Taf4 (TATA-box binding protein associated factor 4) - Rat Genome Database

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Gene: Taf4 (TATA-box binding protein associated factor 4) Rattus norvegicus
Analyze
Symbol: Taf4
Name: TATA-box binding protein associated factor 4
RGD ID: 1588072
Description: Predicted to enable DNA binding activity and aryl hydrocarbon receptor binding activity. Predicted to contribute to RNA polymerase II general transcription initiation factor activity and core promoter sequence-specific DNA binding activity. Predicted to be involved in RNA polymerase II preinitiation complex assembly; mRNA transcription by RNA polymerase II; and positive regulation of transcription initiation by RNA polymerase II. Predicted to act upstream of or within DNA-templated transcription and ovarian follicle development. Predicted to be located in cytosol; male germ cell nucleus; and nucleoplasm. Predicted to be part of MLL1 complex; transcription factor TFIID complex; and transcription factor TFTC complex. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder. Orthologous to human TAF4 (TATA-box binding protein associated factor 4); PARTICIPATES IN RNA polymerase II transcription initiation pathway; INTERACTS WITH bisphenol A; vinclozolin; 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC682097; similar to TBP-associated factor 4; TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor; TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa; Taf4a; transcription initiation factor TFIID subunit 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83187,395,632 - 187,461,042 (-)NCBIGRCr8
mRatBN7.23167,017,992 - 167,083,413 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3167,017,993 - 167,083,356 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3171,395,163 - 171,460,425 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03180,354,234 - 180,419,499 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03177,017,755 - 177,083,016 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03175,300,842 - 175,364,655 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3175,301,879 - 175,327,689 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03181,752,972 - 181,816,580 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera3165,497,297 - 165,560,957 (+)NCBICelera
Cytogenetic Map3q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. A specific role for the TFIID subunit TAF4 and RanBPM in neural progenitor differentiation. Brunkhorst A, etal., Mol Cell Neurosci. 2005 Jun;29(2):250-8.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Structural bioinformatics of the general transcription factor TFIID. Malkowska M, etal., Biochimie. 2013 Apr;95(4):680-91. doi: 10.1016/j.biochi.2012.10.024. Epub 2012 Nov 9.
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:9603525   PMID:10373431   PMID:11557891   PMID:11570813   PMID:12477932   PMID:12665565   PMID:12771217   PMID:14580349   PMID:15601843   PMID:15641800   PMID:15960975   PMID:18722179  
PMID:22323595   PMID:24289924  


Genomics

Comparative Map Data
Taf4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83187,395,632 - 187,461,042 (-)NCBIGRCr8
mRatBN7.23167,017,992 - 167,083,413 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3167,017,993 - 167,083,356 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3171,395,163 - 171,460,425 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03180,354,234 - 180,419,499 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03177,017,755 - 177,083,016 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03175,300,842 - 175,364,655 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3175,301,879 - 175,327,689 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03181,752,972 - 181,816,580 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera3165,497,297 - 165,560,957 (+)NCBICelera
Cytogenetic Map3q43NCBI
TAF4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382061,974,798 - 62,065,881 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2061,953,469 - 62,065,881 (-)EnsemblGRCh38hg38GRCh38
GRCh372060,549,854 - 60,640,937 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362059,983,249 - 60,074,261 (-)NCBINCBI36Build 36hg18NCBI36
Build 342059,983,249 - 60,074,261NCBI
Celera2057,285,893 - 57,375,966 (-)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2057,327,370 - 57,416,991 (-)NCBIHuRef
CHM1_12060,450,922 - 60,541,929 (-)NCBICHM1_1
T2T-CHM13v2.02063,763,185 - 63,856,685 (-)NCBIT2T-CHM13v2.0
Taf4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392179,553,945 - 179,618,519 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2179,553,945 - 179,618,439 (-)EnsemblGRCm39 Ensembl
GRCm382179,912,146 - 179,976,646 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2179,912,152 - 179,976,646 (-)EnsemblGRCm38mm10GRCm38
MGSCv372179,646,851 - 179,711,351 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362179,841,554 - 179,906,054 (-)NCBIMGSCv36mm8
Celera2183,996,374 - 184,059,855 (-)NCBICelera
Cytogenetic Map2H4NCBI
cM Map2102.42NCBI
Taf4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555281,994,249 - 2,020,494 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555281,951,952 - 2,020,592 (+)NCBIChiLan1.0ChiLan1.0
TAF4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22167,757,002 - 67,847,297 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12067,750,123 - 67,840,419 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02058,341,086 - 58,431,623 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12059,662,890 - 59,750,399 (-)NCBIpanpan1.1PanPan1.1panPan2
TAF4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12446,076,744 - 46,107,371 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2446,077,578 - 46,143,828 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2445,314,190 - 45,381,365 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02446,933,627 - 47,000,888 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2446,933,867 - 47,001,098 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12446,035,549 - 46,102,502 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02446,158,437 - 46,225,370 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02446,912,381 - 46,979,578 (-)NCBIUU_Cfam_GSD_1.0
Taf4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640194,240,894 - 194,308,133 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365149,694,509 - 9,722,107 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365149,694,509 - 9,722,101 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAF4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1761,465,822 - 61,529,890 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11761,465,820 - 61,529,963 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21768,993,817 - 69,054,695 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TAF4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.122,167,585 - 2,252,383 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl22,167,341 - 2,252,156 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605050,119,819 - 50,209,736 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Taf4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474127,883,183 - 27,909,304 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474127,881,850 - 27,948,543 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Taf4
230 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3149040888168026850Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3161192952169034231Rat

Markers in Region
D3Hmgc9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23167,068,732 - 167,068,934 (+)MAPPERmRatBN7.2
Rnor_6.03175,351,056 - 175,351,257NCBIRnor6.0
Rnor_5.03181,766,482 - 181,766,683UniSTSRnor5.0
RGSC_v3.43169,027,677 - 169,027,878UniSTSRGSC3.4
Celera3165,510,687 - 165,510,888UniSTS
Cytogenetic Map3 RGD
AI450312  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera3165,560,683 - 165,560,777UniSTS
AW120700  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23167,003,259 - 167,003,338 (+)MAPPERmRatBN7.2
Rnor_6.03175,283,024 - 175,283,102NCBIRnor6.0
Rnor_5.03181,830,975 - 181,831,053UniSTSRnor5.0
RGSC_v3.43168,982,639 - 168,982,717UniSTSRGSC3.4
Celera3165,575,027 - 165,575,105UniSTS
UniSTS:234624  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23167,018,643 - 167,018,846 (+)MAPPERmRatBN7.2
Rnor_6.03175,301,496 - 175,301,698NCBIRnor6.0
Rnor_5.03181,815,724 - 181,815,926UniSTSRnor5.0
Celera3165,560,103 - 165,560,305UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 27 30 22 16 22 66 29 32 11
Low 16 27 19 3 19 8 11 8 6 9 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000082981   ⟹   ENSRNOP00000074471
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3167,017,993 - 167,083,356 (-)Ensembl
Rnor_6.0 Ensembl3175,301,879 - 175,327,689 (-)Ensembl
RefSeq Acc Id: NM_001402170   ⟹   NP_001389099
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83187,395,632 - 187,461,042 (-)NCBI
mRatBN7.23167,017,992 - 167,083,413 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001389099 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88309 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000074471
  ENSRNOP00000074471.2
RefSeq Acc Id: ENSRNOP00000074471   ⟸   ENSRNOT00000082981
RefSeq Acc Id: NP_001389099   ⟸   NM_001402170
- UniProtKB: A0A0G2K849 (UniProtKB/TrEMBL)
Protein Domains
TAFH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K849-F1-model_v2 AlphaFold A0A0G2K849 1-636 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588072 AgrOrtholog
BioCyc Gene G2FUF-46376 BioCyc
Ensembl Genes ENSRNOG00000054497 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000082981 ENTREZGENE
  ENSRNOT00000082981.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.20.10 UniProtKB/TrEMBL
  1.20.120.1110 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7324288 IMAGE-MGC_LOAD
InterPro Histone-fold UniProtKB/TrEMBL
  TAF4 UniProtKB/TrEMBL
  TAF4 UniProtKB/TrEMBL
  TAFH/NHR1_dom_sf UniProtKB/TrEMBL
  TAFH_NHR1 UniProtKB/TrEMBL
MGC_CLONE MGC:109523 IMAGE-MGC_LOAD
NCBI Gene 682097 ENTREZGENE
PANTHER PTHR15138 UniProtKB/TrEMBL
  TATA-BOX-BINDING PROTEIN-ASSOCIATED FACTOR 4 UniProtKB/TrEMBL
Pfam TAF4 UniProtKB/TrEMBL
  TAFH UniProtKB/TrEMBL
PhenoGen Taf4 PhenoGen
PROSITE TAFH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000054497 RatGTEx
SMART TAFH UniProtKB/TrEMBL
Superfamily-SCOP SSF158553 UniProtKB/TrEMBL
  SSF47113 UniProtKB/TrEMBL
UniProt A0A0G2K849 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-09-28 Taf4  TATA-box binding protein associated factor 4  Taf4  TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-09-17 Taf4  TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor  Taf4a  TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-13 Taf4a  TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa  LOC682097  similar to TBP-associated factor 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC682097  similar to TBP-associated factor 4      Symbol and Name status set to provisional 70820 PROVISIONAL