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ONTOLOGY REPORT - ANNOTATIONS


Term:basal transcription machinery binding
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Accession:GO:0001098 term browser browse the term
Definition:Interacting selectively and non-covalently with the basal transcription machinery which is composed of the RNA polymerase core enzyme and the basal transcription factor(s), the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase.
Comment:Note that the definition of basal, or general, transcription factors has typically been done at a small number of well characterized activator-independent promoters. At an activator-dependent promoter, one or more additional factors are generally required in addition to the basal factors.


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basal RNA polymerase II transcription machinery binding term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Llph LLP homolog, long-term synaptic facilitation factor JBrowse link 7 65,004,544 65,009,509 RGD:1624291
RGD:13792537
G LOC100911956 protein LLP homolog JBrowse link 6 125,863,966 125,865,098 RGD:13792537
RNA polymerase II C-terminal domain binding term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Brd4 bromodomain containing 4 JBrowse link 7 14,222,101 14,303,055 RGD:1624291
G Hnrnpu heterogeneous nuclear ribonucleoprotein U JBrowse link 13 96,222,093 96,238,845 RGD:1624291
RGD:13792537
RGD:1600115
G Pcif1 PDX1 C-terminal inhibiting factor 1 JBrowse link 3 161,343,883 161,356,815 RGD:1624291
G Scaf1 SR-related CTD-associated factor 1 JBrowse link 1 100,997,724 101,010,855 RGD:1624291
RGD:13792537
RNA polymerase II C-terminal domain phosphoserine binding term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Leo1 LEO1 homolog, Paf1/RNA polymerase II complex component JBrowse link 8 82,380,906 82,405,293 RGD:13792537
G Rtf1 Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) JBrowse link 3 111,478,350 111,537,941 RGD:13792537
G Scaf4 SR-related CTD-associated factor 4 JBrowse link 11 30,371,713 30,428,073 RGD:1600115
RGD:1624291
G Scaf8 SR-related CTD-associated factor 8 JBrowse link 1 44,017,801 44,120,619 RGD:1600115
RGD:1624291
RNA polymerase II complex binding term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ago1 argonaute RISC component 1 JBrowse link 5 144,444,390 144,479,430 RGD:1624291
G Ago2 argonaute RISC catalytic component 2 JBrowse link 7 114,339,607 114,377,277 RGD:1624291
RGD:1600115
G Ccar2 cell cycle and apoptosis regulator 2 JBrowse link 15 51,818,887 51,834,443 RGD:1624291
RGD:13792537
G Cdc73 cell division cycle 73 JBrowse link 13 60,403,771 60,496,511 RGD:1624291
RGD:1600115
RGD:13792537
G Ctr9 CTR9 homolog, Paf1/RNA polymerase II complex component JBrowse link 1 175,839,140 175,869,167 RGD:13792537
G Dhx9 DExH-box helicase 9 JBrowse link 13 70,885,503 70,922,278 RGD:1624291
G Elof1 elongation factor 1 homolog JBrowse link 8 23,125,987 23,130,980 RGD:13792537
G Elp2 elongator acetyltransferase complex subunit 2 JBrowse link 18 16,544,515 16,581,086 RGD:1624291
G Elp4 elongator acetyltransferase complex subunit 4 JBrowse link 3 95,733,810 95,954,987 RGD:1624291
G Ercc5 ERCC excision repair 5, endonuclease JBrowse link 9 50,928,847 50,970,962 RGD:1624291
G Esrrb estrogen-related receptor beta JBrowse link 6 110,360,940 110,458,406 RGD:1624291
RGD:1600115
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:13792537
G Hnrnpu heterogeneous nuclear ribonucleoprotein U JBrowse link 13 96,222,093 96,238,845 RGD:1624291
RGD:1600115
G Ncoa3 nuclear receptor coactivator 3 JBrowse link 3 162,692,176 162,788,582 RGD:1624291
RGD:1600115
G Paf1 PAF1 homolog, Paf1/RNA polymerase II complex component JBrowse link 1 85,362,421 85,367,999 RGD:1624291
RGD:13792537
RGD:1600115
G Pcf11 PCF11 cleavage and polyadenylation factor subunit JBrowse link 1 157,463,014 157,494,134 RGD:13792537
G Recql5 RecQ like helicase 5 JBrowse link 10 104,443,735 104,482,889 RGD:1624291
RGD:1600115
G Rprd1a regulation of nuclear pre-mRNA domain containing 1A JBrowse link 18 16,450,160 16,497,913 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:13792537
G Rtraf RNA transcription, translation and transport factor JBrowse link 15 4,882,925 4,893,890 RGD:1624291
G Scaf8 SR-related CTD-associated factor 8 JBrowse link 1 44,017,801 44,120,619 RGD:13792537
G Smyd2 SET and MYND domain containing 2 JBrowse link 13 108,642,156 108,686,293 RGD:1624291
RGD:1600115
G Smyd3 SET and MYND domain containing 3 JBrowse link 13 97,330,120 97,807,813 RGD:1624291
G Supt4h1 SPT4 homolog, DSIF elongation factor subunit JBrowse link 10 75,032,365 75,038,547 RGD:13792537
G Uri1 URI1, prefoldin-like chaperone JBrowse link 1 94,346,513 94,404,362 RGD:1624291
G Uvssa UV-stimulated scaffold protein A JBrowse link 14 82,621,028 82,658,912 RGD:1600115
RGD:13792537
RGD:1624291
G Wac WW domain containing adaptor with coiled-coil JBrowse link 17 60,887,606 60,946,630 RGD:1624291
G Wdr43 WD repeat domain 43 JBrowse link 6 23,433,532 23,473,179 RGD:1624291
G Zfp326 zinc finger protein 326 JBrowse link 14
14
4,998,530
5,016,764
5,006,759
5,036,663
RGD:1624291
RGD:13792537
RNA polymerase II complex recruiting activity term browser
Symbol Object Name JBrowse Chr Start Stop Reference
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
RNA polymerase II general transcription initiation factor binding term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ar androgen receptor JBrowse link X 67,656,253 67,828,998 RGD:1600115
RGD:1624291
G Drap1 Dr1 associated protein 1 JBrowse link 1 220,803,783 220,806,480 RGD:1624291
G Tbp TATA box binding protein JBrowse link 1 57,491,381 57,509,335 RGD:1624291
TFIIB-class transcription factor binding term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Crebbp CREB binding protein JBrowse link 10 11,590,994 11,721,039 RGD:1624291
G Esr1 estrogen receptor 1 JBrowse link 1 41,192,029 41,594,799 RGD:1600115
RGD:1624291
G Tbp TATA box binding protein JBrowse link 1 57,491,381 57,509,335 RGD:1624291
G Tcf4 transcription factor 4 JBrowse link 18 65,285,320 65,507,983 RGD:1624291
RGD:1600115
TFIID-class transcription factor complex binding 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 Edf1 endothelial differentiation-related factor 1 JBrowse link 3 2,781,169 2,785,474 RGD:1624291
G Ercc1 ERCC excision repair 1, endonuclease non-catalytic subunit JBrowse link 1 80,256,973 80,268,198 RGD:1624291
G Ercc4 ERCC excision repair 4, endonuclease catalytic subunit JBrowse link 10 2,010,140 2,037,953 RGD:1624291
G Fbl fibrillarin JBrowse link 1 85,103,519 85,112,619 RGD:1624291
G Nop58 NOP58 ribonucleoprotein JBrowse link 9 66,495,881 66,520,521 RGD:1624291
G Ruvbl1 RuvB-like AAA ATPase 1 JBrowse link 4 120,411,917 120,447,458 RGD:1624291
G Ruvbl2 RuvB-like AAA ATPase 2 JBrowse link 1 101,413,766 101,426,970 RGD:1624291
G Tp53 tumor protein p53 JBrowse link 10 56,186,299 56,198,449 RGD:1624291
G Znhit6 zinc finger, HIT-type containing 6 JBrowse link 2 251,453,503 251,484,760 RGD:1624291
TFIIF-class transcription factor complex binding term browser
Symbol Object Name JBrowse Chr Start Stop Reference
G Ctdp1 CTD phosphatase subunit 1 JBrowse link 18 76,922,913 76,985,095 RGD:1624291
G Gtf2f1 general transcription factor IIF subunit 1 JBrowse link 9 10,032,806 10,042,392 RGD:13792537
TFIIH-class transcription factor complex binding 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 Hnrnpu heterogeneous nuclear ribonucleoprotein U JBrowse link 13 96,222,093 96,238,845 RGD:1600115
RGD:13792537
RGD:1624291
G Taf7 TATA-box binding protein associated factor 7 JBrowse link 18 30,779,149 30,781,297 RGD:1624291

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Term Annotations click to browse term
  molecular_function 20377
    binding 16798
      protein binding 14233
        basal transcription machinery binding 59
          bacterial-type RNA polymerase holo enzyme binding 0
          basal RNA polymerase II transcription machinery binding + 59
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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.