BioPAX pathway converted from "RNA Polymerase II Promoter Escape" in the Reactome database. RNA Polymerase II Promoter Escape RNA Polymerase II Promoter Escape This event has been computationally inferred from an event that has been demonstrated in another species.

The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.

More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp Unwinding DNA for the nascent transcript Unwinding DNA for the nascent transcript This event has been computationally inferred from an event that has been demonstrated in another species.

The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.

More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp Converted from EntitySet in Reactome Reactome DB_ID: 30595 1 nucleoplasm GO 0005654 NTP [nucleoplasm] Converted from EntitySet in Reactome. Each synonym is a name of a PhysicalEntity, and each XREF points to one PhysicalEntity CTP [nucleoplasm] UTP [nucleoplasm] ATP [nucleoplasm] GTP [nucleoplasm] Reactome //www.joaskin.com ChEBI 17677 ChEBI 15713 ChEBI 30616 ChEBI 15996 Reactome DB_ID: 10648516 1 pol II transcription complex [nucleoplasm] pol II transcription complex Reactome DB_ID: 109877 1 template DNA with first transcript dinucleotide, opened to +8 position [nucleoplasm] template DNA with first transcript dinucleotide, opened to +8 position Reactome DB_ID: 10648514 1 TFIIE [nucleoplasm] TFIIE Reactome DB_ID: 10648507 1 UniProt:Q557M8 gtf2e1-1 Dictyostelium discoideum NCBI Taxonomy 44689 UniProt Q557M8 Chain Coordinates 2 EQUAL 439 EQUAL Reactome DB_ID: 10648512 1 UniProt:Q54KJ8 gtf2e2 UniProt Q54KJ8 1 EQUAL 291 EQUAL Reactome Database ID Release 77 10648514 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10648514 Reactome R-DDI-109633 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-109633.1 Reactome DB_ID: 10648291 1 TFIIH [nucleoplasm] TFIIH Reactome DB_ID: 10648269 1 UniProt:Q86IB5 gtf2h3 UniProt Q86IB5 1 EQUAL 308 EQUAL Reactome DB_ID: 10648274 1 UniProt:Q86KZ2 gtf2h2 UniProt Q86KZ2 1 EQUAL 395 EQUAL Reactome DB_ID: 10648264 1 UniProt:O00835 repB UniProt O00835 1 EQUAL 782 EQUAL Reactome DB_ID: 10648284 1 UniProt:Q55FP1 gtf2h1 UniProt Q55FP1 1 EQUAL 548 EQUAL Reactome DB_ID: 10648254 1 CAK(核浆) CAK Reactome DB_ID: 10648247 1 UniProt:Q55F19 cycH UniProt Q55F19 1 EQUAL 323 EQUAL Reactome DB_ID: 10648242 1 UniProt:P54685 cdk7 UniProt P54685 1 EQUAL 346 EQUAL Reactome DB_ID: 10648252 1 UniProt:Q54I13 mnat1 UniProt Q54I13 1 EQUAL 309 EQUAL Reactome Database ID Release 77 10648254 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10648254 Reactome R-DDI-69221 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-69221.1 Reactome DB_ID: 10648289 1 UniProt:Q55CT8 gtf2h5 UniProt Q55CT8 1 EQUAL 71 EQUAL Reactome DB_ID: 10648279 1 UniProt:Q54C29 gtf2h4 UniProt Q54C29 1 EQUAL 462 EQUAL Reactome DB_ID: 10648259 1 UniProt:Q55G81 repD UniProt Q55G81 1 EQUAL 760 EQUAL Reactome Database ID Release 77 10648291 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10648291 Reactome R-DDI-109634 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-109634.1 Reactome DB_ID: 10646488 1 RNA Polymerase II (unphosphorylated):TFIIF complex [nucleoplasm] RNA Polymerase II (unphosphorylated):TFIIF complex Reactome DB_ID: 10646486 1 RNA Polymerase II holoenzyme complex (unphosphorylated) [nucleoplasm] RNA Polymerase II holoenzyme complex (unphosphorylated) Reactome DB_ID: 10646452 1 UniProt:Q54EH2 polr2e UniProt Q54EH2 1 EQUAL 210 EQUAL Reactome DB_ID: 10646484 1 UniProt:P35084 polr2a UniProt P35084 1 EQUAL 1970 EQUAL Reactome DB_ID: 10646412 1 UniProt:Q86JJ5 polr2j UniProt Q86JJ5 1 EQUAL 117 EQUAL Reactome DB_ID: 10646432 1 UniProt:Q54P04 polr2g UniProt Q54P04 1 EQUAL 172 EQUAL Reactome DB_ID: 10646457 1 UniProt:Q54FA8 polr2f UniProt Q54FA8 2 EQUAL 127 EQUAL Reactome DB_ID: 10646417 1 UniProt:Q55GG8 rpb9 UniProt Q55GG8 1 EQUAL 125 EQUAL Reactome DB_ID: 10646437 1 UniProt:Q54DH7 polr2c UniProt Q54DH7 2 EQUAL 275 EQUAL Reactome DB_ID: 10646447 1 UniProt:Q54R66 polr2k UniProt Q54R66 1 EQUAL 58 EQUAL Reactome DB_ID: 10646427 1 UniProt:Q54S04 polr2d UniProt Q54S04 1 EQUAL 142 EQUAL Reactome DB_ID: 10646422 1 UniProt:Q54J75 polr2b UniProt Q54J75 1 EQUAL 1174 EQUAL Reactome DB_ID: 10646442 1 UniProt:Q54YW8 polr2h UniProt Q54YW8 2 EQUAL 150 EQUAL Reactome DB_ID: 10646462 1 UniProt:Q55AB6 polr2l UniProt Q55AB6 1 EQUAL 67 EQUAL Reactome Database ID Release 77 10646486 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10646486 Reactome R-DDI-113401 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-113401.1 Reactome DB_ID: 10646476 1 TFIIF [nucleoplasm] TFIIF Reactome DB_ID: 10646469 1 UniProt:Q54WV4 gtf2f1 UniProt Q54WV4 2 EQUAL 517 EQUAL Reactome DB_ID: 10646474 1 UniProt:Q54KT7 gtf2f2 UniProt Q54KT7 2 EQUAL 249 EQUAL Reactome Database ID Release 77 10646476 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10646476 Reactome R-DDI-109631 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-109631.1 Reactome Database ID Release 77 10646488 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10646488 Reactome R-DDI-71307 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-71307.1 Reactome DB_ID: 10648502 1 TFIID [nucleoplasm] TFIID Reactome DB_ID: 10648496 1 UniProt:Q55BH6 TAF7 UniProt Q55BH6 1 EQUAL 349 EQUAL Reactome DB_ID: 10648465 1 Ghost homologue of TAF10 [nucleoplasm] Ghost homologue of TAF10 Reactome DB_ID: 10648489 1 UniProt:Q54DH8 taf1 UniProt Q54DH8 1 EQUAL 1872 EQUAL Reactome DB_ID: 10648484 1 UniProt:Q55A39 TAF9 UniProt Q55A39 1 EQUAL 251 EQUAL Reactome DB_ID: 10648482 1 Ghost homologue of TAF3 [nucleoplasm] Ghost homologue of TAF3 Reactome DB_ID: 10648475 1 1 EQUAL 264 EQUAL Reactome DB_ID: 10648448 1 UniProt:Q54X70 UniProt Q54X70 1 EQUAL 1085 EQUAL Reactome DB_ID: 10648453 1 UniProt:Q54CN8 taf13 UniProt Q54CN8 1 EQUAL 124 EQUAL Reactome DB_ID: 10648458 1 UniProt:Q555L9 TAF12 UniProt Q555L9 1 EQUAL 161 EQUAL Reactome DB_ID: 10648463 1 UniProt:Q54XM9 taf11 UniProt Q54XM9 1 EQUAL 211 EQUAL Reactome DB_ID: 10648480 1 UniProt:C7G081 taf2 UniProt C7G081 1 EQUAL 1199 EQUAL Reactome DB_ID: 10648446 1 1 EQUAL 862 EQUAL Reactome DB_ID: 10648500 1 Ghost homologue of TAF15 [nucleoplasm] Ghost homologue of TAF15 Reactome DB_ID: 10648229 1 UniProt:P26355 tbpA UniProt P26355 1 EQUAL 339 EQUAL Reactome DB_ID: 10648441 1 UniProt:Q54KH7 TAF5 UniProt Q54KH7 1 EQUAL 800 EQUAL Reactome DB_ID: 10648470 1 UniProt:Q54IW7 TAF6 UniProt Q54IW7 1 EQUAL 677 EQUAL Reactome Database ID Release 77 10648502 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10648502 Reactome R-DDI-109626 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-109626.1 Reactome DB_ID: 10648431 1 TFIIA [nucleoplasm] TFIIA Reactome DB_ID: 10648424 1 UniProt:Q54G80 gtf2a1 UniProt Q54G80 275 EQUAL 376 EQUAL Reactome DB_ID: 10648422 1 1 EQUAL 274 EQUAL Reactome DB_ID: 10648429 1 UniProt:Q54ND1 gtf2a2 UniProt Q54ND1 1 EQUAL 109 EQUAL Reactome Database ID Release 77 10648431 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10648431 Reactome R-DDI-109629 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-109629.1 Reactome DB_ID: 10648436 1 UniProt:Q54FD6 gtf2b UniProt Q54FD6 1 EQUAL 316 EQUAL Reactome Database ID Release 77 10648516 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10648516 Reactome R-DDI-109878 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-109878.1 Reactome DB_ID: 113541 1 diphosphoric acid [ChEBI:29888] diphosphoric acid ChEBI 29888 Reactome DB_ID: 10648516 1 PHYSIOL-LEFT-TO-RIGHT ACTIVATION Reactome DB_ID: 10648291 GO 0043138 GO molecular function Reactome Database ID Release 77 10649302 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10649302 Reactome Database ID Release 77 10698845 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10698845 Reactome R-DDI-9613497 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-9613497.1 The human BTF2 basic transcription factor (also called TFIIH), is required for class1 gene transcription of transcripts. TFIIH has an adenosine triphosphate-dependent DNA helicase activity. The helicase activity is closely associated with the multi-subunit BTF2/TFIIH transcription factor which also has a CTD protein kinase activity. 8465201 Pubmed 1993 DNA repair helicase: a component of BTF2 (TFIIH) basic transcription factor Schaeffer, L Roy, R Humbert, S Moncollin, V Vermeulen, W Hoeijmakers, J H Chambon, P Egly, JM Science 260:58-63 11784853 Pubmed 2002 Translocation after synthesis of a four-nucleotide RNA commits RNA polymerase II to promoter escape. Kugel, JF Goodrich, JA Mol Cell Biol 22:762-73 9405375 Pubmed 1998 Three transitions in the RNA polymerase II transcription complex during initiation. Holstege, FC Fiedler, U Timmers, HT EMBO J 16:7468-80 inferred by electronic annotation IEA GO IEA 2.7.7.6 Addition of the third nucleotide on the nascent transcript Addition of the third nucleotide on the nascent transcript This event has been computationally inferred from an event that has been demonstrated in another species.

The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.

More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp Converted from EntitySet in Reactome Reactome DB_ID: 30595 1 Reactome DB_ID: 10648516 1 Reactome DB_ID: 113541 1 Reactome DB_ID: 10649161 1 pol II transcription complex containing 3 Nucleotide long transcript [nucleoplasm] pol II transcription complex containing 3 Nucleotide long transcript Reactome DB_ID: 75858 1 template DNA:3 nucleotide transcript hybrid [nucleoplasm] template DNA:3 nucleotide transcript hybrid Reactome DB_ID: 10648514 1 Reactome DB_ID: 10648291 1 Reactome DB_ID: 10646488 1 Reactome DB_ID: 10648502 1 Reactome DB_ID: 10648431 1 Reactome DB_ID: 10648436 1 1 EQUAL 316 EQUAL Reactome Database ID Release 77 10649161 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10649161 Reactome R-DDI-75878 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-75878.1 PHYSIOL-LEFT-TO-RIGHT ACTIVATION Reactome DB_ID: 10646488 GO 0003899 GO molecular function Reactome Database ID Release 77 10649162 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10649162 Reactome Database ID Release 77 10649164 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10649164 Reactome R-DDI-75850 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-75850.1 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. inferred by electronic annotation IEA GO IEA Unwinding of DNA for the Nascent Transcript: Second Transition Unwinding of DNA for the Nascent Transcript: Second Transition This event has been computationally inferred from an event that has been demonstrated in another species.

The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.

More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp Reactome DB_ID: 10649161 1 Reactome DB_ID: 29358 1 ATP(4-) [ChEBI:30616] ATP(4-) Adenosine 5'-triphosphate atp ATP Reactome DB_ID: 113541 1 Reactome DB_ID: 164121 1 adenosine 5'-monophosphate [ChEBI:16027] adenosine 5'-monophosphate ChEBI 16027 Reactome DB_ID: 10649161 1 PHYSIOL-LEFT-TO-RIGHT ACTIVATION Reactome DB_ID: 10648291 Reactome Database ID Release 77 10698843 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10698843 Reactome R-DDI-9613494 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-9613494.1 The human BTF2 basic transcription factor (also called TFIIH), is required for class1 gene transcription of the second round of transcripts. TFIIH has an adenosine triphosphate-dependent DNA helicase activity. The helicase activity is closely associated with the multi-subunit BTF2/TFIIH transcription factor which also has a CTD protein kinase activity. inferred by electronic annotation IEA GO IEA 2.7.7.6 Addition of the fourth nucleotide on the Nascent Transcript: Second Transition Addition of the fourth nucleotide on the Nascent Transcript: Second Transition This event has been computationally inferred from an event that has been demonstrated in another species.

The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.

More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp Converted from EntitySet in Reactome Reactome DB_ID: 30595 1 Reactome DB_ID: 10649161 1 Reactome DB_ID: 113541 1 Reactome DB_ID: 10648436 1 1 EQUAL 316 EQUAL Reactome DB_ID: 10649201 1 pol II transcription complex containing 4 nucleotide long transcript [nucleoplasm] pol II transcription complex containing 4 nucleotide long transcript Reactome DB_ID: 10648514 1 Reactome DB_ID: 10648291 1 Reactome DB_ID: 10646488 1 Reactome DB_ID: 10648502 1 Reactome DB_ID: 10648431 1 Reactome DB_ID: 75884 1 template DNA:4 nucleotide transcript hybrid [nucleoplasm] template DNA:4 nucleotide transcript hybrid Reactome Database ID Release 77 10649201 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10649201 Reactome R-DDI-75881 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-75881.1 PHYSIOL-LEFT-TO-RIGHT ACTIVATION Reactome DB_ID: 10646488 Reactome Database ID Release 77 10649203 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10649203 Reactome R-DDI-75869 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-75869.1 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. inferred by electronic annotation IEA GO IEA 2.7.7.6 Addition of Nucleotides 5 through 9 on the growing Transcript Addition of Nucleotides 5 through 9 on the growing Transcript This event has been computationally inferred from an event that has been demonstrated in another species.

The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.

More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp Converted from EntitySet in Reactome Reactome DB_ID: 30595 5 Reactome DB_ID: 10649201 1 Reactome DB_ID: 113541 5 Reactome DB_ID: 10648514 1 Reactome DB_ID: 10648502 1 Reactome DB_ID: 10648431 1 Reactome DB_ID: 10649230 1 pol II transcription complex containing 9 nucleotide long transcript [nucleoplasm] pol II transcription complex containing 9 nucleotide long transcript Reactome DB_ID: 75888 1 template DNA:9 nucleotide transcript hybrid [nucleoplasm] template DNA:9 nucleotide transcript hybrid Reactome DB_ID: 10648291 1 Reactome DB_ID: 10646488 1 Reactome Database ID Release 77 10649230 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10649230 Reactome R-DDI-75882 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-75882.1 PHYSIOL-LEFT-TO-RIGHT ACTIVATION Reactome DB_ID: 10646488 Reactome Database ID Release 77 10649232 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10649232 Reactome R-DDI-75873 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-75873.1 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. 7601352 Pubmed 1995 Recycling of the general transcription factors during RNA polymerase II transcription. Zawel, L Kumar, KP Reinberg, Danny Genes Dev 9:1479-90 9256425 Pubmed 1997 A role for TFIIH in controlling the activity of early RNA polymerase II elongation complexes. Dvir, A Conaway, Ron C Conaway, Joan W Proc Natl Acad Sci U S A 94:9006-10 11739720 Pubmed 2001 Strong natural pausing by RNA polymerase II within 10 bases of transcription start may result in repeated slippage and reextension of the nascent RNA. Pal, M Luse, DS Mol Cell Biol 22:30-40 inferred by electronic annotation IEA GO IEA 2.7.7.6 Addition of nucleotides 10 and 11 on the growing transcript: Third Transition Addition of nucleotides 10 and 11 on the growing transcript: Third Transition This event has been computationally inferred from an event that has been demonstrated in another species.

The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.

More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp Converted from EntitySet in Reactome Reactome DB_ID: 30595 2 Reactome DB_ID: 10649230 1 Reactome DB_ID: 113541 2 Reactome DB_ID: 10649868 1 pol II transcription complex containing 11 nucleotide long transcript [nucleoplasm] pol II transcription complex containing 11 nucleotide long transcript Reactome DB_ID: 75901 1 template DNA:11 nucleotide transcript hybrid [nucleoplasm] template DNA:11 nucleotide transcript hybrid Reactome DB_ID: 10648291 1 Reactome DB_ID: 10646488 1 Reactome Database ID Release 77 10649868 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10649868 Reactome R-DDI-75902 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-75902.1 PHYSIOL-LEFT-TO-RIGHT ACTIVATION Reactome DB_ID: 10646488 Reactome Database ID Release 77 10649870 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10649870 Reactome R-DDI-76576 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-76576.1 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. inferred by electronic annotation IEA GO IEA 2.7.7.6 Addition of nucleotides between position +11 and +30 Addition of nucleotides between position +11 and +30 This event has been computationally inferred from an event that has been demonstrated in another species.

The inference is based on the homology mapping from PANTHER. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation.

More details and caveats of the event inference in Reactome. For details on PANTHER see also: http://www.pantherdb.org/about.jsp Converted from EntitySet in Reactome Reactome DB_ID: 30595 1 Reactome DB_ID: 10649868 1 Reactome DB_ID: 10649905 1 Pol II transcription complex containing extruded transcript to +30 [nucleoplasm] Pol II transcription complex containing extruded transcript to +30 Reactome DB_ID: 111260 1 template DNA:30 nt transcript hybrid [nucleoplasm] template DNA:30 nt transcript hybrid Reactome DB_ID: 10648291 1 Reactome DB_ID: 10646488 1 Reactome Database ID Release 77 10649905 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10649905 Reactome R-DDI-157171 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-157171.1 Reactome DB_ID: 113541 1 PHYSIOL-LEFT-TO-RIGHT ACTIVATION Reactome DB_ID: 10646488 Reactome Database ID Release 77 10650361 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10650361 Reactome R-DDI-111264 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-111264.1 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. 11486021 Pubmed 2001 Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence. Pal, M McKean, D Luse, DS Mol Cell Biol 21:5815-25 9353262 Pubmed 1997 Promoter escape by RNA polymerase II. Formation of an escape-competent transcriptional intermediate is a prerequisite for exit of polymerase from the promoter. Dvir, A Tan, S Conaway, Joan W Conaway, Ron C J Biol Chem 272:28175-8 11433015 Pubmed 2001 Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation. Fiedler, U Timmers, HT Nucleic Acids Res 29:2706-14 inferred by electronic annotation IEA GO IEA Reactome Database ID Release 77 10700637 数据库标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser?DB=gk_current&ID=10700637 Reactome R-DDI-73776 1 Reactome稳定的标识符。使用这个URL连接到the web page of this instance in Reactome: //www.joaskin.com/cgi-bin/eventbrowser_st_id?ST_ID=R-DDI-73776.1 GO 0006368 GO biological process RNA Polymerase II promoter escape occurs after the first phosphodiester bond has been created. inferred by electronic annotation IEA GO IEA