Taf4b (TATA-box binding protein associated factor 4b) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Taf4b (TATA-box binding protein associated factor 4b) Rattus norvegicus
Analyze
Symbol: Taf4b
Name: TATA-box binding protein associated factor 4b
RGD ID: 1562997
Description: Predicted to enable DNA binding activity and NF-kappaB binding activity. Predicted to contribute to RNA polymerase II general transcription initiation factor activity. Predicted to be involved in positive regulation of stem cell proliferation; positive regulation of transcription initiation by RNA polymerase II; and transcription by RNA polymerase II. Predicted to be located in fibrillar center and nucleoplasm. Predicted to be part of transcription factor TFIID complex. Human ortholog(s) of this gene implicated in spermatogenic failure 13. Orthologous to human TAF4B (TATA-box binding protein associated factor 4b); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC291773; RGD1562997; similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105); similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (TAFII105); TAF4B RNA polymerase II, TATA box binding protein (TBP)-associated factor; TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa; transcription initiation factor TFIID subunit 4B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8186,227,299 - 6,360,970 (+)NCBIGRCr8
mRatBN7.2185,952,737 - 6,086,408 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl185,952,769 - 6,068,307 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0186,206,939 - 6,338,794 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl186,207,280 - 6,318,219 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0186,168,668 - 6,280,010 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4186,071,848 - 6,168,486 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera185,982,341 - 6,115,631 (+)NCBICelera
Cytogenetic Map18p13NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10849440   PMID:15601843   PMID:23350932  


Genomics

Comparative Map Data
Taf4b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8186,227,299 - 6,360,970 (+)NCBIGRCr8
mRatBN7.2185,952,737 - 6,086,408 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl185,952,769 - 6,068,307 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0186,206,939 - 6,338,794 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl186,207,280 - 6,318,219 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0186,168,668 - 6,280,010 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4186,071,848 - 6,168,486 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera185,982,341 - 6,115,631 (+)NCBICelera
Cytogenetic Map18p13NCBI
TAF4B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381826,226,445 - 26,391,685 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1826,226,445 - 26,391,685 (+)EnsemblGRCh38hg38GRCh38
GRCh371823,806,409 - 23,971,649 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361822,060,407 - 22,225,647 (+)NCBINCBI36Build 36hg18NCBI36
Build 341822,061,093 - 22,224,126NCBI
Celera1820,617,414 - 20,782,254 (+)NCBICelera
Cytogenetic Map18q11.2NCBI
HuRef1820,657,331 - 20,821,816 (+)NCBIHuRef
CHM1_11823,733,723 - 23,899,102 (+)NCBICHM1_1
T2T-CHM13v2.01826,421,246 - 26,585,805 (+)NCBIT2T-CHM13v2.0
Taf4b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391814,916,302 - 15,035,160 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1814,916,302 - 15,033,416 (+)EnsemblGRCm39 Ensembl
GRCm381814,783,201 - 14,960,424 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1814,783,245 - 14,900,359 (+)EnsemblGRCm38mm10GRCm38
MGSCv371814,941,754 - 15,058,868 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361814,926,263 - 15,043,377 (+)NCBIMGSCv36mm8
Celera1815,005,590 - 15,122,615 (+)NCBICelera
Cytogenetic Map18A1NCBI
cM Map188.28NCBI
Taf4b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540214,296,202 - 14,425,321 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540214,296,202 - 14,425,298 (+)NCBIChiLan1.0ChiLan1.0
TAF4B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21743,653,166 - 43,820,276 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11829,345,762 - 29,513,872 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01819,480,844 - 19,648,936 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11823,089,239 - 23,254,247 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1823,089,736 - 23,254,518 (+)Ensemblpanpan1.1panPan2
TAF4B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1762,276,885 - 62,402,838 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl762,278,061 - 62,402,375 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha761,710,878 - 61,836,411 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0762,326,267 - 62,452,063 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl762,320,097 - 62,452,478 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1761,998,731 - 62,124,071 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0762,011,647 - 62,137,195 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0762,314,451 - 62,440,300 (-)NCBIUU_Cfam_GSD_1.0
Taf4b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494458,288,608 - 58,419,879 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365505,396,188 - 5,527,556 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365505,396,239 - 5,527,540 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TAF4B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6110,855,636 - 110,971,994 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16110,855,636 - 110,972,798 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.26103,817,752 - 103,934,684 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TAF4B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11854,198,730 - 54,357,101 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1854,200,414 - 54,356,611 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605028,927,788 - 29,089,238 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Taf4b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247706,031,028 - 6,162,937 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247705,955,159 - 6,163,060 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Taf4b
718 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:12
Count of miRNA genes:11
Interacting mature miRNAs:12
Transcripts:ENSRNOT00000037955
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589153Insul31Insulin level QTL 317.150.05blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)18142547119Rat
2312598Bp340Blood pressure QTL 3400.05arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)18130558703Rat
2300180Bmd67Bone mineral density QTL 674.80.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)18134291613Rat
8552968Pigfal19Plasma insulin-like growth factor 1 level QTL 1911.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)18125758124Rat
9590248Scort10Serum corticosterone level QTL 1019.710.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)18125758124Rat
2299160Iddm35Insulin dependent diabetes mellitus QTL 352.79blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)18420794160377792Rat
2312568Glom21Glomerulus QTL 2120.005kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)18518585840503530Rat
61388Bp2Blood pressure QTL 23.23arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)18135374722Rat
2293661Bss50Bone structure and strength QTL 504.640.0003lumbar vertebra size trait (VT:0010518)lumbar vertebra trabecular cross-sectional area (CMO:0001692)18134291613Rat
1641910Colcr3Colorectal carcinoma resistance QTL 35.020.000007intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)18224947722066430Rat

Markers in Region
RH128256  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2186,065,564 - 6,065,731 (+)MAPPERmRatBN7.2
Rnor_6.0186,317,961 - 6,318,127NCBIRnor6.0
Rnor_5.0186,279,755 - 6,279,921UniSTSRnor5.0
RGSC_v3.4186,168,231 - 6,168,397UniSTSRGSC3.4
Celera186,094,839 - 6,095,005UniSTS
RH 3.4 Map1842.3UniSTS
Cytogenetic Map18p13UniSTS
BM392071  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8186,339,124 - 6,339,309 (+)Marker Load Pipeline
mRatBN7.2186,064,561 - 6,064,746 (+)MAPPERmRatBN7.2
Rnor_6.0186,316,958 - 6,317,142NCBIRnor6.0
Rnor_5.0186,278,752 - 6,278,936UniSTSRnor5.0
RGSC_v3.4186,167,227 - 6,167,411UniSTSRGSC3.4
Celera186,093,835 - 6,094,019UniSTS
RH 3.4 Map1880.7UniSTS
Cytogenetic Map18p13UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000037955   ⟹   ENSRNOP00000031359
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl185,952,769 - 6,068,307 (+)Ensembl
Rnor_6.0 Ensembl186,207,280 - 6,318,219 (+)Ensembl
RefSeq Acc Id: NM_001426974   ⟹   NP_001413903
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8186,227,378 - 6,340,383 (+)NCBI
RefSeq Acc Id: XM_006254440   ⟹   XP_006254502
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8186,227,929 - 6,340,373 (+)NCBI
mRatBN7.2185,953,357 - 6,065,820 (+)NCBI
Rnor_6.0186,207,476 - 6,319,323 (+)NCBI
Rnor_5.0186,168,668 - 6,280,010 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771990   ⟹   XP_008770212
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8186,227,299 - 6,360,968 (+)NCBI
mRatBN7.2185,952,737 - 6,086,407 (+)NCBI
Rnor_6.0186,206,939 - 6,338,794 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039097304   ⟹   XP_038953232
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8186,227,299 - 6,360,970 (+)NCBI
mRatBN7.2185,952,737 - 6,086,408 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001413903 (Get FASTA)   NCBI Sequence Viewer  
  XP_006254502 (Get FASTA)   NCBI Sequence Viewer  
  XP_008770212 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953232 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000031359.7
RefSeq Acc Id: XP_006254502   ⟸   XM_006254440
- Peptide Label: isoform X2
- UniProtKB: F1LT11 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008770212   ⟸   XM_008771990
- Peptide Label: isoform X1
- UniProtKB: F1LT11 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000031359   ⟸   ENSRNOT00000037955
RefSeq Acc Id: XP_038953232   ⟸   XM_039097304
- Peptide Label: isoform X1
- UniProtKB: F1LT11 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001413903   ⟸   NM_001426974
- UniProtKB: F1LT11 (UniProtKB/TrEMBL)
Protein Domains
TAFH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LT11-F1-model_v2 AlphaFold F1LT11 1-828 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:1562997 AgrOrtholog
BioCyc Gene G2FUF-8300 BioCyc
Ensembl Genes ENSRNOG00000026023 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037955.7 UniProtKB/TrEMBL
Gene3D-CATH 1.10.20.10 UniProtKB/TrEMBL
  1.20.120.1110 UniProtKB/TrEMBL
InterPro Histone-fold UniProtKB/TrEMBL
  TAF4 UniProtKB/TrEMBL
  TAF4 UniProtKB/TrEMBL
  TAFH/NHR1_dom_sf UniProtKB/TrEMBL
  TAFH_NHR1 UniProtKB/TrEMBL
NCBI Gene 291773 ENTREZGENE
PANTHER PTHR15138 UniProtKB/TrEMBL
  TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 4B UniProtKB/TrEMBL
Pfam TAF4 UniProtKB/TrEMBL
  TAFH UniProtKB/TrEMBL
PhenoGen Taf4b PhenoGen
PROSITE TAFH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000026023 RatGTEx
SMART TAFH UniProtKB/TrEMBL
Superfamily-SCOP Histone-fold UniProtKB/TrEMBL
  SSF158553 UniProtKB/TrEMBL
UniProt F1LT11 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Taf4b  TATA-box binding protein associated factor 4b  Taf4b  TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-12 Taf4b  TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa  RGD1562997  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1562997  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105)   RGD1562997_predicted  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-10 RGD1562997_predicted  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (predicted)    similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (TAFII105) (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1562997_predicted  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (TAFII105) (predicted)  LOC291773  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (TAFII105)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC291773  similar to Transcription initiation factor TFIID 105 kDa subunit (TAFII-105) (TAFII105)      Symbol and Name status set to provisional 70820 PROVISIONAL