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ONTOLOGY REPORT - ANNOTATIONS


Term:RNA polymerase II, holoenzyme
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Accession:GO:0016591 term browser browse the term
Definition:A nuclear DNA-directed RNA polymerase complex containing an RNA polymerase II core enzyme as well as additional proteins and transcription factor complexes, that are capable of promoter recognition and transcription initiation from an RNA polymerase II promoter in vivo. These additional components may include general transcription factor complexes TFIIA, TFIID, TFIIE, TFIIF, or TFIIH, as well as Mediator, SWI/SNF, GCN5, or SRBs and confer the ability to recognize promoters.
Synonyms:exact_synonym: DNA-directed RNA polymerase II, holoenzyme


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RNA polymerase II, holoenzyme term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G AABR07043557.1 RGD:1600115
G Myo6 myosin VI JBrowse link 8 87,583,649 87,731,271 RGD:1624291
G Myzap myocardial zonula adherens protein JBrowse link 8 78,009,019 78,096,409 RGD:1600115
G Polr2m RNA polymerase II subunit M JBrowse link 8 77,985,190 77,992,621 RGD:1600115
RGD:1624291
G Recql5 RecQ like helicase 5 JBrowse link 10 104,443,735 104,482,889 RGD:1624291
G Rpap2 RNA polymerase II associated protein 2 JBrowse link 14 3,125,595 3,204,590 RGD:1600115
RGD:1624291
G Rprd1a regulation of nuclear pre-mRNA domain containing 1A JBrowse link 18 16,450,160 16,497,913 RGD:1624291
RGD:13792537
G Rprd1b regulation of nuclear pre-mRNA domain containing 1B JBrowse link 3 154,507,029 154,553,312 RGD:1624291
RGD:13792537
G Rprd2 regulation of nuclear pre-mRNA domain containing 2 JBrowse link 2 197,882,666 197,937,844 RGD:1624291
RGD:13792537
Cdc73/Paf1 complex term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Cdc73 cell division cycle 73 JBrowse link 13 60,403,771 60,496,511 RGD:1600115
RGD:13792537
RGD:1624291
G Ctr9 CTR9 homolog, Paf1/RNA polymerase II complex component JBrowse link 1 175,839,140 175,869,167 RGD:1624291
RGD:13792537
G Leo1 LEO1 homolog, Paf1/RNA polymerase II complex component JBrowse link 8 82,380,906 82,405,293 RGD:1600115
RGD:1624291
G Paf1 PAF1 homolog, Paf1/RNA polymerase II complex component JBrowse link 1 85,362,421 85,367,999 RGD:1600115
RGD:1624291
RGD:13792537
G Pex2 peroxisomal biogenesis factor 2 JBrowse link 2 98,251,756 98,269,185 RGD:1624291
G Rtf1 Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) JBrowse link 3 111,478,350 111,537,941 RGD:1624291
RGD:13792537
G Setd5 SET domain containing 5 JBrowse link 4 145,017,549 145,095,247 RGD:1624291
G Wdr61 WD repeat domain 61 JBrowse link 8 59,296,339 59,313,663 RGD:1624291
RGD:1600115
core TFIIH complex portion of holo TFIIH complex term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Gtf2h2 general transcription factor IIH subunit 2 JBrowse link 2 30,494,718 30,522,716 RGD:1600115
G Gtf2h3 general transcription factor IIH subunit 3 JBrowse link 12 37,427,556 37,444,027 RGD:1624291
RGD:1600115
G Gtf2h4 general transcription factor 2H subunit 4 JBrowse link 20 3,582,688 3,588,373 RGD:1624291
RNA polymerase II, core complex term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G AABR07006025.1 RGD:13792537
G AABR07042789.1 RGD:13792537
G AC109542.1 RGD:13792537
G LOC100912534 DNA-directed RNA polymerases I, II, and III subunit RPABC3-like JBrowse link 11 82,856,537 82,860,991 RGD:13792537
G LOC103690054 DNA-directed RNA polymerase II subunit RPB9 JBrowse link 1 91,041,173 91,042,258 RGD:13792537
G Polr2a RNA polymerase II subunit A JBrowse link 10 56,339,277 56,364,888 RGD:1624291
RGD:13792537
G Polr2b RNA polymerase II subunit B JBrowse link 14 33,070,104 33,107,792 RGD:1624291
RGD:13792537
G Polr2c RNA polymerase II subunit C JBrowse link 19 10,575,060 10,581,842 RGD:1624291
RGD:13792537
G Polr2d RNA polymerase II subunit D JBrowse link 18 24,570,762 24,577,894 RGD:1624291
RGD:13792537
G Polr2e RNA polymerase II, I and III subunit E JBrowse link 7 12,532,785 12,536,797 RGD:1624291
RGD:13792537
RGD:1600115
G Polr2f RNA polymerase II, I and III subunit F JBrowse link 7 120,380,543 120,392,214 RGD:1299534
RGD:13792537
RGD:1600115
RGD:1624291
G Polr2g RNA polymerase II subunit G JBrowse link 1 224,991,250 224,998,355 RGD:1624291
RGD:13792537
RGD:1600115
G Polr2h RNA polymerase II, I and III subunit H JBrowse link 11 83,877,760 83,882,208 RGD:1624291
RGD:13792537
G Polr2i RNA polymerase II subunit I JBrowse link 1 88,686,812 88,688,249 RGD:1624291
RGD:13792537
G Polr2j RNA polymerase II subunit J JBrowse link 12 23,587,222 23,592,774 RGD:1624291
RGD:13792537
G Polr2k RNA polymerase II, I and III subunit K JBrowse link 7 74,939,010 74,992,594 RGD:1624291
RGD:13792537
G Polr2l RNA polymerase II, I and III subunit L JBrowse link 1 214,451,966 214,453,974 RGD:1624291
G Polr2l-ps1 polymerase (RNA) II (DNA directed) polypeptide L, pseudogene 1 JBrowse link 19 8,943,599 8,943,966 RGD:13792537
G Polr2m RNA polymerase II subunit M JBrowse link 8 77,985,190 77,992,621 RGD:1624291
transcription factor TFIIA complex term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Gtf2a1 general transcription factor 2A subunit 1 JBrowse link 6 115,321,110 115,352,659 RGD:1624291
RGD:13792537
G Gtf2a1l general transcription factor 2A subunit 1 like JBrowse link 6 12,412,198 12,468,613 RGD:1624291
RGD:13792537
G Gtf2a2 general transcription factor 2A subunit 2 JBrowse link 8 76,422,341 76,435,587 RGD:1600115
RGD:13792537
RGD:1624291
G LOC103695118 transcription initiation factor IIA subunit 2 RGD:13792537
RGD:1600115
G Tbp TATA box binding protein JBrowse link 1 57,491,381 57,509,335 RGD:1624291
G Tbpl1 TATA-box binding protein like 1 JBrowse link 1 23,977,154 24,002,512 RGD:1624291
transcription factor TFIID complex term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G AABR07063323.1 RGD:13792537
G Ercc2 ERCC excision repair 2, TFIIH core complex helicase subunit JBrowse link 1 80,293,574 80,307,334 RGD:1624291
G Ercc3 ERCC excision repair 3, TFIIH core complex helicase subunit JBrowse link 18 25,037,668 25,068,380 RGD:1624291
G Gtf2a1 general transcription factor 2A subunit 1 JBrowse link 6 115,321,110 115,352,659 RGD:1624291
G Gtf2a2 general transcription factor 2A subunit 2 JBrowse link 8 76,422,341 76,435,587 RGD:1624291
G Gtf2b general transcription factor IIB JBrowse link 2 248,709,433 248,727,741 RGD:1600115
RGD:1624291
G Gtf2e1 general transcription factor IIE subunit 1 JBrowse link 11 66,078,786 66,111,394 RGD:1624291
G Gtf2e2 general transcription factor IIE subunit 2 JBrowse link 16 62,113,846 62,164,339 RGD:1624291
G Gtf2f1 general transcription factor IIF subunit 1 JBrowse link 9 10,032,806 10,042,392 RGD:1624291
G Gtf2h3 general transcription factor IIH subunit 3 JBrowse link 12 37,427,556 37,444,027 RGD:1624291
G Gtf2h4 general transcription factor 2H subunit 4 JBrowse link 20 3,582,688 3,588,373 RGD:1624291
G Gtf2h5 general transcription factor IIH subunit 5 JBrowse link 1 46,978,345 46,985,032 RGD:1624291
RGD:13792537
G LOC690283 similar to TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor JBrowse link 1 60,105,788 60,108,103 RGD:13792537
G Supt3h SPT3 homolog, SAGA and STAGA complex component JBrowse link 9 18,249,565 18,604,814 RGD:13792537
G Taf1 TATA-box binding protein associated factor 1 JBrowse link X 71,412,291 71,486,456 RGD:1624291
G Taf10 TATA-box binding protein associated factor 10 JBrowse link 1 170,585,160 170,586,428 RGD:1624291
G Taf11 TATA-box binding protein associated factor 11 JBrowse link 20 7,476,648 7,484,417 RGD:13792537
RGD:1624291
G Taf12 TATA-box binding protein associated factor 12 JBrowse link 5 150,459,701 150,476,521 RGD:13792537
RGD:1624291
G Taf13 TATA-box binding protein associated factor 13 JBrowse link 2 211,359,623 211,370,285 RGD:13792537
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 Taf3 TATA-box binding protein associated factor 3 JBrowse link 17 72,240,785 72,393,448 RGD:1624291
G Taf4 TATA-box binding protein associated factor 4 JBrowse link 3 175,300,842 175,364,655 RGD:13792537
RGD:1624291
G Taf4b TATA-box binding protein associated factor 4b JBrowse link 18 6,206,939 6,338,794 RGD:13792537
RGD:1624291
G Taf5 TATA-box binding protein associated factor 5 JBrowse link 1 266,844,480 266,859,965 RGD:13792537
RGD:1624291
G Taf5l TATA-box binding protein associated factor 5 like JBrowse link 19 56,781,854 56,801,005 RGD:13792537
G Taf6 TATA-box binding protein associated factor 6 JBrowse link 12 19,320,269 19,328,706 RGD:1600115
RGD:1624291
RGD:13792537
G Taf6l TATA-box binding protein associated factor 6 like JBrowse link 1 224,974,238 224,986,819 RGD:1600115
G Taf7 TATA-box binding protein associated factor 7 JBrowse link 18 30,779,149 30,781,297 RGD:1624291
RGD:13792537
G Taf7l TATA-box binding protein associated factor 7-like JBrowse link X 105,292,338 105,308,554 RGD:13792537
G Taf7l-ps1 TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, pseudogene 1 JBrowse link 7 59,138,768 59,139,910 RGD:13792537
G Taf7l2 Taf7l2 RGD:13792537
G Taf8 TATA-box binding protein associated factor 8 JBrowse link 9 15,513,048 15,532,992 RGD:1624291
G Taf9 TATA-box binding protein associated factor 9 JBrowse link 2 30,664,407 30,668,414 RGD:13792537
RGD:1624291
G Taf9b TATA-box binding protein associated factor 9b JBrowse link X 77,281,234 77,295,238 RGD:13792537
RGD:1624291
G Tbp TATA box binding protein JBrowse link 1 57,491,381 57,509,335 RGD:2306552
RGD:13792537
RGD:1624291
G Tbpl1 TATA-box binding protein like 1 JBrowse link 1 23,977,154 24,002,512 RGD:13792537
G Tbpl2 TATA box binding protein-like 2 JBrowse link 3 1,095,883 1,116,677 RGD:13792537
G Tcea1 transcription elongation factor A1 JBrowse link 5 14,511,183 14,548,494 RGD:1624291
G Tp53 tumor protein p53 JBrowse link 10 56,186,299 56,198,449 RGD:1624291
transcription factor TFIIE complex 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
G Gtf2e2 general transcription factor IIE subunit 2 JBrowse link 16 62,113,846 62,164,339 RGD:13792537
transcription factor TFIIF complex term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Gtf2f1 general transcription factor IIF subunit 1 JBrowse link 9 10,032,806 10,042,392 RGD:13792537
G Gtf2f2 general transcription factor IIF subunit 2 JBrowse link 15 57,942,057 58,068,892 RGD:1600115
RGD:13792537
transcription factor TFIIH holo complex term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G AABR07063323.1 RGD:13792537
G Ccnh cyclin H JBrowse link 2 13,593,100 13,613,910 RGD:1624291
RGD:13792537
RGD:1600115
G Cdk7 cyclin-dependent kinase 7 JBrowse link 2 30,710,642 30,735,522 RGD:9590319
RGD:1600115
RGD:1624291
G Ercc2 ERCC excision repair 2, TFIIH core complex helicase subunit JBrowse link 1 80,293,574 80,307,334 RGD:1624291
G Ercc3 ERCC excision repair 3, TFIIH core complex helicase subunit JBrowse link 18 25,037,668 25,068,380 RGD:1600115
RGD:1624291
RGD:13792537
G Gtf2f2 general transcription factor IIF subunit 2 JBrowse link 15 57,942,057 58,068,892 RGD:9590319
G Gtf2h1 general transcription factor IIH subunit 1 JBrowse link 1 102,849,618 102,877,939 RGD:9590319
RGD:13792537
RGD:1624291
G Gtf2h2 general transcription factor IIH subunit 2 JBrowse link 2 30,494,718 30,522,716 RGD:1600115
RGD:13792537
G Gtf2h3 general transcription factor IIH subunit 3 JBrowse link 12 37,427,556 37,444,027 RGD:1624291
RGD:13792537
RGD:1600115
G Gtf2h4 general transcription factor 2H subunit 4 JBrowse link 20 3,582,688 3,588,373 RGD:1624291
RGD:13792537
G Gtf2h5 general transcription factor IIH subunit 5 JBrowse link 1 46,978,345 46,985,032 RGD:13792537
G Mnat1 MNAT1 component of CDK activating kinase JBrowse link 6 95,995,341 96,153,331 RGD:1624291
RGD:13792537
transcription factor TFIIK complex term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ccnh cyclin H JBrowse link 2 13,593,100 13,613,910 RGD:13792537
RGD:1624291
G Cdk7 cyclin-dependent kinase 7 JBrowse link 2 30,710,642 30,735,522 RGD:1600115
RGD:13792537
RGD:1624291
G Mnat1 MNAT1 component of CDK activating kinase JBrowse link 6 95,995,341 96,153,331 RGD:1624291
transcription factor TFTC complex term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Kat2a lysine acetyltransferase 2A JBrowse link 10 88,611,586 88,619,558 RGD:1624291
G LOC690283 similar to TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor JBrowse link 1 60,105,788 60,108,103 RGD:1600115
G Supt3h SPT3 homolog, SAGA and STAGA complex component JBrowse link 9 18,249,565 18,604,814 RGD:1624291
RGD:1600115
G Tada3 transcriptional adaptor 3 JBrowse link 4 145,318,417 145,330,291 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 Taf2 TATA-box binding protein associated factor 2 JBrowse link 7 94,698,987 94,755,924 RGD:1624291
G Taf4 TATA-box binding protein associated factor 4 JBrowse link 3 175,300,842 175,364,655 RGD:1624291
G Taf5 TATA-box binding protein associated factor 5 JBrowse link 1 266,844,480 266,859,965 RGD:1624291
G Taf5l TATA-box binding protein associated factor 5 like JBrowse link 19 56,781,854 56,801,005 RGD:1624291
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 Taf9 TATA-box binding protein associated factor 9 JBrowse link 2 30,664,407 30,668,414 RGD:1624291
G Taf9b TATA-box binding protein associated factor 9b JBrowse link X 77,281,234 77,295,238 RGD:1624291
G Trrap transformation/transcription domain-associated protein JBrowse link 12 11,537,950 11,627,563 RGD:1624291

Term paths to the root
Path 1
Term Annotations click to browse term
  cellular_component 20300
    cellular anatomical entity 19956
      nucleoplasm 3399
        RNA polymerase II, holoenzyme 85
          Cdc73/Paf1 complex 8
          RNA polymerase II, core complex 19
          transcription factor TFIIA complex 6
          transcription factor TFIID complex + 39
          transcription factor TFIIE complex 2
          transcription factor TFIIF complex 2
          transcription factor TFIIH holo complex + 12
          transcription factor TFTC complex 15
Path 2
Term Annotations click to browse term
  cellular_component 20300
    protein-containing complex 6095
      catalytic complex 1479
        transferase complex 823
          transferase complex, transferring phosphorus-containing groups 267
            RNA polymerase complex 111
              DNA-directed RNA polymerase complex 109
                nuclear DNA-directed RNA polymerase complex 108
                  RNA polymerase II, holoenzyme 85
                    Cdc73/Paf1 complex 8
                    RNA polymerase II, core complex 19
                    transcription factor TFIIA complex 6
                    transcription factor TFIID complex + 39
                    transcription factor TFIIE complex 2
                    transcription factor TFIIF complex 2
                    transcription factor TFIIH holo complex + 12
                    transcription factor TFTC complex 15
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.