CF IINTPNELFA CDK9 POLR2A GTF2E2 SUPT4H1 TBP POLR2B GTP TAF7L IWS1 POLR2C GTF2E1 p-SUPT5H GTF2F2 TAF13 GTF2H2 TAF10 TAF13 ZC3H11A ERCC3 POLR2H NCBP1 POLR2G UTP TAF6 TFIIDPOLR2K TAF13 POLR2L POLR2G POLR2D NELFA GTF2H4 TCEB3B SUPT6H CTR9 GTF2H5 ATP POLR2F GTF2B POLR2F SUPT6HPOLR2A NELFB CE:Pol II CTD:Spt5complexCDK7 POLR2H CDC73 ERCC3 GTF2H4 POLR2L GTF2H3 POLR2J POLR2F RNPS1 CF I - 68 kDa subunit POLR2L THOC7 POLR2C TAF7 GTF2H1 TAF7 TCEB1 WDR61 ELLU2AF1L4 CPSF3 TAF13 GTF2E1 POLR2G POLR2G TAF7L POLR2E SUPT4H1 CSTF2T POLR2G GTF2A1(275-376) SUPT4H1 POLR2K GTF2F2 NELFA POLR2G TCEA1 NELFENELFE CTR9 TAF9B SUPT16H POLR2D SRSF11 ERCC3 NCBP2 pol II openpre-initiationcomplexWDR33 GTF2H1 TAF4 CPSF3 EAF2 CDK7 POLR2K POLR2J template DNA:4-9nucleotidetranscript hybridERCC3 GTF2H1 POLR2G GTF2A2 GTF2F1 ERCC2 POLR2F POLR2B GTF2F2 TAF4B DSIF complexEAF1 LSM11 POLR2C PiGTF2F2 TFIIHNTPNELFE POLR2K NELFCD POLR2J POLR2C GTP TAF9 POLR2H CDK7 TAF5 MLLT3 SSRP1 TAF7 POLR2C UTP NCBP1 GTF2B SSRP1 TAF7L GTF2H4 TAF3 CCNK GTF2H4 GTF2E2 POLR2G DDX39A POLR2G GTF2F2 TAF3 TFIIETCEB2 POLR2H TCEB3CL2 NCBP2 GTF2H3 POLR2F POLR2E ATP POLR2H p-S5-POLR2A POLR2L TCEB1 GTF2H2 POLR2G POLR2A TCEB3CL DHX38 TAF5 GTF2A1(1-274) POLR2B NELFB NELFB TAF9B CDK7 MLLT1 GTF2F1 TAF12 POLR2A GTF2H5 GTP POLR2H POLR2J POLR2B TAF10 GTF2H1 POLR2I RNA Pol II withphosphorylated CTD:CE complexTAF6 GenericTranscriptionPathwayGTF2F2 GTF2F1 ATPGTF2F1 GTF2H2 POLR2I CDK9 POLR2E MLLT3 GTF2H2 EIF4A3 POLR2E TAF2 CTP p-S2,S5-POLR2A TCEB3C TAF10 TAF10 NELFB TAF12 GTF2H4 GTF2A2 GTF2H3 NELFBNCBP2 TCEA1TCEB3CL Elongating transcript prior to cleavage TAF4B MNAT1 POLR2K POLR2C TCEB3CL EAF2 TAF11 UTP POLR2C GTF2H4 ATP MAGOH POLR2E THOC5 POLR2G POLR2J MNAT1 CCNH PAF1 POLR2H GTF2F2 NELFCD GTP TCEA1 CCNT2 MAGOHB CDK7 GTF2B ATP U2AF1 Mature intronlesstranscript derivedHistonepre-mRNA:CBCcomplexTAF10 POLR2L POLR2I POLR2J CTP TCEA1 GTF2E2 FIP1L1 CDC40 CSTF2 p-SUPT5H POLR2F CCNH ERCC3 CPSF7 POLR2D THOC3 SSRP1 template:capped transcript hybrid POLR2B GTF2F2 SNRPG POLR2F GTF2H4 FIP1L1 GTF2A2 POLR2B MLLT3 NTPTAF4B 3' end cleaved,ligated exoncontaining complexPOLR2L POLR2I POLR2B GTF2F1 POLR2I SNRPF TAF3 SUPT16H TAF7L POLR2F PAPOLA POLR2F PPiPOLR2E TAF4B NCBP1 MNAT1 GTF2F1 GTF2H2 CCNH template DNA:30 nt transcript hybrid template DNA with first transcript dinucleotide, opened to +8 position GTF2A1(275-376) GTF2F2 SNRPD3 POLR2K TAF4 GTF2H4 THOC3 CDC73 POLR2B GTF2E2 NCBP2 POLR2C TAF4 TAF1L CDK7 CTR9 TAF4 ERCC3 POLR2C TAF1L POLR2H MatureIntronlesstranscriptderivedHistonemRNA:SLBP:CBP80:CBP20CTR9 NELFAGTF2F2 POLR2G PCF11 TAF3 GTP CTDP1 GTF2H2 POLR2H TAF9 TFIIDp-SUPT5H GTF2F2 TCEB2 MLLT1GTF2H3 MAGOH CTP p-SUPT5H CSTF1 GTF2E2 CF I - 68 kDa subunit CSTF1 POLR2B POLR2F THOC1 UTP CCNH POLR2I POLR2L p-SUPT5H template DNA:30 nt transcript hybrid CTP POLR2D POLR2K GTF2F1 CDC73 PAF1 GTF2H5 GTF2A2 WDR33 TBP GTF2E1 TAF1L UTP POLR2L POLR2H TAF1L CCNT1 MNAT1 RBM8A ERCC2 TAF6 RTF1 TAF9 CTDP1 MNAT1 RBM8A POLR2K ERCC2 CDK7 TAF13 Elongating transcript in processive Pol II mediated elongation POLR2J TCEB3CL2 CSTF2T IWS1 POLR2F POLR2K GTF2F2 p-S2,S5-POLR2A ERCC2 TAF6 SRSF2 TAF12 TAF9B POLR2I GTF2F1 NCBP1 3'-end cleaved mRNA with spliced exons POLR2K DDX39A POLR2K RTF1 GTF2H3 TCEB1 UTP TAF4 ATP polIIpromoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complexGTF2E1 TCEB1 TAF2 AFF4 p-S2,S5-POLR2A SNRPG ELL GTF2H5 TAF5 POLR2L capped pre-mRNA NTPTAF1 POLR2D GTF2H5 MNAT1 intronless pre-mRNAcleavage complexPOLR2B SNRPG CDK7 GTF2E2 GTF2H3 ERCC2 ELL POLR2E GTF2H4 CCNT1 GTF2H1 GTF2H3 ERCC2 POLR2E ZNF473 DDX39B TBP POLR2K NELFE TAF7L POLR2D GTF2F2 SNRPB GTP POLR2I EAF2 NCBP1 MNAT1 NTPERCC3 CTP EAF1GTF2H1 CCNK NELFE POLR2K GTF2H5 LSM10 Pol II transcriptioncomplex containingtranscript to +30POLR2I ERCC3 CCNT1 GTF2F2 U7 snRNP:ZNF473POLR2J TCEB2CDK7 POLR2C GTF2A1(1-274) TAF9B POLR2J POLR2F CTP Arrested processiveelongation complexGTF2F1 POLR2B TCEB3C NELFB CCNH TCEB1 POLR2E TAF12 POLR2F RTF1 TAF6 GTF2H3 TAF9 TAF13 GTF2F1 532, 6, 10, 17, 18, 22...3053535, 24, 791, 2169715, 24, 7913, 5158533535356, 715, 24, 79567432, 55, 77, 8230535, 24, 794, 7, 11, 25, 33...32, 55, 77, 8253535, 24, 79


Description

View original pathway at:Reactome.

Comments

Reactome-Converter 
Pathway is converted from Reactome ID: 73857
Reactome-version 
Reactome version: 62

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Bibliography

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  1. Martinez E, Ge H, Tao Y, Yuan CX, Palhan V, Roeder RG.; ''Novel cofactors and TFIIA mediate functional core promoter selectivity by the human TAFII150-containing TFIID complex.''; PubMed Europe PMC Scholia
  2. Mandal SS, Cho H, Kim S, Cabane K, Reinberg D.; ''FCP1, a phosphatase specific for the heptapeptide repeat of the largest subunit of RNA polymerase II, stimulates transcription elongation.''; PubMed Europe PMC Scholia
  3. Dvir A, Conaway RC, Conaway JW.; ''A role for TFIIH in controlling the activity of early RNA polymerase II elongation complexes.''; PubMed Europe PMC Scholia
  4. Kibel A, Iliopoulos O, DeCaprio JA, Kaelin WG.; ''Binding of the von Hippel-Lindau tumor suppressor protein to Elongin B and C.''; PubMed Europe PMC Scholia
  5. Roeder RG.; ''Transcriptional regulation and the role of diverse coactivators in animal cells.''; PubMed Europe PMC Scholia
  6. Rosenfeld MG, Lunyak VV, Glass CK.; ''Sensors and signals: a coactivator/corepressor/epigenetic code for integrating signal-dependent programs of transcriptional response.''; PubMed Europe PMC Scholia
  7. Mousson F, Kolkman A, Pijnappel WW, Timmers HT, Heck AJ.; ''Quantitative proteomics reveals regulation of dynamic components within TATA-binding protein (TBP) transcription complexes.''; PubMed Europe PMC Scholia
  8. Gnatt AL, Cramer P, Fu J, Bushnell DA, Kornberg RD.; ''Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution.''; PubMed Europe PMC Scholia
  9. Yu M, Yang W, Ni T, Tang Z, Nakadai T, Zhu J, Roeder RG.; ''RNA polymerase II-associated factor 1 regulates the release and phosphorylation of paused RNA polymerase II.''; PubMed Europe PMC Scholia
  10. Yao C, Choi EA, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, Shi Y.; ''Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3' processing.''; PubMed Europe PMC Scholia
  11. Hernandez N.; ''Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription.''; PubMed Europe PMC Scholia
  12. Bray SJ.; ''Notch signalling: a simple pathway becomes complex.''; PubMed Europe PMC Scholia
  13. Yamazaki K, Guo L, Sugahara K, Zhang C, Enzan H, Nakabeppu Y, Kitajima S, Aso T.; ''Identification and biochemical characterization of a novel transcription elongation factor, Elongin A3.''; PubMed Europe PMC Scholia
  14. Justice NJ, Jan YN.; ''Variations on the Notch pathway in neural development.''; PubMed Europe PMC Scholia
  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 complex
ComplexR-HSA-72177 (Reactome)
3'-end cleaved mRNA with spliced exons R-ALL-71998 (Reactome)
ADPMetaboliteCHEBI:16761 (ChEBI)
AFF4 ProteinQ9UHB7 (Uniprot-TrEMBL)
AFF4ProteinQ9UHB7 (Uniprot-TrEMBL)
ALYREF ProteinQ86V81 (Uniprot-TrEMBL)
ATP MetaboliteCHEBI:15422 (ChEBI)
ATPMetaboliteCHEBI:15422 (ChEBI)
Aborted early elongation complexComplexR-HSA-113410 (Reactome)
Aborted elongation

complex after

arrest
ComplexR-HSA-113722 (Reactome)
Arrested processive elongation complexComplexR-HSA-113721 (Reactome)
CASC3 ProteinO15234 (Uniprot-TrEMBL)
CCNH ProteinP51946 (Uniprot-TrEMBL)
CCNK ProteinO75909 (Uniprot-TrEMBL)
CCNT1 ProteinO60563 (Uniprot-TrEMBL)
CCNT1,CCNT2,CCNKComplexR-HSA-6807466 (Reactome)
CCNT2 ProteinO60583 (Uniprot-TrEMBL)
CDC40 ProteinO60508 (Uniprot-TrEMBL)
CDC73 ProteinQ6P1J9 (Uniprot-TrEMBL)
CDK7 ProteinP50613 (Uniprot-TrEMBL)
CDK9 ProteinP50750 (Uniprot-TrEMBL)
CDK9ProteinP50750 (Uniprot-TrEMBL)
CE:Pol II CTD:Spt5 complexComplexR-HSA-77061 (Reactome) Spt5 reacts with Guanyl Transferase (GT) of the capping enzyme (CE).
CF I - 68 kDa subunit R-HSA-72013 (Reactome)
CF I - 72 kDa subunit R-HSA-72014 (Reactome)
CF IIComplexR-HSA-72020 (Reactome)
CF IComplexR-HSA-72015 (Reactome)
CHTOP ProteinQ9Y3Y2 (Uniprot-TrEMBL)
CLP1 ProteinQ92989 (Uniprot-TrEMBL)
CPSF1 ProteinQ10570 (Uniprot-TrEMBL)
CPSF2 ProteinQ9P2I0 (Uniprot-TrEMBL)
CPSF3 ProteinQ9UKF6 (Uniprot-TrEMBL)
CPSF4 ProteinO95639 (Uniprot-TrEMBL)
CPSF7 ProteinQ8N684 (Uniprot-TrEMBL)
CSTF1 ProteinQ05048 (Uniprot-TrEMBL)
CSTF2 ProteinP33240 (Uniprot-TrEMBL)
CSTF2T ProteinQ9H0L4 (Uniprot-TrEMBL)
CSTF3 ProteinQ12996 (Uniprot-TrEMBL)
CTDP1 ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTDP1ProteinQ9Y5B0 (Uniprot-TrEMBL)
CTP MetaboliteCHEBI:17677 (ChEBI)
CTR9 ProteinQ6PD62 (Uniprot-TrEMBL)
Cap Binding Complex (CBC)ComplexR-HSA-77088 (Reactome)
Capped

Intronless Histone

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

Histone pre-mRNA:CBC:ZFP100

Complex
ComplexR-HSA-112045 (Reactome)
Capped intronless pre-mRNA R-ALL-112158 (Reactome)
CstFComplexR-HSA-72006 (Reactome)
DDX39A ProteinO00148 (Uniprot-TrEMBL)
DDX39B ProteinQ13838 (Uniprot-TrEMBL)
DHX38 ProteinQ92620 (Uniprot-TrEMBL)
DNA containing Pol

II promoter with transcript with 2

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

Polymerase II

promoter
R-ALL-109627 (Reactome)
DNA containing RNA Polymerase II promoter R-ALL-109627 (Reactome)
DSIF complexComplexR-HSA-112420 (Reactome)
DSIF:NELF:early elongation complexComplexR-HSA-113408 (Reactome)
EAF1 ProteinQ96JC9 (Uniprot-TrEMBL)
EAF1ProteinQ96JC9 (Uniprot-TrEMBL)
EAF2 ProteinQ96CJ1 (Uniprot-TrEMBL)
EAF2ProteinQ96CJ1 (Uniprot-TrEMBL)
EIF4A3 ProteinP38919 (Uniprot-TrEMBL)
ELL ProteinP55199 (Uniprot-TrEMBL)
ELLProteinP55199 (Uniprot-TrEMBL)
ERCC2 ProteinP18074 (Uniprot-TrEMBL)
ERCC3 ProteinP19447 (Uniprot-TrEMBL)
Early elongation

complex with hyperphosphorylated

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

with separated and uncleaved

transcript
ComplexR-HSA-113726 (Reactome)
Elongation complexComplexR-HSA-112433 (Reactome)
Elongin AComplexR-HSA-8867795 (Reactome)
Elongin B:C complexComplexR-HSA-112424 (Reactome)
Elongin ComplexComplexR-HSA-112425 (Reactome)
FACT complexComplexR-HSA-112417 (Reactome)
FIP1L1 ProteinQ6UN15 (Uniprot-TrEMBL)
FYTTD1 ProteinQ96QD9 (Uniprot-TrEMBL)
GTF2A1(1-274) ProteinP52655 (Uniprot-TrEMBL)
GTF2A1(275-376) ProteinP52655 (Uniprot-TrEMBL)
GTF2A2 ProteinP52657 (Uniprot-TrEMBL)
GTF2B ProteinQ00403 (Uniprot-TrEMBL)
GTF2BProteinQ00403 (Uniprot-TrEMBL)
GTF2E1 ProteinP29083 (Uniprot-TrEMBL)
GTF2E2 ProteinP29084 (Uniprot-TrEMBL)
GTF2F1 ProteinP35269 (Uniprot-TrEMBL)
GTF2F2 ProteinP13984 (Uniprot-TrEMBL)
GTF2H1 ProteinP32780 (Uniprot-TrEMBL)
GTF2H2 ProteinQ13888 (Uniprot-TrEMBL)
GTF2H3 ProteinQ13889 (Uniprot-TrEMBL)
GTF2H4 ProteinQ92759 (Uniprot-TrEMBL)
GTF2H5 ProteinQ6ZYL4 (Uniprot-TrEMBL)
GTP MetaboliteCHEBI:15996 (ChEBI)
Generic

Transcription

Pathway
PathwayR-HSA-212436 (Reactome) OVERVIEW OF TRANSCRIPTION REGULATION:

Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or tissue-specific regulation of differential gene transcription is mediated (reviewed in Naar, 2001. Kadonaga, 2004, Maston, 2006, Barolo, 2002; Roeder, 2005, Rosenfeld, 2006). Of the three major classes of DNA polymerase involved in eukaryotic gene transcription, Polymerase II generally regulates protein-encoding genes. Figure 1 shows a diagram of the various components involved in cell-specific regulation of Pol-II gene transcription.

Core Promoter: Pol II-regulated genes typically have a Core Promoter where Pol II and a variety of general factors bind to specific DNA motifs:
i: the TATA box (TATA DNA sequence), which is bound by the "TATA-binding protein" (TBP).
ii: the Initiator motif (INR), where Pol II and certain other core factors bind, is present in many Pol II-regulated genes.
iii: the Downstream Promoter Element (DPE), which is present in a subset of Pol II genes, and where additional core factors bind.
The core promoter binding factors are generally ubiquitously expressed, although there are exceptions to this.

Proximal Promoter: immediately upstream (5') of the core promoter, Pol II target genes often have a Proximal Promoter region that spans up to 500 base pairs (b.p.), or even to 1000 b.p.. This region contains a number of functional DNA binding sites for a specific set of transcription activator (TA) and transcription repressor (TR) proteins. These TA and TR factors are generally cell- or tissue-specific in expression, rather than ubiquitous, so that the presence of their cognate binding sites in the proximal promoter region programs cell- or tissue-specific expression of the target gene, perhaps in conjunction with TA and TR complexes bound in distal enhancer regions.

Distal Enhancer(s): many or most Pol II regulated genes in higher eukaryotes have one or more distal Enhancer regions which are essential for proper regulation of the gene, often in a cell or tissue-specific pattern. Like the proximal promoter region, each of the distal enhancer regions typically contain a cluster of binding sites for specific TA and/or TR DNA-binding factors, rather than just a single site.

Enhancers generally have three defining characteristics:
i: They can be located very long distances from the promoter of the target gene they regulate, sometimes as far as 100 Kb, or more.
ii: They can be either upstream (5') or downstream (3') of the target gene, including within introns of that gene.
iii: They can function in either orientation in the DNA.

Combinatorial mechanisms of transcription regulation: The specific combination of TA and TR binding sites within the proximal promoter and/or distal enhancer(s) provides a "combinatorial transcription code" that mediates cell- or tissue-specific expression of the associated target gene. Each promoter or enhancer region mediates expression in a specific subset of the overall expression pattern. In at least some cases, each enhancer region functions completely independently of the others, so that the overall expression pattern is a linear combination of the expression patterns of each of the enhancer modules.

Co-Activator and Co-Repressor Complexes: DNA-bound TA and TR proteins typically recruit the assembly of specific Co-Activator (Co-A) and Co-Repressor (Co-R) Complexes, respectively, which are essential for regulating target gene transcription. Both Co-A's and Co-R's are multi-protein complexes that contain several specific protein components.

Co-Activator complexes generally contain at lease one component protein that has Histone Acetyl Transferase (HAT) enzymatic activity. This functions to acetylate Histones and/or other chromatin-associated factors, which typically increases that transcription activation of the target gene. By contrast, Co-Repressor complexes generally contain at lease one component protein that has Histone De-Acetylase (HDAC) enzymatic activity. This functions to de-acetylate Histones and/or other chromatin-associated factors. This typically increases the transcription repression of the target gene.

Adaptor (Mediator) complexes: In addition to the co-activator complexes that assemble on particular cell-specific TA factors, - there are at least two additional transcriptional co-activator complexes common to most cells. One of these is the Mediator complex, which functions as an "adaptor" complex that bridges between the tissue-specific co-activator complexes assembled in the proximal promoter (or distal enhancers). The human Mediator complex has been shown to contain at least 19 protein distinct components. Different combinations of these co-activator proteins are also found to be components of specific transcription Co-Activator complexes, such as the DRIP, TRAP and ARC complexes described below.

TBP/TAF complex: Another large Co-A complex is the "TBP-associated factors" (TAFs) that assemble on TBP (TATA-Binding Protein), which is bound to the TATA box present in many promoters. There are at least 23 human TAF proteins that have been identified. Many of these are ubiquitously expressed, but TAFs can also be expressed in a cell or tissue-specific pattern.


Specific Coactivator Complexes for DNA-binding Transcription Factors.

A number of specific co-activator complexes for DNA-binding transcription factors have been identified, including DRIP, TRAP, and ARC (reviewed in Bourbon, 2004, Blazek, 2005, Conaway, 2005, and Malik, 2005). The DRIP co-activator complex was originally identified and named as a specific complex associated with the Vitamin D Receptor member of the nuclear receptor family of transcription factors (Rachez, 1998). Similarly, the TRAP co-activator complex was originally identified as a complex that associates with the thyroid receptor (Yuan, 1998). It was later determined that all of the components of the DRIP complex are also present in the TRAP complex, and the ARC complex (discussed further below). For example, the DRIP205 and TRAP220 proteins were show to be identical, as were specific pairs of the other components of these complexes (Rachez, 1999).

In addition, these various transcription co-activator proteins identified in mammalian cells were found to be the orthologues or homologues of the Mediator ("adaptor") complex proteins (reviewed in Bourbon, 2004). The Mediator proteins were originally identified in yeast by Kornberg and colleagues, as complexes associated with DNA polymerase (Kelleher, 1990). In higher organisms, Adapter complexes bridge between the basal transcription factors (including Pol II) and tissue-specific transcription factors (TFs) bound to sites within upstream Proximal Promoter regions or distal Enhancer regions (Figure 1). However, many of the Mediator homologues can also be found in complexes associated with specific transcription factors in higher organisms. A unified nomenclature system for these adapter / co-activator proteins now labels them Mediator 1 through Mediator 31 (Bourbon, 2004). For example, the DRIP205 / TRAP220 proteins are now identified as Mediator 1 (Rachez, 1999), based on homology with yeast Mediator 1.


Example Pathway: Specific Regulation of Target Genes During Notch Signaling:

One well-studied example of cell-specific regulation of gene transcription is selective regulation of target genes during Notch signaling. Notch signaling was first identified in Drosophila, where it has been studied in detail at the genetic, molecular, biochemical and cellular levels (reviewed in Justice, 2002; Bray, 2006; Schweisguth, 2004; Louvri, 2006). In Drosophila, Notch signaling to the nucleus is thought always to be mediated by one specific DNA binding transcription factor, Suppressor of Hairless. In mammals, the homologous genes are called CBF1 (or RBPJkappa), while in worms they are called Lag-1, so that the acronym "CSL" has been given to this conserved transcription factor family. There are at least two human CSL homologues, which are now named RBPJ and RBPJL.

In Drosophila, Su(H) is known to be bifunctional, in that it represses target gene transcription in the absence of Notch signaling, but activates target genes during Notch signaling. At least some of the mammalian CSL homologues are believed also to be bifunctional, and to mediate target gene repression in the absence of Notch signaling, and activation in the presence of Notch signaling.

Notch Co-Activator and Co-Repressor complexes: This repression is mediated by at least one specific co-repressor complexes (Co-R) bound to CSL in the absence of Notch signaling. In Drosophila, this co-repressor complex consists of at least three distinct co-repressor proteins: Hairless, Groucho, and dCtBP (Drosophila C-terminal Binding Protein). Hairless has been show to bind directly to Su(H), and Groucho and dCtBP have been shown to bind directly to Hairless (Barolo, 2002). All three of the co-repressor proteins have been shown to be necessary for proper gene regulation during Notch signaling in vivo (Nagel, 2005).

In mammals, the same general pathway and mechanisms are observed, where CSL proteins are bifunctional DNA binding transcription factors (TFs), that bind to Co-Repressor complexes to mediate repression in the absence of Notch signaling, and bind to Co-Activator complexes to mediate activation in the presence of Notch signaling. However, in mammals, there may be multiple co-repressor complexes, rather than the single Hairless co-repressor complex that has been observed in Drosophila.

During Notch signaling in all systems, the Notch transmembrane receptor is cleaved and the Notch intracellular domain (NICD) translocates to the nucleus, where it there functions as a specific transcription co-activator for CSL proteins. In the nucleus, NICD replaces the Co-R complex bound to CSL, thus resulting in de-repression of Notch target genes in the nucleus (Figure 2). Once bound to CSL, NICD and CSL proteins recruit an additional co-activator protein, Mastermind, to form a CSL-NICD-Mam ternary co-activator (Co-A) complex. This Co-R complex was initially thought to be sufficient to mediate activation of at least some Notch target genes. However, there now is evidence that still other co-activators and additional DNA-binding transcription factors are required in at least some contexts (reviewed in Barolo, 2002).

Thus, CSL is a good example of a bifunctional DNA-binding transcription factor that mediates repression of specific targets genes in one context, but activation of the same targets in another context. This bifunctionality is mediated by the association of specific Co-Repressor complexes vs. specific Co-Activator complexes in different contexts, namely in the absence or presence of Notch signaling.
IWS1 ProteinQ96ST2 (Uniprot-TrEMBL)
IWS1ProteinQ96ST2 (Uniprot-TrEMBL)
Intronless Histone pre-mRNA R-ALL-110756 (Reactome)
LEO1 ProteinQ8WVC0 (Uniprot-TrEMBL)
LSM10 ProteinQ969L4 (Uniprot-TrEMBL)
LSM11 ProteinP83369 (Uniprot-TrEMBL)
LUZP4 ProteinQ9P127 (Uniprot-TrEMBL)
MAGOH ProteinP61326 (Uniprot-TrEMBL)
MAGOHB ProteinQ96A72 (Uniprot-TrEMBL)
MLLT1 ProteinQ03111 (Uniprot-TrEMBL)
MLLT1ProteinQ03111 (Uniprot-TrEMBL)
MLLT3 ProteinP42568 (Uniprot-TrEMBL)
MLLT3ProteinP42568 (Uniprot-TrEMBL)
MNAT1 ProteinP51948 (Uniprot-TrEMBL)
Mature

Intronless transcript derived Histone

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

transcript derived Histone pre-mRNA:CBC

complex
ComplexR-HSA-156959 (Reactome)
NCBP1 ProteinQ09161 (Uniprot-TrEMBL)
NCBP2 ProteinP52298 (Uniprot-TrEMBL)
NELF complexComplexR-HSA-112432 (Reactome)
NELFA ProteinQ9H3P2 (Uniprot-TrEMBL)
NELFAProteinQ9H3P2 (Uniprot-TrEMBL)
NELFB ProteinQ8WX92 (Uniprot-TrEMBL)
NELFBProteinQ8WX92 (Uniprot-TrEMBL)
NELFCD ProteinQ8IXH7 (Uniprot-TrEMBL)
NELFCDProteinQ8IXH7 (Uniprot-TrEMBL)
NELFE ProteinP18615 (Uniprot-TrEMBL)
NELFEProteinP18615 (Uniprot-TrEMBL)
NTPComplexR-ALL-30595 (Reactome)
NUDT21 ProteinO43809 (Uniprot-TrEMBL)
Open DNA -10 to +2 containing RNA Polymerase II promoter R-ALL-109875 (Reactome)
P-TEFb complexComplexR-HSA-112431 (Reactome)
PABPN1 ProteinQ86U42 (Uniprot-TrEMBL)
PAF1 ProteinQ8N7H5 (Uniprot-TrEMBL)
PAF1CComplexR-HSA-8866690 (Reactome)
PAPOLA ProteinP51003 (Uniprot-TrEMBL)
PCF11 ProteinO94913 (Uniprot-TrEMBL)
POLDIP3 ProteinQ9BY77 (Uniprot-TrEMBL)
POLR2A ProteinP24928 (Uniprot-TrEMBL)
POLR2B ProteinP30876 (Uniprot-TrEMBL)
POLR2C ProteinP19387 (Uniprot-TrEMBL)
POLR2D ProteinO15514 (Uniprot-TrEMBL)
POLR2E ProteinP19388 (Uniprot-TrEMBL)
POLR2F ProteinP61218 (Uniprot-TrEMBL)
POLR2G ProteinP62487 (Uniprot-TrEMBL)
POLR2H ProteinP52434 (Uniprot-TrEMBL)
POLR2I ProteinP36954 (Uniprot-TrEMBL)
POLR2J ProteinP52435 (Uniprot-TrEMBL)
POLR2K ProteinP53803 (Uniprot-TrEMBL)
POLR2L ProteinP62875 (Uniprot-TrEMBL)
PPiMetaboliteCHEBI:29888 (ChEBI)
Paused processive elongation complexComplexR-HSA-113720 (Reactome)
PiMetaboliteCHEBI:18367 (ChEBI)
Pol II Initiation

complex with phosphodiester-PPi

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

complex containing extruded transcript

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

complex containing

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

complex with (ser5) phosphorylated CTD containing extruded

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

Pol II

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

Pol II

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

Polymerase II

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

Polymerase II holoenzyme complex

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

phosphorylated CTD: CE complex with

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

phosphorylated CTD:

CE complex
ComplexR-HSA-77053 (Reactome)
RNA polymerase II

transcribes snRNA

genes
PathwayR-HSA-6807505 (Reactome) Small nuclear RNAs (snRNAs) play key roles in splicing and some of them, specifically the U1 and U2 snRNAs, are encoded by multicopy snRNA gene clusters containing tandem arrays of genes, about 30 in the RNU1 cluster (Bernstein et al. 1985) and about 10-20 in the RNU2 cluster (Van Ardsell and Weiner 1984). Whereas U6 snRNA genes are transcribed by RNA polymerase III, U1,U2, U4, U4atac, U5, U11, and U12 genes are transcribed by RNA polymerase II. Transcription of the U1 and U2 genes has been most extensively studied and the other snRNA genes as well as other genes with similar promoter structures, for example the SNORD13 gene, are inferred to be transcribed by similar reactions. The snRNA genes transcribed by RNA polymerase II are distinguished from mRNA-encoding genes by the presence of a proximal sequence element (PSE) rather than a TATA box and the presence of the Integrator complex rather than the Mediator complex (reviewed in Egloff et al. 2008, Jawdeker and Henry 2008).
The snRNA genes are among the most rapidly transcribed genes in the genome. The 5' transcribed region of the U2 snRNA gene is largely single-stranded during interphase and metaphase (Pavelitz et al. 2008) and chromatin within the transcribed region is cleared of nucleosomes (O'Reilly et al. 2014). Transcriptional activation of the RNA polymerase II transcribed snRNA genes begins with binding of transcription factors to the distal sequence element (DSE) of the promoter (reviewed in Hernandez 2001, Egloff et al. 2008, Jawdeker and Henry 2008). The factors, which include POU2F1 (Oct-1), POU2F2 (Oct-2), ZNF143 (Staf) and Sp1, promote binding of the SNAPc complex (also known as PTF and PBP) to the PSE. SNAPc helps clear the gene of nucleosomes (O'Reilly et al. 2014) and recruits initiation factors (TFIIA, TFIIB, TFIIE, TFIIF, and snTAFc:TBP) which recruit RNA polymerase II. Phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (reviewed in Egloff and Murphy 2008) by CDK7 recruits RPAP2 and the Integrator complex, which is required for later processing of the 3' end of the pre-snRNA transcript (reviewed in Chen and Wagner 2010, Baillat and Wagner 2015). The Little Elongation Complex (LEC) also appears to bind around the time of transcription initiation (Hu et al. 2013). As transcription proceeds, RPAP2 dephosphorylates serine-5 and P-TEFb phosphorylates serine-2 of the CTD. As transcription reaches the end of the snRNA gene serine-7 of the CTD is phosphorylated. These marks serve to bind protein complexes and are required for 3' processing of the pre-snRNA (reviewed in Egloff and Murphy 2008). After transcription proceeds through the conserved 3' processing sequence of the pre-snRNA the Integrator complex cleaves the pre-snRNA. Transcription then terminates downstream in a less well characterized reaction that requires elements of the polyadenylation system.
RNGTT ProteinO60942 (Uniprot-TrEMBL)
RNGTTProteinO60942 (Uniprot-TrEMBL)
RNMT ProteinO43148 (Uniprot-TrEMBL)
RNMTProteinO43148 (Uniprot-TrEMBL)
RNPS1 ProteinQ15287 (Uniprot-TrEMBL)
RTF1 ProteinQ92541 (Uniprot-TrEMBL)
SARNP ProteinP82979 (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)
SUPT6H ProteinQ7KZ85 (Uniprot-TrEMBL)
SUPT6HProteinQ7KZ85 (Uniprot-TrEMBL)
SYMPK ProteinQ92797 (Uniprot-TrEMBL)
Spliced mRNA:CBC:EJC:TREXComplexR-HSA-8850671 (Reactome)
TAF1 ProteinP21675 (Uniprot-TrEMBL)
TAF10 ProteinQ12962 (Uniprot-TrEMBL)
TAF11 ProteinQ15544 (Uniprot-TrEMBL)
TAF12 ProteinQ16514 (Uniprot-TrEMBL)
TAF13 ProteinQ15543 (Uniprot-TrEMBL)
TAF1L ProteinQ8IZX4 (Uniprot-TrEMBL)
TAF2 ProteinQ6P1X5 (Uniprot-TrEMBL)
TAF3 ProteinQ5VWG9 (Uniprot-TrEMBL)
TAF4 ProteinO00268 (Uniprot-TrEMBL)
TAF4B ProteinQ92750 (Uniprot-TrEMBL)
TAF5 ProteinQ15542 (Uniprot-TrEMBL)
TAF6 ProteinP49848 (Uniprot-TrEMBL)
TAF7 ProteinQ15545 (Uniprot-TrEMBL)
TAF7L ProteinQ5H9L4 (Uniprot-TrEMBL)
TAF9 ProteinQ16594 (Uniprot-TrEMBL)
TAF9B ProteinQ9HBM6 (Uniprot-TrEMBL)
TBP ProteinP20226 (Uniprot-TrEMBL)
TCEA1 ProteinP23193 (Uniprot-TrEMBL)
TCEA1ProteinP23193 (Uniprot-TrEMBL)
TCEB1 ProteinQ15369 (Uniprot-TrEMBL)
TCEB1ProteinQ15369 (Uniprot-TrEMBL)
TCEB2 ProteinQ15370 (Uniprot-TrEMBL)
TCEB2ProteinQ15370 (Uniprot-TrEMBL)
TCEB3 ProteinQ14241 (Uniprot-TrEMBL)
TCEB3B ProteinQ8IYF1 (Uniprot-TrEMBL)
TCEB3C ProteinQ8NG57 (Uniprot-TrEMBL)
TCEB3CL ProteinQ3SY89 (Uniprot-TrEMBL)
TCEB3CL2 ProteinA6NLF2 (Uniprot-TrEMBL)
TFIIAComplexR-HSA-109629 (Reactome)
TFIIDComplexR-HSA-109626 (Reactome)
TFIIEComplexR-HSA-109633 (Reactome)
TFIIFComplexR-HSA-109631 (Reactome)
TFIIHComplexR-HSA-109634 (Reactome)
THOC1 ProteinQ96FV9 (Uniprot-TrEMBL)
THOC2 ProteinQ8NI27 (Uniprot-TrEMBL)
THOC3 ProteinQ96J01 (Uniprot-TrEMBL)
THOC5 ProteinQ13769 (Uniprot-TrEMBL)
THOC6 ProteinQ86W42 (Uniprot-TrEMBL)
THOC7 ProteinQ6I9Y2 (Uniprot-TrEMBL)
Template DNA hybrid with phosphodiester-PPi intermediate R-ALL-83602 (Reactome)
U2AF1 ProteinQ01081 (Uniprot-TrEMBL)
U2AF1L4 ProteinQ8WU68 (Uniprot-TrEMBL)
U2AF2 ProteinP26368 (Uniprot-TrEMBL)
U7 snRNA R-ALL-110761 (Reactome)
U7 snRNP:ZNF473ComplexR-HSA-110765 (Reactome)
UPF3B ProteinQ9BZI7 (Uniprot-TrEMBL)
UTP MetaboliteCHEBI:15713 (ChEBI)
WDR33 ProteinQ9C0J8 (Uniprot-TrEMBL)
WDR61 ProteinQ9GZS3 (Uniprot-TrEMBL)
ZC3H11A ProteinO75152 (Uniprot-TrEMBL)
ZNF473 ProteinQ8WTR7 (Uniprot-TrEMBL)
capped

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

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

substrate:nascent

mRNA hybrid
R-ALL-110291 (Reactome)
downstream

intronless mRNA

fragment
R-ALL-112165 (Reactome)
hSLU7 ProteinO95391 (Uniprot-TrEMBL)
hTra2 R-HSA-72063 (Reactome)
intronless pre-mRNA cleavage complexComplexR-HSA-112162 (Reactome)
mRNA 3'-end cleavage factorComplexR-HSA-72075 (Reactome)
mRNA with spliced exons R-ALL-72156 (Reactome)
p-S2,S5-POLR2A ProteinP24928 (Uniprot-TrEMBL) The C-terminal domain (CTD) of POLR2A contains about 52 repeats of the consensus heptad YSPTSPS. Serines-2 and 5 of the heptads are phosphorylated in RNA polymerase II initiating transcription of protein coding genes. The exact repeats that are phosphorylated are not known.
p-S5-POLR2A ProteinP24928 (Uniprot-TrEMBL)
p-SUPT5H ProteinO00267 (Uniprot-TrEMBL)
p-SUPT5HProteinO00267 (Uniprot-TrEMBL)
pol

II

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

II

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

II

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

promoter:TFIID

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

pre-initiation

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

pre-initiation

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

complex containing 11 nucleotide long

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

complex containing 3 Nucleotide long

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

complex containing 4 nucleotide long

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

complex containing 4-9 nucleotide long

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

complex containing 9 nucleotide long

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

first transcript dinucleotide, opened to +8

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

nucleotide

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

mRNA

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

Annotated Interactions

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

ligated exon

containing complex
ArrowR-HSA-72180 (Reactome)
ADPArrowR-HSA-75949 (Reactome)
AFF4ArrowR-HSA-113429 (Reactome)
AFF4R-HSA-112381 (Reactome)
ATPR-HSA-75949 (Reactome)
Aborted early elongation complexArrowR-HSA-113409 (Reactome)
Aborted elongation

complex after

arrest
ArrowR-HSA-112395 (Reactome)
Arrested processive elongation complexArrowR-HSA-113414 (Reactome)
Arrested processive elongation complexR-HSA-112395 (Reactome)
Arrested processive elongation complexR-HSA-113413 (Reactome)
CCNT1,CCNT2,CCNKR-HSA-112430 (Reactome)
CDK9R-HSA-112430 (Reactome)
CE:Pol II CTD:Spt5 complexArrowR-HSA-77073 (Reactome)
CF IArrowR-HSA-72180 (Reactome)
CF IArrowR-HSA-77592 (Reactome)
CF IIArrowR-HSA-72180 (Reactome)
CF IIArrowR-HSA-77592 (Reactome)
CTDP1ArrowR-HSA-113429 (Reactome)
CTDP1R-HSA-112383 (Reactome)
CTDP1mim-catalysisR-HSA-112383 (Reactome)
Cap Binding Complex (CBC)ArrowR-HSA-112381 (Reactome)
Capped

Intronless Histone

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

Histone pre-mRNA:CBC:ZFP100

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

II promoter with transcript with 2

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

Polymerase II

promoter
R-HSA-109636 (Reactome)
DSIF complexArrowR-HSA-112434 (Reactome)
DSIF complexArrowR-HSA-113429 (Reactome)
DSIF complexR-HSA-113407 (Reactome)
DSIF:NELF:early elongation complexArrowR-HSA-113402 (Reactome)
DSIF:NELF:early elongation complexR-HSA-112381 (Reactome)
DSIF:NELF:early elongation complexR-HSA-113409 (Reactome)
EAF1ArrowR-HSA-113429 (Reactome)
EAF1R-HSA-112381 (Reactome)
EAF2ArrowR-HSA-113429 (Reactome)
EAF2R-HSA-112381 (Reactome)
ELLArrowR-HSA-113429 (Reactome)
ELLR-HSA-112381 (Reactome)
Early elongation

complex with hyperphosphorylated

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

complex with hyperphosphorylated

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

with separated and uncleaved

transcript
ArrowR-HSA-112396 (Reactome)
Elongation complexArrowR-HSA-112379 (Reactome)
Elongation complexR-HSA-112385 (Reactome)
Elongin AR-HSA-112436 (Reactome)
Elongin B:C complexArrowR-HSA-112435 (Reactome)
Elongin B:C complexR-HSA-112436 (Reactome)
Elongin ComplexArrowR-HSA-112436 (Reactome)
Elongin ComplexArrowR-HSA-113429 (Reactome)
Elongin ComplexR-HSA-112379 (Reactome)
FACT complexArrowR-HSA-112429 (Reactome)
FACT complexArrowR-HSA-113429 (Reactome)
FACT complexR-HSA-112379 (Reactome)
GTF2BArrowR-HSA-73946 (Reactome)
GTF2BArrowR-HSA-75856 (Reactome)
GTF2BArrowR-HSA-75869 (Reactome)
GTF2BR-HSA-109637 (Reactome)
IWS1ArrowR-HSA-113429 (Reactome)
IWS1R-HSA-112379 (Reactome)
MLLT1ArrowR-HSA-113429 (Reactome)
MLLT1R-HSA-112381 (Reactome)
MLLT3ArrowR-HSA-113429 (Reactome)
MLLT3R-HSA-112381 (Reactome)
Mature

Intronless transcript derived Histone

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

transcript derived Histone pre-mRNA:CBC

complex
ArrowR-HSA-111437 (Reactome)
NELF complexArrowR-HSA-112437 (Reactome)
NELF complexArrowR-HSA-113429 (Reactome)
NELF complexR-HSA-113402 (Reactome)
NELFAR-HSA-112437 (Reactome)
NELFBR-HSA-112437 (Reactome)
NELFCDR-HSA-112437 (Reactome)
NELFER-HSA-112437 (Reactome)
NTPArrowR-HSA-113402 (Reactome)
NTPArrowR-HSA-113412 (Reactome)
NTPArrowR-HSA-113429 (Reactome)
NTPR-HSA-111264 (Reactome)
NTPR-HSA-112385 (Reactome)
NTPR-HSA-113402 (Reactome)
NTPR-HSA-113412 (Reactome)
NTPR-HSA-75850 (Reactome)
NTPR-HSA-75861 (Reactome)
NTPR-HSA-75869 (Reactome)
NTPR-HSA-75873 (Reactome)
NTPR-HSA-76576 (Reactome)
P-TEFb complexArrowR-HSA-112430 (Reactome)
P-TEFb complexArrowR-HSA-113429 (Reactome)
P-TEFb complexR-HSA-112381 (Reactome)
P-TEFb complexmim-catalysisR-HSA-112381 (Reactome)
PAF1CArrowR-HSA-113429 (Reactome)
PAF1CR-HSA-112379 (Reactome)
PPiArrowR-HSA-111264 (Reactome)
PPiArrowR-HSA-75850 (Reactome)
PPiArrowR-HSA-75864 (Reactome)
PPiArrowR-HSA-75869 (Reactome)
PPiArrowR-HSA-75873 (Reactome)
PPiArrowR-HSA-76576 (Reactome)
Paused processive elongation complexArrowR-HSA-113411 (Reactome)
Paused processive elongation complexR-HSA-112392 (Reactome)
PiArrowR-HSA-75949 (Reactome)
Pol II Initiation

complex with phosphodiester-PPi

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

complex with phosphodiester-PPi

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

complex containing extruded transcript

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

complex containing extruded transcript

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

complex containing extruded transcript

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

complex containing

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

complex containing

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

complex with (ser5) phosphorylated CTD containing extruded

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

complex with (ser5) phosphorylated CTD containing extruded

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

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

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

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

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

R-HSA-109638 (Reactome) The general transcription factor TFIIF has a high affinity for the RNA Polymerase II holoenzyme. TFIIF stabilizes the preinitiation complex, and suppresses non-specific binding of RNA Pol II to DNA, and is thus critical for start site recognition.
R-HSA-109639 (Reactome) The binding of TFIIH completes the assembly of the preinitiation complex (PIC) for RNA Polymerase II transcription. Although RNA polymerase binds the TATA box on the promoter DNA, no initiation of transcription occurs until TFIIH is bound to the PIC. TFIIH is the only factor with known enzymatic activities.
R-HSA-111264 (Reactome) RNA polymerase II transcription complexes are susceptible to transcriptional stalling and arrest, when extending nascent transcripts to 30-nt. This susceptibility depends on presence on down-stream DNA, the particular DNA-sequence of the template and presence of transcription factors. Transcription factor TFIIH remains associated to the RNA pol II elongation complex until position +30. At this stage transcription elongation factor TFIIS can rescue stalled transcription elongation complexes. The transcription bubble varies between 13- and 22-nt in size.
R-HSA-111437 (Reactome) Processing is initiated once the U7 snRNP is loaded onto the pre-mRNA. The pre-mRNA HDE makes base-pairing contacts with the 5�² end of U7 snRNA. Binding of the U7 snRNP to the pre-mRNA is stabilized by interactions between a U7 snRNP protein, hZFP100 and other trans-acting factors, including the factor that catalyzes the cleavage reaction, which have yet to be defined. The cleavage occurs in the presence of EDTA as does the cleavage reaction in polyadenylation, it is likely that this reaction is catalyzed by a protein. There may well be additional proteins associated with the U7 snRNP, since the in vitro processing occurs in the absence of SLBP, it is possible that all the other factors required for processing are associated with the active form of the U7 snRNP.
R-HSA-112379 (Reactome) At the beginning of this reaction, 1 molecule of 'FACT complex', 1 molecule of 'Elongin Complex', 1 molecule of 'Early elongation complex with hyperphosphorylated Pol II CTD', 1 molecule of 'TFIIH', 1 molecule of 'RNA polymerase II elongation factor ELL', and 1 molecule of 'TFIIS protein' are present. At the end of this reaction, 1 molecule of 'Elongation complex' is present.

This reaction takes place in the 'nucleus'.

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

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

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus' (Kamakaka et al.1993, Orphanides et al.1998).

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

This reaction takes place in the 'nucleus'.

R-HSA-112434 (Reactome) At the beginning of this reaction, 1 molecule of 'SUPT5H protein', and 1 molecule of 'SPT4H1 protein' are present. At the end of this reaction, 1 molecule of 'DSIF complex' is present (Wada et al. 1998).

This reaction takes place in the 'nucleus'.

R-HSA-112435 (Reactome) At the beginning of this reaction, 1 molecule of 'Elongin B protein', and 1 molecule of 'Elongin C protein' are present. At the end of this reaction, 1 molecule of 'Elongin B:C complex' is present. This reaction takes place in the 'nucleus' (Aso et al., 1995; Duan et al., 1995b; Kibel et al., 1995).
R-HSA-112436 (Reactome) At the beginning of this reaction, 1 molecule of 'Elongin A1 protein', and 1 molecule of 'Elongin B:C complex' are present. At the end of this reaction, 1 molecule of 'Elongin Complex' is present.

This reaction takes place in the 'nucleus' (Kibel et al. 1995, Aso et al. 1995, Duan et al. 1995).

R-HSA-112437 (Reactome) At the beginning of this reaction, 1 molecule of 'NELF-A protein', 1 molecule of 'RD protein', 1 molecule of 'NELF-B protein', and 1 molecule of 'NELF-C/D protein' are present. At the end of this reaction, 1 molecule of 'NELF complex' is present(Yamaguchi et al.1999).

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus' (Woudstra et al. 2002).

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

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

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

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

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

This reaction takes place in the 'nucleus'.

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

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

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

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

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

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

This reaction takes place in the 'nucleus'.

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

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

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

This reaction takes place in the 'nucleus'.

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

This reaction takes place in the 'nucleus'.

R-HSA-77071 (Reactome) Phosphorylation of serine 5 residue at the CTD of pol II largest subunit is an important step signaling the end of initiation and escape into processive elongation processes. Cdk7 protein subunit of TFIIH phosphorylates RNA Pol II CTD serine 5 residues on its heptad repeats (Buratowski 2009).
R-HSA-77073 (Reactome) The capping enzyme interacts with the Spt5 subunit of transcription elongation factor DSIF. This interaction may couple the capping reaction with promoter escape or elongation, thereby acting as a "checkpoint" to assure that capping has occurred before the polymerase proceeds to make the rest of the transcript (Gonatopoulos-Pournatzis et al.2011).
R-HSA-77586 (Reactome) Processing is initiated once the SLBP (bound to the stem loop) and the U7 snRNP (bound to the HDE) are both loaded onto the pre-mRNA. The pre-mRNA HDE makes base-pairing contacts with the 5�² end of U7 snRNA. Binding of the U7 snRNP to the pre-mRNA is stabilized by interactions between a U7 snRNP protein, hZFP100 and SLBP. It should be noted that there must be other trans-acting factors, including the factor that catalyzes the cleavage reaction, which have yet to be defined. The cleavage occurs in the presence of EDTA as does the cleavage reaction in polyadenylation, it is likely that this reaction is catalyzed by a protein. There may well be additional proteins associated with the U7 snRNP, and since in some conditions in vitro processing occurs in the absence of SLBP, it is possible that all the other factors required for processing are associated with the active form of the U7 snRNP.
R-HSA-77592 (Reactome) The polypeptide catalyzing the hydrolysis of the phosphodiester bond remains to be identified. Cleavage produces a 3'-OH on the upstream fragment and a 5'-phosphate on the downstream fragment. At some unknown point after cleavage, the downstream fragment, CstF, CF I and CF II are thought to be released, whereas CPSF and poly(A) polymerase remain to carry out polyadenylation.
RNA

Pol II

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

Pol II

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

Pol II

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

Pol II

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

Polymerase II

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

Polymerase II

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

Polymerase II

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

Polymerase II

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

Polymerase II

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

Polymerase II

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

Polymerase II

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

Polymerase II

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

Polymerase II

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

Polymerase II holoenzyme complex

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

phosphorylated CTD: CE complex with

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

phosphorylated CTD: CE complex with

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

phosphorylated CTD:

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

phosphorylated CTD:

CE complex
R-HSA-77068 (Reactome)
RNGTTR-HSA-77069 (Reactome)
RNMTR-HSA-77073 (Reactome)
SSRP1R-HSA-112429 (Reactome)
SUPT16HR-HSA-112429 (Reactome)
SUPT4H1R-HSA-112434 (Reactome)
SUPT6HArrowR-HSA-113429 (Reactome)
SUPT6HR-HSA-112379 (Reactome)
Spliced mRNA:CBC:EJC:TREXR-HSA-72180 (Reactome)
TCEA1ArrowR-HSA-113429 (Reactome)
TCEA1R-HSA-112379 (Reactome)
TCEB1R-HSA-112435 (Reactome)
TCEB2R-HSA-112435 (Reactome)
TFIIAArrowR-HSA-73946 (Reactome)
TFIIAArrowR-HSA-75856 (Reactome)
TFIIAArrowR-HSA-75873 (Reactome)
TFIIAR-HSA-109637 (Reactome)
TFIIDArrowR-HSA-73946 (Reactome)
TFIIDArrowR-HSA-75856 (Reactome)
TFIIDArrowR-HSA-75873 (Reactome)
TFIIDR-HSA-109636 (Reactome)
TFIIEArrowR-HSA-73946 (Reactome)
TFIIEArrowR-HSA-75856 (Reactome)
TFIIEArrowR-HSA-75873 (Reactome)
TFIIEArrowR-HSA-75891 (Reactome)
TFIIER-HSA-75095 (Reactome)
TFIIFArrowR-HSA-113429 (Reactome)
TFIIHArrowR-HSA-112383 (Reactome)
TFIIHArrowR-HSA-112385 (Reactome)
TFIIHArrowR-HSA-73946 (Reactome)
TFIIHArrowR-HSA-75856 (Reactome)
TFIIHArrowR-HSA-75891 (Reactome)
TFIIHR-HSA-109639 (Reactome)
TFIIHR-HSA-112379 (Reactome)
TFIIHR-HSA-112383 (Reactome)
TFIIHmim-catalysisR-HSA-75850 (Reactome)
TFIIHmim-catalysisR-HSA-75869 (Reactome)
TFIIHmim-catalysisR-HSA-75949 (Reactome)
U7 snRNP:ZNF473ArrowR-HSA-111437 (Reactome)
U7 snRNP:ZNF473ArrowR-HSA-77586 (Reactome)
capped

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

complex
R-HSA-112383 (Reactome)
damaged DNA

substrate:nascent

mRNA hybrid
ArrowR-HSA-113429 (Reactome)
downstream

intronless mRNA

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

II

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

II

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

II

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

II

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

II

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

II

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

promoter:TFIID

complex
ArrowR-HSA-109636 (Reactome)
pol II

promoter:TFIID

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

pre-initiation

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

pre-initiation

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

pre-initiation

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

pre-initiation

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

pre-initiation

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

pre-initiation

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

complex containing 11 nucleotide long

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

complex containing 11 nucleotide long

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

complex containing 3 Nucleotide long

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

complex containing 3 Nucleotide long

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

complex containing 4 nucleotide long

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

complex containing 4 nucleotide long

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

complex containing 4-9 nucleotide long

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

complex containing 9 nucleotide long

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

complex containing 9 nucleotide long

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

first transcript dinucleotide, opened to +8

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

nucleotide

transcript hybrid
ArrowR-HSA-75891 (Reactome)
upstream

mRNA

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