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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:Binding to a component of 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 Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Llph LLP homolog, long-term synaptic facilitation factor enables ISO
IBA		 (MGI:5796065|PMID:26961175)
GO_REF:0000033		 RGD
GO_Central		 PMID:26961175 GO_REF:0000033 MGI:5796065 NCBI chr 7:55,735,317...55,740,341
Ensembl chr 7:55,735,400...55,740,339 		JBrowse link
RNA polymerase II C-terminal domain binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Brd4 bromodomain containing 4 enables ISO (PMID:22509028)
PR:P08775 (PMID:22509028)		 RGD PMID:22509028 NCBI chr 7:11,216,446...11,296,029
Ensembl chr 7:11,216,446...11,295,539 		JBrowse link
G Hnrnpu heterogeneous nuclear ribonucleoprotein U enables ISS
ISO		 GO_REF:0000024
(MGI:5908336|PMID:21235343)		 UniProt
RGD		 PMID:21235343 GO_REF:0000024 MGI:5908336 NCBI chr13:90,069,058...90,086,905
Ensembl chr13:90,074,181...90,086,588 		JBrowse link
G Pcif1 phosphorylated CTD interacting factor 1 enables ISO (PMID:18294453), (PMID:30467178) RGD PMID:18294453 PMID:30467178 NCBI chr 3:153,614,147...153,627,079
Ensembl chr 3:153,614,147...153,627,079 		JBrowse link
G Rprd1a regulation of nuclear pre-mRNA domain containing 1A enables IEA GO_REF:0000002 InterPro GO_REF:0000002 NCBI chr18:15,791,418...15,839,338
Ensembl chr18:15,791,418...15,839,338 		JBrowse link
G Rprd1b regulation of nuclear pre-mRNA domain containing 1B enables IEA GO_REF:0000002 InterPro GO_REF:0000002 NCBI chr 3:146,682,975...146,729,251
Ensembl chr 3:146,682,922...146,786,452 		JBrowse link
G Rprd2 regulation of nuclear pre-mRNA domain containing 2 enables IEA GO_REF:0000002 InterPro GO_REF:0000002 NCBI chr 2:183,311,132...183,367,959
Ensembl chr 2:183,293,114...183,367,407 		JBrowse link
G Scaf1 SR-related CTD-associated factor 1 enables ISO
IBA		 UniProtKB:P24928 (PMID:15992770)
GO_REF:0000033		 RGD
GO_Central		 PMID:15992770 GO_REF:0000033 NCBI chr 1:95,485,448...95,499,389
Ensembl chr 1:95,485,448...95,496,029 		JBrowse link
RNA polymerase II C-terminal domain phosphoserine binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Leo1 LEO1 homolog, Paf1/RNA polymerase II complex component enables IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 8:76,199,547...76,223,983
Ensembl chr 8:76,199,099...76,223,983 		JBrowse link
G Pcif1 phosphorylated CTD interacting factor 1 enables ISO (PMID:32814042) RGD PMID:32814042 NCBI chr 3:153,614,147...153,627,079
Ensembl chr 3:153,614,147...153,627,079 		JBrowse link
G Rtf1 Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) enables IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 3:106,659,363...106,718,956
Ensembl chr 3:106,659,308...106,718,970 		JBrowse link
G Scaf4 SR-related CTD-associated factor 4 enables ISO
ISS
IEA
IBA		 (PMID:31104839)
GO_REF:0000024
GO_REF:0000107
GO_REF:0000033		 RGD
UniProt
Ensembl
GO_Central		 PMID:31104839 GO_REF:0000024 GO_REF:0000033 GO_REF:0000107 NCBI chr11:29,460,479...29,521,153
Ensembl chr11:29,465,106...29,521,153 		JBrowse link
G Scaf8 SR-related CTD-associated factor 8 enables ISO
ISS
IEA		 (PMID:31104839)
GO_REF:0000024
GO_REF:0000107		 RGD
UniProt
Ensembl		 PMID:31104839 GO_REF:0000024 GO_REF:0000107 NCBI chr 1:43,727,686...43,855,889
Ensembl chr 1:43,727,794...43,804,977 		JBrowse link
RNA polymerase II complex binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ago1 argonaute RISC component 1 enables ISO (PMID:25336585) RGD PMID:25336585 NCBI chr 5:138,722,111...138,757,118
Ensembl chr 5:138,722,111...138,773,546 		JBrowse link
G Ago2 argonaute RISC catalytic component 2 enables IEA
ISO		 GO_REF:0000107
(PMID:25336585)		 Ensembl
RGD		 PMID:25336585 GO_REF:0000107 NCBI chr 7:105,018,202...105,105,118
Ensembl chr 7:105,029,120...105,104,974 		JBrowse link
G Ccar2 cell cycle and apoptosis regulator 2 enables ISO (PMID:22446626) RGD PMID:22446626 NCBI chr15:45,212,797...45,228,001
Ensembl chr15:45,212,803...45,227,636 		JBrowse link
G Cdc73 cell division cycle 73 enables ISS
IBA
IEA
ISO		 GO_REF:0000024
GO_REF:0000033
GO_REF:0000107
(PMID:15923622)		 UniProt
GO_Central
Ensembl
RGD		 PMID:15923622 GO_REF:0000024 GO_REF:0000033 GO_REF:0000107 NCBI chr13:55,357,226...55,449,690
Ensembl chr13:55,357,226...55,449,656 		JBrowse link
G Ctr9 CTR9 homolog, Paf1/RNA polymerase II complex component enables IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 1:165,137,277...165,167,303
Ensembl chr 1:165,137,215...165,167,303 		JBrowse link
G Dhx9 DExH-box helicase 9 enables ISO (PMID:11416126) RGD PMID:11416126 NCBI chr13:65,602,322...65,639,098
Ensembl chr13:65,602,323...65,639,069 		JBrowse link
G Elof1 elongation factor 1 enables IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 8:20,645,336...20,650,888
Ensembl chr 8:20,645,336...20,650,579 		JBrowse link
G Elp2 elongator acetyltransferase complex subunit 2 contributes_to ISO (PMID:11714725) RGD PMID:11714725 NCBI chr18:15,885,940...15,921,564
Ensembl chr18:15,885,934...15,921,599 		JBrowse link
G Elp4 elongator acetyltransferase complex subunit 4 contributes_to ISO (PMID:11714725) RGD PMID:11714725 NCBI chr 3:92,162,271...92,385,251
Ensembl chr 3:92,162,280...92,385,243 		JBrowse link
G Ercc5 ERCC excision repair 5, endonuclease enables ISO (PMID:16246722) RGD PMID:16246722 NCBI chr 9:46,309,477...46,354,478
Ensembl chr 9:46,309,389...46,354,472 		JBrowse link
G Esrrb estrogen-related receptor beta enables ISS
ISO		 GO_REF:0000024
(MGI:5440110|PMID:23019124)		 UniProt
RGD		 PMID:23019124 GO_REF:0000024 MGI:5440110 NCBI chr 6:106,007,701...106,163,136
Ensembl chr 6:106,008,095...106,160,791 		JBrowse link
G Gtf2b general transcription factor IIB enables ISO
IEA
ISS		 (PMID:8413225), (PMID:8504927)
GO_REF:0000107
GO_REF:0000024		 RGD
Ensembl
UniProt		 PMID:8413225 PMID:8504927 GO_REF:0000024 GO_REF:0000107 NCBI chr 2:231,767,317...231,785,626
Ensembl chr 2:231,767,238...231,785,651 		JBrowse link
G Hnrnpu heterogeneous nuclear ribonucleoprotein U enables ISO
IEA		 (PMID:10490622)
GO_REF:0000107		 RGD
Ensembl		 PMID:10490622 GO_REF:0000107 NCBI chr13:90,069,058...90,086,905
Ensembl chr13:90,074,181...90,086,588 		JBrowse link
G Ncoa3 nuclear receptor coactivator 3 enables ISS
ISO		 GO_REF:0000024
(MGI:5440110|PMID:23019124)		 UniProt
RGD		 PMID:23019124 GO_REF:0000024 MGI:5440110 NCBI chr 3:154,738,566...154,821,395
Ensembl chr 3:154,738,581...154,818,594 		JBrowse link
G Paf1 PAF1 homolog, Paf1/RNA polymerase II complex component enables ISO
IBA
ISS		 (PMID:15923622)
GO_REF:0000033
GO_REF:0000024		 RGD
GO_Central
UniProt		 PMID:15923622 GO_REF:0000024 GO_REF:0000033 NCBI chr 1:83,683,654...83,689,233
Ensembl chr 1:83,668,813...83,689,237 		JBrowse link
G Pcf11 PCF11 cleavage and polyadenylation factor subunit enables ISO
IBA		 (PMID:29196535)
GO_REF:0000033		 RGD
GO_Central		 PMID:29196535 GO_REF:0000033 NCBI chr 1:146,694,045...146,724,030
Ensembl chr 1:146,697,646...146,724,124 		JBrowse link
G Polr2m RNA polymerase II subunit M enables ISO (PMID:26789250) RGD PMID:26789250 NCBI chr 8:72,131,992...72,139,423
Ensembl chr 8:72,131,530...72,243,036 		JBrowse link
G Recql5 RecQ like helicase 5 enables ISS
ISO		 GO_REF:0000024
(PMID:23748380)		 UniProt
RGD		 PMID:23748380 GO_REF:0000024 NCBI chr10:101,126,544...101,165,739
Ensembl chr10:101,126,547...101,165,652 		JBrowse link
G Rprd1a regulation of nuclear pre-mRNA domain containing 1A enables IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr18:15,791,418...15,839,338
Ensembl chr18:15,791,418...15,839,338 		JBrowse link
G Rprd1b regulation of nuclear pre-mRNA domain containing 1B enables ISO
IBA		 (PMID:22264791)
GO_REF:0000033		 RGD
GO_Central		 PMID:22264791 GO_REF:0000033 NCBI chr 3:146,682,975...146,729,251
Ensembl chr 3:146,682,922...146,786,452 		JBrowse link
G Rprd2 regulation of nuclear pre-mRNA domain containing 2 enables IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 2:183,311,132...183,367,959
Ensembl chr 2:183,293,114...183,367,407 		JBrowse link
G Rtraf RNA transcription, translation and transport factor enables ISO (PMID:16950395) RGD PMID:16950395 NCBI chr15:4,447,243...4,457,973
Ensembl chr15:4,442,573...4,457,972 		JBrowse link
G Scaf8 SR-related CTD-associated factor 8 enables IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 1:43,727,686...43,855,889
Ensembl chr 1:43,727,794...43,804,977 		JBrowse link
G Smyd2 SET and MYND domain containing 2 enables ISS
ISO		 GO_REF:0000024
(MGI:4440782|PMID:20305823)		 UniProt
RGD		 PMID:20305823 GO_REF:0000024 MGI:4440782 NCBI chr13:101,425,270...101,466,576
Ensembl chr13:101,425,273...101,466,576 		JBrowse link
G Smyd3 SET and MYND domain containing 3 enables ISO (PMID:23752591) RGD PMID:23752591 NCBI chr13:90,709,263...91,266,209
Ensembl chr13:90,709,270...91,266,253 		JBrowse link
G Supt4h1 SPT4 homolog, DSIF elongation factor subunit enables IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr10:72,539,323...72,545,582
Ensembl chr10:72,539,382...72,545,831 		JBrowse link
G Uri1 URI1, prefoldin-like chaperone enables ISO (PMID:9819440) RGD PMID:9819440 NCBI chr 1:90,646,392...90,704,811
Ensembl chr 1:90,646,393...90,709,026 		JBrowse link
G Uvssa UV-stimulated scaffold protein A enables ISO
IBA
IEA
ISS		 (PMID:22466610), (PMID:22466611), (PMID:22466612)
GO_REF:0000033
GO_REF:0000107
GO_REF:0000024		 RGD
GO_Central
Ensembl
UniProt		 PMID:22466610 PMID:22466611 PMID:22466612 GO_REF:0000024 GO_REF:0000033 GO_REF:0000107 NCBI chr14:77,309,188...77,351,922
Ensembl chr14:77,314,056...77,351,903 		JBrowse link
G Wac WW domain containing adaptor with coiled-coil enables ISO
IBA		 (PMID:21329877)
GO_REF:0000033		 RGD
GO_Central		 PMID:21329877 GO_REF:0000033 NCBI chr17:55,922,686...55,984,286
Ensembl chr17:55,923,123...55,982,301 		JBrowse link
G Wdr43 WD repeat domain 43 enables ISO (MGI:6323527|PMID:31128943) RGD PMID:31128943 MGI:6323527 NCBI chr 6:23,845,499...23,884,846
Ensembl chr 6:23,845,499...23,884,846 		JBrowse link
G Zfp326 zinc finger protein 326 enables ISO (PMID:22446626) RGD PMID:22446626 NCBI chr14:3,941,210...3,980,419
Ensembl chr14:3,941,958...3,980,384 		JBrowse link
RNA polymerase II general transcription initiation factor binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ar androgen receptor enables ISO
IEA		 UniProtKB:P21675 (PMID:20181722)
GO_REF:0000107		 RGD
Ensembl		 PMID:20181722 GO_REF:0000107 NCBI chr  X:63,104,771...63,273,934
Ensembl chr  X:63,104,771...63,273,925 		JBrowse link
G Drap1 Dr1 associated protein 1 enables ISO UniProtKB:Q01658 (PMID:8608938), (PMID:8670811) RGD PMID:8608938 PMID:8670811 NCBI chr 1:202,731,775...202,734,468
Ensembl chr 1:202,731,788...202,734,425 		JBrowse link
G Gtf2a1 general transcription factor 2A subunit 1 enables ISO UniProtKB:P52657 (PMID:8626665) RGD PMID:8626665 NCBI chr 6:110,488,891...110,521,502
Ensembl chr 6:110,488,931...110,521,511 		JBrowse link
G Gtf2a2 general transcription factor 2A subunit 2 enables ISO UniProtKB:P52655 (PMID:8626665) RGD PMID:8626665 NCBI chr 8:70,662,447...70,675,576
Ensembl chr 8:70,662,428...70,675,569 		JBrowse link
G Gtf2f1 general transcription factor IIF subunit 1 enables ISO UniProtKB:P21675 (PMID:8625415) RGD PMID:8625415 NCBI chr 9:1,844,027...1,853,455
Ensembl chr 9:1,843,901...1,853,423 		JBrowse link
G Taf1 TATA-box binding protein associated factor 1 enables ISO UniProtKB:P35269 (PMID:8625415) RGD PMID:8625415 NCBI chr  X:66,640,915...66,716,543
Ensembl chr  X:66,640,982...66,716,543 		JBrowse link
G Tbp TATA box binding protein enables ISO UniProtKB:P52655|UniProtKB:P52657|UniProtKB:Q01658|UniProtKB:Q14919|UniProtKB:Q15543|UniProtKB:Q15544 (PMID:29111974), (PMID:7724559), (PMID:8626665), (PMID:8670811) RGD PMID:7724559 PMID:8626665 PMID:8670811 PMID:29111974 NCBI chr 1:56,463,330...56,480,430
Ensembl chr 1:56,463,618...56,510,016 		JBrowse link
TFIIB-class transcription factor binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Crebbp CREB binding protein enables ISO PR:P62915 (PMID:7913207) RGD PMID:7913207 NCBI chr10:11,335,551...11,461,888
Ensembl chr10:11,335,953...11,461,888 		JBrowse link
G Esr1 estrogen receptor 1 enables ISO
IEA		 UniProtKB:P03372 (PMID:9841876)
GO_REF:0000107		 RGD
Ensembl		 PMID:9841876 GO_REF:0000107 NCBI chr 1:41,106,335...41,499,104
Ensembl chr 1:41,210,475...41,495,002 		JBrowse link
G Foxf2 forkhead box F2 enables ISO UniProtKB:Q00403 (PMID:9722567) RGD PMID:9722567 NCBI chr17:32,835,730...32,842,547
Ensembl chr17:32,836,777...32,842,176 		JBrowse link
G Nolc1 nucleolar and coiled-body phosphoprotein 1 IDA Gtf2b RGD PMID:8972203 RGD:2303819 NCBI chr 1:244,921,275...244,932,089
Ensembl chr 1:244,921,377...244,932,088 		JBrowse link
G Tbp TATA box binding protein enables ISO UniProtKB:Q00403 (PMID:9841876) RGD PMID:9841876 NCBI chr 1:56,463,330...56,480,430
Ensembl chr 1:56,463,618...56,510,016 		JBrowse link
G Tcf4 transcription factor 4 enables ISO (MGI:85411|PMID:8978694) RGD PMID:8978694 MGI:85411 NCBI chr18:62,941,739...63,288,126
Ensembl chr18:62,943,782...63,284,425 		JBrowse link
TFIID-class transcription factor complex binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ahr aryl hydrocarbon receptor enables ISO
IEA		 UniProtKB:O00268|UniProtKB:P20226|UniProtKB:P49848 (PMID:15641800)
GO_REF:0000107		 RGD
Ensembl		 PMID:15641800 GO_REF:0000107 NCBI chr 6:52,234,089...52,271,568
Ensembl chr 6:52,234,089...52,271,568 		JBrowse link
G Edf1 endothelial differentiation-related factor 1 enables ISO
IEA		 (PMID:12040021)
GO_REF:0000107		 RGD
Ensembl		 PMID:12040021 GO_REF:0000107 NCBI chr 3:8,377,058...8,381,363
Ensembl chr 3:8,366,613...8,381,363 		JBrowse link
G Ercc1 ERCC excision repair 1, endonuclease non-catalytic subunit enables ISO (PMID:22323595) RGD PMID:22323595 NCBI chr 1:78,971,310...79,007,963
Ensembl chr 1:78,996,390...79,007,963 		JBrowse link
G Ercc4 ERCC excision repair 4, endonuclease catalytic subunit enables ISO (PMID:22323595) RGD PMID:22323595 NCBI chr10:2,416,259...2,448,364
Ensembl chr10:2,419,038...2,448,369 		JBrowse link
G Fbl fibrillarin enables ISO
IEA		 UniProtKB:Q16594 (PMID:17636026)
GO_REF:0000107		 RGD
Ensembl		 PMID:17636026 GO_REF:0000107 NCBI chr 1:83,469,832...83,478,932
Ensembl chr 1:83,469,832...83,478,932 		JBrowse link
G Nop58 NOP58 ribonucleoprotein enables ISO UniProtKB:Q16594 (PMID:17636026) RGD PMID:17636026 NCBI chr 9:61,120,939...61,144,810
Ensembl chr 9:61,120,929...61,144,810 		JBrowse link
G Ruvbl1 RuvB-like AAA ATPase 1 enables ISO UniProtKB:Q16594 (MGI:5700302|PMID:17636026) RGD PMID:17636026 MGI:5700302 NCBI chr 4:120,932,486...120,967,400
Ensembl chr 4:120,932,417...121,029,384 		JBrowse link
G Ruvbl2 RuvB-like AAA ATPase 2 enables ISO UniProtKB:Q16594 (MGI:5700302|PMID:17636026) RGD PMID:17636026 MGI:5700302 NCBI chr 1:95,902,014...95,915,247
Ensembl chr 1:95,901,701...95,915,342 		JBrowse link
G Tp53 tumor protein p53 enables ISO
IEA		 UniProtKB:P21675 (PMID:24289924)
GO_REF:0000107		 RGD
Ensembl		 PMID:24289924 GO_REF:0000107 NCBI chr10:54,300,070...54,311,525
Ensembl chr10:54,300,048...54,311,524 		JBrowse link
G Znhit6 zinc finger, HIT-type containing 6 enables ISO UniProtKB:Q16594 (PMID:17636026) RGD PMID:17636026 NCBI chr 2:234,486,686...234,517,952
Ensembl chr 2:234,486,704...234,517,960 		JBrowse link
TFIIF-class transcription factor complex binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ctdp1 CTD phosphatase subunit 1 enables ISO UniProtKB:P35269 (PMID:12732728), (PMID:15723517) RGD PMID:12732728 PMID:15723517 NCBI chr18:73,854,277...73,916,232
Ensembl chr18:73,854,282...73,916,457 		JBrowse link
G Gtf2f1 general transcription factor IIF subunit 1 enables IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 9:1,844,027...1,853,455
Ensembl chr 9:1,843,901...1,853,423 		JBrowse link
TFIIH-class transcription factor complex binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Gtf2e2 general transcription factor IIE subunit 2 contributes_to IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr16:58,399,307...58,449,467
Ensembl chr16:58,399,107...58,449,371 		JBrowse link
G Hnrnpu heterogeneous nuclear ribonucleoprotein U enables ISO
IEA		 (PMID:10490622)
GO_REF:0000107		 RGD
Ensembl		 PMID:10490622 GO_REF:0000107 NCBI chr13:90,069,058...90,086,905
Ensembl chr13:90,074,181...90,086,588 		JBrowse link
G Taf7 TATA-box binding protein associated factor 7 enables ISO (PMID:18391197) RGD PMID:18391197 NCBI chr18:29,459,937...29,462,086
Ensembl chr18:29,452,943...29,462,134 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  molecular_function 20483
    binding 17534
      protein binding 14557
        basal transcription machinery binding 63
          bacterial-type RNA polymerase holo enzyme binding 0
          basal RNA polymerase II transcription machinery binding + 63
paths to the root