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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 IBA
ISO
PMID:21873635
(MGI:5796065|PMID:26961175)
RGD PMID:26961175 PMID:21873635 MGI:5796065, RGD:13792537 NCBI chr 7:55,735,317...55,740,341
Ensembl chr 7:55,735,400...55,740,339
JBrowse link
G LOC100911956 protein LLP homolog enables IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 6:121,118,419...121,119,529
Ensembl chr 6:121,118,450...121,119,528
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 PR:P08775 (MGI:5319557|PMID:22509028)
(PMID:22509028)
RGD PMID:22509028 MGI:5319557 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
IBA
GO_REF:0000024
(MGI:5908336|PMID:21235343)
PMID:21873635
UniProt
RGD
PMID:21235343 PMID:21873635 GO_REF:0000024 MGI:5908336, RGD:13792537 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 Scaf1 SR-related CTD-associated factor 1 enables ISO
IBA
UniProtKB:P24928 (PMID:15992770)
PMID:21873635
RGD PMID:15992770 PMID:21873635 RGD:13792537 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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 3:106,659,363...106,718,970
Ensembl chr 3:106,659,308...106,718,970
JBrowse link
G Scaf4 SR-related CTD-associated factor 4 enables ISO
ISS
(PMID:31104839)
GO_REF:0000024
RGD
UniProt
PMID:31104839 GO_REF:0000024 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
IEA
ISS
(PMID:31104839)
GO_REF:0000107
GO_REF:0000024
RGD
Ensembl
UniProt
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...105,105,120
Ensembl chr 7:105,029,120...105,104,974
JBrowse link
G Ccar2 cell cycle and apoptosis regulator 2 enables ISO
IBA
(PMID:22446626)
PMID:21873635
RGD PMID:22446626 PMID:21873635 RGD:13792537 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 IBA
IEA
ISO
ISS
PMID:21873635
GO_REF:0000107
(PMID:15923622)
GO_REF:0000024
Ensembl
RGD
UniProt
PMID:15923622 PMID:21873635 GO_REF:0000024 GO_REF:0000107, RGD:13792537 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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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 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 6:106,007,662...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 IEA
ISO
GO_REF:0000107
(PMID:10490622)
Ensembl
RGD
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 IBA
ISS
ISO
PMID:21873635
GO_REF:0000024
(PMID:15923622)
UniProt
RGD
PMID:15923622 PMID:21873635 GO_REF:0000024, RGD:13792537 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 IBA PMID:21873635 GO_Central PMID:21873635 RGD:13792537 NCBI chr 1:146,694,045...146,724,030
Ensembl chr 1:146,697,646...146,724,124
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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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)
PMID:21873635
RGD PMID:22264791 PMID:21873635 RGD:13792537 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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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 (MGI:5500979|PMID:23752591) RGD PMID:23752591 MGI:5500979 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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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 IBA
IEA
ISS
ISO
PMID:21873635
GO_REF:0000107
GO_REF:0000024
(PMID:22466610), (PMID:22466611), (PMID:22466612)
Ensembl
UniProt
RGD
PMID:22466610 PMID:22466611 PMID:22466612 PMID:21873635 GO_REF:0000024 GO_REF:0000107, RGD:13792537 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)
PMID:21873635
RGD PMID:21329877 PMID:21873635 RGD:13792537 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
IEA
UniProtKB:P52657 (PMID:8626665)
GO_REF:0000107
RGD
Ensembl
PMID:8626665 GO_REF:0000107 NCBI chr 6:110,488,891...110,521,059
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 8:70,662,395...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 (MGI:67494|PMID:7913207) RGD PMID:7913207 MGI:67494 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...32,842,555 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 UniProtKB:O00268|UniProtKB:P49848 (PMID:15641800) RGD PMID:15641800 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 (PMID:12040021) RGD PMID:12040021 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 (MGI:5314556|PMID:22323595) RGD PMID:22323595 MGI:5314556 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 (MGI:5314556|PMID:22323595) RGD PMID:22323595 MGI:5314556 NCBI chr10:2,416,259...2,448,364 JBrowse link
G Fbl fibrillarin enables ISO UniProtKB:Q16594 (PMID:17636026) RGD PMID:17636026 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...95,915,364
Ensembl chr 1:95,901,701...95,915,342
JBrowse link
G Tp53 tumor protein p53 enables ISO UniProtKB:P21675 (PMID:24289924) RGD PMID:24289924 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 PMID:21873635 GO_Central PMID:21873635 RGD:13792537 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 Hnrnpu heterogeneous nuclear ribonucleoprotein U enables ISO
IEA
IBA
(PMID:10490622)
GO_REF:0000107
PMID:21873635
RGD
Ensembl
PMID:10490622 PMID:21873635 GO_REF:0000107, RGD:13792537 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 19910
    binding 16997
      protein binding 14384
        basal transcription machinery binding 62
          bacterial-type RNA polymerase holo enzyme binding 0
          basal RNA polymerase II transcription machinery binding + 62
paths to the root