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ONTOLOGY REPORT - ANNOTATIONS


Term:DNA-templated transcription, initiation
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Accession:GO:0006352 term browser browse the term
Definition:Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
Comment:Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation.
Synonyms:exact_synonym: DNA-dependent RNA polymerase complex assembly at promoter;   initiation of DNA-dependent transcription
 related_synonym: transcription initiation factor activity;   transcription initiation, DNA-dependent
 xref: MIPS_funcat:11.02.03.01.01


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DNA-templated transcription, initiation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Brf1 BRF1, RNA polymerase III transcription initiation factor subunit JBrowse link 6 137,762,230 137,808,573 RGD:13792537
G Brf2 BRF2, RNA polymerase III transcription initiation factor subunit JBrowse link 16 69,089,955 69,094,678 RGD:13792537
G Gtf2b general transcription factor IIB JBrowse link 2 248,709,433 248,727,741 RGD:13792537
G Hist1h2ao histone cluster 1, H2ao JBrowse link 17 44,744,534 44,744,931 RGD:1600115
G Hist1h4b histone cluster 1 H4 family member B JBrowse link 17 44,522,144 44,526,587 RGD:1600115
G Hist1h4m histone cluster 1, H4m RGD:1600115
G Hist2h4 histone cluster 2, H4 JBrowse link 2 198,411,955 198,412,350 RGD:1600115
G Hist2h4a histone cluster 2 H4 family member A JBrowse link 4 170,800,539 170,800,979 RGD:1600115
G LOC100912489 histone H4-like JBrowse link 4 170,144,871 170,145,311 RGD:1600115
G LOC100912564 histone H4-like JBrowse link 4 170,182,634 170,183,074 RGD:1600115
G Myc MYC proto-oncogene, bHLH transcription factor JBrowse link 7 102,586,313 102,591,240 RGD:69897
G Ncoa6 nuclear receptor coactivator 6 JBrowse link 3 150,919,317 150,990,391 RGD:1600115
RGD:1624291
G RGD1562378 histone H4 variant H4-v.1 JBrowse link 4 170,762,862 170,763,962 RGD:1600115
G Rrn3 RRN3 homolog, RNA polymerase I transcription factor JBrowse link 10 3,170,387 3,214,648 RGD:1624291
G Rsf1 remodeling and spacing factor 1 JBrowse link 1 162,549,222 162,671,962 RGD:1624291
RGD:1600115
G Smarca5 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 JBrowse link 19 30,936,703 30,969,454 RGD:1624291
G Taf10 TATA-box binding protein associated factor 10 JBrowse link 1 170,585,160 170,586,428 RGD:1624291
G Taf12 TATA-box binding protein associated factor 12 JBrowse link 5 150,459,701 150,476,521 RGD:1624291
G Taf4 TATA-box binding protein associated factor 4 JBrowse link 3 175,300,842 175,364,655 RGD:1624291
G Taf4b TATA-box binding protein associated factor 4b JBrowse link 18 6,206,939 6,338,794 RGD:1600115
G Taf5 TATA-box binding protein associated factor 5 JBrowse link 1 266,844,480 266,859,965 RGD:1624291
G Taf6 TATA-box binding protein associated factor 6 JBrowse link 12 19,320,269 19,328,706 RGD:1624291
G Taf7 TATA-box binding protein associated factor 7 JBrowse link 18 30,779,149 30,781,297 RGD:1624291
G Taf9 TATA-box binding protein associated factor 9 JBrowse link 2 30,664,407 30,668,414 RGD:1600115
G Taf9b TATA-box binding protein associated factor 9b JBrowse link X 77,281,234 77,295,238 RGD:1600115
G Tbpl1 TATA-box binding protein like 1 JBrowse link 1 23,977,154 24,002,512 RGD:1600115
G Tcf4 transcription factor 4 JBrowse link 18 65,285,320 65,507,983 RGD:1624291
negative regulation of DNA-templated transcription, initiation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Morc1 MORC family CW-type zinc finger 1 JBrowse link 11 54,762,654 55,044,581 RGD:1624291
RGD:1600115
G Thra thyroid hormone receptor alpha JBrowse link 10 86,657,285 86,684,935 RGD:1624291
negative regulation of RNA polymerase II transcriptional preinitiation complex assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Hmgb1 high mobility group box 1 JBrowse link 12 7,082,529 7,090,246 RGD:1624291
G Thra thyroid hormone receptor alpha JBrowse link 10 86,657,285 86,684,935 RGD:1600115
RGD:1624291
negative regulation of transcription initiation from RNA polymerase II promoter term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ctnnbip1 catenin, beta-interacting protein 1 JBrowse link 5 166,464,170 166,513,030 RGD:1624291
RGD:1600115
G Hey2 hes-related family bHLH transcription factor with YRPW motif 2 JBrowse link 1 29,191,170 29,201,257 RGD:1624291
RGD:1600115
G Zfp451 zinc finger protein 451 JBrowse link 9 38,395,464 38,451,585 RGD:1624291
RGD:1600115
positive regulation of DNA-templated transcription, initiation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Bclaf1 BCL2-associated transcription factor 1 JBrowse link 1 15,799,753 15,828,838 RGD:1624291
G Cebpa CCAAT/enhancer binding protein alpha JBrowse link 1 91,363,492 91,366,164 RGD:1624291
G Ctnnb1 catenin beta 1 JBrowse link 8 129,601,511 129,628,378 RGD:1624291
RGD:1600115
G Fosl1 FOS like 1, AP-1 transcription factor subunit JBrowse link 1 220,826,560 220,835,066 RGD:1624291
RGD:1600115
G Jun Jun proto-oncogene, AP-1 transcription factor subunit JBrowse link 5 114,011,184 114,014,277 RGD:1624291
RGD:1600115
G Mitf melanocyte inducing transcription factor JBrowse link 4 130,172,484 130,425,496 RGD:1624291
RGD:1600115
G Setx senataxin JBrowse link 3 7,680,430 7,731,815 RGD:1624291
RGD:1600115
G Twist1 twist family bHLH transcription factor 1 JBrowse link 6 53,401,241 53,403,235 RGD:1624291
RGD:1600115
positive regulation of RNA polymerase II transcriptional preinitiation complex assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ahr aryl hydrocarbon receptor JBrowse link 6 54,963,990 55,001,806 RGD:1624291
G Cand1 cullin-associated and neddylation-dissociated 1 JBrowse link 7 62,124,362 62,162,451 RGD:8553447
G Creb1 cAMP responsive element binding protein 1 JBrowse link 9 71,229,753 71,298,994 RGD:1625706
G Esr1 estrogen receptor 1 JBrowse link 1 41,192,029 41,594,799 RGD:1600115
RGD:1624291
G Gtf2f2 general transcription factor IIF subunit 2 JBrowse link 15 57,942,057 58,068,892 RGD:9681417
G Ikzf1 IKAROS family zinc finger 1 JBrowse link 14 91,782,281 91,867,828 RGD:1624291
G Psmc2 proteasome 26S subunit, ATPase 2 JBrowse link 4 9,867,132 9,881,383 RGD:13792537
G Psmc3 proteasome 26S subunit, ATPase 3 JBrowse link 3 79,876,938 79,882,319 RGD:13792537
G Psmc4 proteasome 26S subunit, ATPase 4 JBrowse link 1 84,978,220 84,986,536 RGD:13792537
G Psmc5 proteasome 26S subunit, ATPase 5 JBrowse link 10 94,445,877 94,451,811 RGD:13792537
G Psmc6 proteasome 26S subunit, ATPase 6 JBrowse link 15 19,667,453 19,688,916 RGD:13792537
G Tp53 tumor protein p53 JBrowse link 10 56,186,299 56,198,449 RGD:1624291
G Wnt10b Wnt family member 10B JBrowse link 7 140,448,284 140,466,159 RGD:1624291
RGD:1600115
positive regulation of transcription initiation from RNA polymerase II promoter term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Dhx36 DEAH-box helicase 36 JBrowse link 2 152,785,844 152,824,549 RGD:1600115
RGD:1624291
G Gtf2b general transcription factor IIB JBrowse link 2 248,709,433 248,727,741 RGD:1600115
RGD:1624291
G Hnf1a HNF1 homeobox A JBrowse link 12 47,407,811 47,433,342 RGD:1624291
G Hnf1b HNF1 homeobox B JBrowse link 10 71,159,863 71,218,902 RGD:1624291
RGD:1600115
G Irf8 interferon regulatory factor 8 JBrowse link 19 54,314,859 54,336,643 RGD:1624291
G Nkx2-5 NK2 homeobox 5 JBrowse link 10 16,635,989 16,638,758 RGD:1624291
RGD:1600115
G Paxip1 PAX interacting protein 1 JBrowse link 4 3,956,931 4,008,326 RGD:1624291
RGD:1600115
G Srf serum response factor JBrowse link 9 16,737,637 16,747,226 RGD:1624291
RGD:1600115
G Sub1 SUB1 regulator of transcription JBrowse link 2 62,019,902 62,034,704 RGD:13792537
G Taf6 TATA-box binding protein associated factor 6 JBrowse link 12 19,320,269 19,328,706 RGD:1624291
regulation of DNA-templated transcription, initiation term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Rrn3 RRN3 homolog, RNA polymerase I transcription factor JBrowse link 10 3,170,387 3,214,648 RGD:1624291
RGD:1600115
regulation of RNA polymerase II transcriptional preinitiation complex assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Atf7ip activating transcription factor 7 interacting protein JBrowse link 4 170,476,998 170,563,063 RGD:1624291
RGD:1600115
G Dr1 down-regulator of transcription 1 JBrowse link 14 2,463,651 2,475,004 RGD:13792537
G LOC100910207 protein Dr1-like JBrowse link 14 1,621,021 1,632,432 RGD:13792537
RNA polymerase I preinitiation complex assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Baz2a bromodomain adjacent to zinc finger domain, 2A JBrowse link 7 2,518,267 2,548,840 RGD:1600115
G Pih1d1 PIH1 domain containing 1 JBrowse link 1 101,151,240 101,156,806 RGD:1600115
G Polr1e RNA polymerase I subunit E JBrowse link 5 60,572,573 60,588,097 RGD:1624291
RGD:13792537
G Rrn3 RRN3 homolog, RNA polymerase I transcription factor JBrowse link 10 3,170,387 3,214,648 RGD:1600115
G Smarca4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 JBrowse link 8 22,648,323 22,739,468 RGD:1600115
G Taf1b TATA-box binding protein associated factor, RNA polymerase I subunit B JBrowse link 6 43,644,931 43,722,124 RGD:1600115
RGD:1624291
G Taf1c TATA-box binding protein associated factor, RNA polymerase 1 subunit C JBrowse link 19 52,246,061 52,252,642 RGD:1600115
G Ubtf upstream binding transcription factor JBrowse link 10 90,250,275 90,265,772 RGD:1600115
RNA polymerase II preinitiation complex assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Gtf2a2 general transcription factor 2A subunit 2 JBrowse link 8 76,422,341 76,435,587 RGD:1624291
RGD:13792537
G Gtf2b general transcription factor IIB JBrowse link 2 248,709,433 248,727,741 RGD:1600115
RGD:13792537
RGD:1624291
G LOC103695118 transcription initiation factor IIA subunit 2 RGD:13792537
G Med6 mediator complex subunit 6 JBrowse link 6 105,302,558 105,316,024 RGD:13792537
G Sgf29 SAGA complex associated factor 29 JBrowse link 1 198,066,974 198,100,494 RGD:1600115
G Taf11 TATA-box binding protein associated factor 11 JBrowse link 20 7,476,648 7,484,417 RGD:13792537
G Taf12 TATA-box binding protein associated factor 12 JBrowse link 5 150,459,701 150,476,521 RGD:13792537
G Taf6 TATA-box binding protein associated factor 6 JBrowse link 12 19,320,269 19,328,706 RGD:13792537
G Taf6l TATA-box binding protein associated factor 6 like JBrowse link 1 224,974,238 224,986,819 RGD:13792537
G Taf7 TATA-box binding protein associated factor 7 JBrowse link 18 30,779,149 30,781,297 RGD:13792537
G Taf7l TATA-box binding protein associated factor 7-like JBrowse link X 105,292,338 105,308,554 RGD:13792537
G Tbp TATA box binding protein JBrowse link 1 57,491,381 57,509,335 RGD:1624291
RGD:1600115
G Tp53 tumor protein p53 JBrowse link 10 56,186,299 56,198,449 RGD:1624291
RNA polymerase III preinitiation complex assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Bdp1 B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB JBrowse link 2 30,248,458 30,340,211 RGD:13792537
G Brf1 BRF1, RNA polymerase III transcription initiation factor subunit JBrowse link 6 137,762,230 137,808,573 RGD:13792537
G Brf2 BRF2, RNA polymerase III transcription initiation factor subunit JBrowse link 16 69,089,955 69,094,678 RGD:13792537
G Gtf3c3 general transcription factor IIIC subunit 3 JBrowse link 9 60,999,159 61,033,612 RGD:1600115
G Gtf3c5 general transcription factor IIIC subunit 5 JBrowse link 3 7,144,354 7,164,678 RGD:1600115
G Tbp TATA box binding protein JBrowse link 1 57,491,381 57,509,335 RGD:13792537
G Tbpl2 TATA box binding protein-like 2 JBrowse link 3 1,095,883 1,116,677 RGD:13792537
transcription initiation from mitochondrial promoter term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Tfam transcription factor A, mitochondrial JBrowse link 20 18,594,057 18,606,106 RGD:1624291
RGD:1600115
G Tfb2m transcription factor B2, mitochondrial JBrowse link 13 97,820,493 97,838,275 RGD:1624291
RGD:1600115
transcription initiation from RNA polymerase I promoter term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Cavin1 caveolae associated protein 1 JBrowse link 10 88,862,513 88,874,495 RGD:1600115
RGD:8554461
RGD:1624291
G Lipe lipase E, hormone sensitive type JBrowse link 1 82,248,031 82,266,727 RGD:8554461
G Rrn3 RRN3 homolog, RNA polymerase I transcription factor JBrowse link 10 3,170,387 3,214,648 RGD:1624291
RGD:13792537
G Ttf1 transcription termination factor 1 JBrowse link 3 7,635,630 7,660,153 RGD:1624291
RGD:1600115
transcription initiation from RNA polymerase II promoter term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ercc3 ERCC excision repair 3, TFIIH core complex helicase subunit JBrowse link 18 25,037,668 25,068,380 RGD:13792537
G Gtf2a1 general transcription factor 2A subunit 1 JBrowse link 6 115,321,110 115,352,659 RGD:1600115
G Gtf2a1l general transcription factor 2A subunit 1 like JBrowse link 6 12,412,198 12,468,613 RGD:1600115
G Gtf2a2 general transcription factor 2A subunit 2 JBrowse link 8 76,422,341 76,435,587 RGD:1600115
G Gtf2b general transcription factor IIB JBrowse link 2 248,709,433 248,727,741 RGD:1600115
RGD:1624291
G Gtf2e2 general transcription factor IIE subunit 2 JBrowse link 16 62,113,846 62,164,339 RGD:13792537
G Gtf2f1 general transcription factor IIF subunit 1 JBrowse link 9 10,032,806 10,042,392 RGD:1600115
G Gtf2f2 general transcription factor IIF subunit 2 JBrowse link 15 57,942,057 58,068,892 RGD:1600115
G LOC103690054 DNA-directed RNA polymerase II subunit RPB9 JBrowse link 1 91,041,173 91,042,258 RGD:13792537
G Maz MYC associated zinc finger protein JBrowse link 1 198,456,699 198,460,126 RGD:1624291
RGD:1600115
G Med1 mediator complex subunit 1 JBrowse link 10 86,101,560 86,145,271 RGD:1624291
RGD:1600115
G Med12 mediator complex subunit 12 JBrowse link X 71,174,653 71,197,812 RGD:1624291
RGD:1600115
G Med13 mediator complex subunit 13 JBrowse link 10 73,702,327 73,787,084 RGD:1624291
RGD:1600115
G Med14 mediator complex subunit 14 JBrowse link X 10,964,035 11,082,403 RGD:1624291
RGD:1600115
G Med16 mediator complex subunit 16 JBrowse link 7 12,619,739 12,632,241 RGD:1624291
RGD:1600115
G Med17 mediator complex subunit 17 JBrowse link 8 13,522,257 13,835,302 RGD:1624291
G Med24 mediator complex subunit 24 JBrowse link 10 86,620,166 86,658,014 RGD:1624291
G Med30 mediator complex subunit 30 JBrowse link 7 92,234,584 92,260,019 RGD:1624291
RGD:13792537
G Med4 mediator complex subunit 4 JBrowse link 15 55,406,543 55,416,816 RGD:1624291
RGD:1600115
G Polr2d RNA polymerase II subunit D JBrowse link 18 24,570,762 24,577,894 RGD:13792537
G Polr2g RNA polymerase II subunit G JBrowse link 1 224,991,250 224,998,355 RGD:13792537
G Polr2i RNA polymerase II subunit I JBrowse link 1 88,686,812 88,688,249 RGD:13792537
G Taf10 TATA-box binding protein associated factor 10 JBrowse link 1 170,585,160 170,586,428 RGD:1624291
RGD:1600115
G Taf12 TATA-box binding protein associated factor 12 JBrowse link 5 150,459,701 150,476,521 RGD:1624291
G Taf2 TATA-box binding protein associated factor 2 JBrowse link 7 94,698,987 94,755,924 RGD:1624291
RGD:13792537
G Taf4 TATA-box binding protein associated factor 4 JBrowse link 3 175,300,842 175,364,655 RGD:1624291
RGD:1600115
G Taf5 TATA-box binding protein associated factor 5 JBrowse link 1 266,844,480 266,859,965 RGD:1624291
RGD:1600115
G Taf6 TATA-box binding protein associated factor 6 JBrowse link 12 19,320,269 19,328,706 RGD:1600115
RGD:1624291
G Taf7 TATA-box binding protein associated factor 7 JBrowse link 18 30,779,149 30,781,297 RGD:1624291
G Tcf4 transcription factor 4 JBrowse link 18 65,285,320 65,507,983 RGD:1624291
RGD:1600115
G Thrap3 thyroid hormone receptor associated protein 3 JBrowse link 5 144,178,248 144,221,318 RGD:1624291
RGD:1600115
transcription initiation from RNA polymerase III promoter term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Crcp CGRP receptor component JBrowse link 12 30,125,237 30,160,857 RGD:1600115
RGD:13792537
G Gtf3c1 general transcription factor IIIC subunit 1 JBrowse link 1 197,032,473 197,098,676 RGD:13792537
G Polr3h RNA polymerase III subunit H JBrowse link 7 123,146,248 123,156,558 RGD:13792537
G Snapc5 small nuclear RNA activating complex, polypeptide 5 JBrowse link 8 69,127,708 69,131,539 RGD:1600115
transcription preinitiation complex assembly term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Gtf2b general transcription factor IIB JBrowse link 2 248,709,433 248,727,741 RGD:1600115
transcriptional open complex formation at RNA polymerase II promoter term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Gtf2e1 general transcription factor IIE subunit 1 JBrowse link 11 66,078,786 66,111,394 RGD:13792537
transcriptional start site selection at RNA polymerase II promoter term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Gtf2b general transcription factor IIB JBrowse link 2 248,709,433 248,727,741 RGD:1600115
RGD:13792537
RGD:1624291

Term paths to the root
Path 1
Term Annotations click to browse term
  biological_process 18008
    metabolic process 10729
      organic substance metabolic process 10177
        macromolecule metabolic process 8720
          gene expression 4958
            transcription, DNA-templated 3068
              DNA-templated transcription, initiation 115
                DNA-templated transcriptional open complex formation + 1
                DNA-templated transcriptional start site selection + 1
                negative regulation of DNA-templated transcription, initiation + 6
                positive regulation of DNA-templated transcription, initiation + 31
                regulation of DNA-templated transcription, initiation + 41
                transcription initiation from RNA polymerase I promoter + 11
                transcription initiation from RNA polymerase II promoter + 67
                transcription initiation from RNA polymerase III promoter + 11
                transcription initiation from bacterial-type RNA polymerase promoter + 0
                transcription initiation from mitochondrial promoter 2
                transcription preinitiation complex assembly + 44
Path 2
Term Annotations click to browse term
  biological_process 18008
    cellular process 16139
      cellular metabolic process 9809
        heterocycle metabolic process 5044
          nucleobase-containing compound metabolic process 4896
            nucleic acid metabolic process 4447
              RNA metabolic process 3980
                RNA biosynthetic process 3124
                  nucleic acid-templated transcription 3112
                    transcription, DNA-templated 3068
                      DNA-templated transcription, initiation 115
                        DNA-templated transcriptional open complex formation + 1
                        DNA-templated transcriptional start site selection + 1
                        negative regulation of DNA-templated transcription, initiation + 6
                        positive regulation of DNA-templated transcription, initiation + 31
                        regulation of DNA-templated transcription, initiation + 41
                        transcription initiation from RNA polymerase I promoter + 11
                        transcription initiation from RNA polymerase II promoter + 67
                        transcription initiation from RNA polymerase III promoter + 11
                        transcription initiation from bacterial-type RNA polymerase promoter + 0
                        transcription initiation from mitochondrial promoter 2
                        transcription preinitiation complex assembly + 44
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.