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TAF4B TATA-box binding protein associated factor 4b [ Homo sapiens (human) ]

Gene ID: 6875, updated on 12-Oct-2019

Summary

Official Symbol
TAF4Bprovided by HGNC
Official Full Name
TATA-box binding protein associated factor 4bprovided by HGNC
Primary source
HGNC:HGNC:11538
See related
Ensembl:ENSG00000141384 MIM:601689
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SPGF13; TAF2C2; TAFII105
Summary
TATA binding protein (TBP) and TBP-associated factors (TAFs) participate in the formation of the TFIID protein complex, which is involved in initiation of transcription of genes by RNA polymerase II. This gene encodes a cell type-specific TAF that may be responsible for mediating transcription by a subset of activators in B cells. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]
Expression
Broad expression in testis (RPKM 5.0), lymph node (RPKM 3.4) and 24 other tissues See more
Orthologs

Genomic context

See TAF4B in Genome Data Viewer
Location:
18q11.2
Exon count:
18
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 18 NC_000018.10 (26226445..26391685)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (23806409..23971649)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene proteasome 20S subunit alpha 8 Neighboring gene dihydrofolate reductase pseudogene 1 Neighboring gene nucleophosmin 1 pseudogene 2 Neighboring gene SINHCAF pseudogene 1 Neighboring gene zinc finger protein 347 pseudogene Neighboring gene RNA, U6 small nuclear 1289, pseudogene Neighboring gene uncharacterized LOC105372034 Neighboring gene uncharacterized LOC107985142

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Spermatogenic failure 13
MedGen: C4014449 OMIM: 615841 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide search for common SNP x SNP interactions on the risk of venous thrombosis.
NHGRI GWA Catalog
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
NHGRI GWA Catalog
Genome-wide association study identifies genetic risk underlying primary rhegmatogenous retinal detachment.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat Interaction of TFIID with the HIV-1 LTR, and therefore presumably HIV-1 Tat protein, is primarily dependent on the LTR TATA element and may also be stabilized or regulated by flanking E box motifs and basic helix-loop-helix proteins such as AP-4 and E47 PubMed
tat TATA binding protein (TBP)-associated factors (TAFs) in the TFIID complex are required for activation by transcription factors, but are dispensable for HIV-1 Tat LTR transactivation function PubMed
tat A novel function of LBP-1, restricting HIV-1 transcription at the level of elongation by preventing the binding of TFIID to the promoter, is suppressed by HIV-1 Tat, indicating Tat helps recruit TFIID to the HIV-1 LTR PubMed
tat HIV-1 Tat stabilizes the interaction of TFIIA with TFIID, and TFIIA and TFIID are required to reconstitute Tat-specific and TAR-dependent activation of HIV transcription in vitro PubMed
tat HIV-1 Tat binds, through amino acids 36-50, directly to the TBP subunit of the TFIID holoenzyme complex (which includes at least TFIID subunits p250, p125, p70, TBP, and p30), and increases the interaction of TFIID with the HIV-1 LTR promoter PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
NF-kappaB binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
 
transcription factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
oogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of signal transduction by p53 class mediator TAS
Traceable Author Statement
more info
 
spermatogenesis IEA
Inferred from Electronic Annotation
more info
 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
fibrillar center IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
transcription factor TFIID complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
transcription initiation factor TFIID subunit 4B
Names
TAF(II)105
TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa
TATA box binding protein (TBP)-associated factor 4B
TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD
transcription initiation factor TFIID 105 kDa subunit

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_034162.1 RefSeqGene

    Range
    4563..169803
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001293725.2NP_001280654.1  transcription initiation factor TFIID subunit 4B isoform 1

    See identical proteins and their annotated locations for NP_001280654.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC016839, AC121320, AY888048, BC016360
    Consensus CDS
    CCDS77170.1
    UniProtKB/Swiss-Prot
    Q92750
    UniProtKB/TrEMBL
    J3KTH2
    Related
    ENSP00000462980.1, ENST00000578121.5
    Conserved Domains (2) summary
    pfam05236
    Location:621862
    TAF4; Transcription initiation factor TFIID component TAF4 family
    pfam07531
    Location:258346
    TAFH; NHR1 homology to TAF
  2. NM_005640.3NP_005631.1  transcription initiation factor TFIID subunit 4B isoform 2

    See identical proteins and their annotated locations for NP_005631.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC016839, AY888048, BC016360
    Consensus CDS
    CCDS42421.1
    UniProtKB/Swiss-Prot
    Q92750
    Related
    ENSP00000269142.5, ENST00000269142.9
    Conserved Domains (2) summary
    pfam05236
    Location:616857
    TAF4; Transcription initiation factor TFIID component TAF4 family
    pfam07531
    Location:258346
    TAFH; NHR1 homology to TAF

RNA

  1. NR_121653.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate exon and uses an alternate splice junction at the 5' end of an exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC016839, AC121320, AY888048, BC016360
    Related
    ENST00000418698.3

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p13 Primary Assembly

    Range
    26226445..26391685
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024451239.1XP_024307007.1  transcription initiation factor TFIID subunit 4B isoform X1

    Conserved Domains (3) summary
    pfam05236
    Location:616801
    TAF4; Transcription initiation factor TFIID component TAF4 family
    pfam07531
    Location:258346
    TAFH; NHR1 homology to TAF
    cl26464
    Location:14154
    Atrophin-1; Atrophin-1 family
  2. XM_011526153.2XP_011524455.1  transcription initiation factor TFIID subunit 4B isoform X4

    Conserved Domains (1) summary
    pfam07531
    Location:258346
    TAFH; NHR1 homology to TAF
  3. XM_017025932.1XP_016881421.1  transcription initiation factor TFIID subunit 4B isoform X3

  4. XM_005258339.3XP_005258396.1  transcription initiation factor TFIID subunit 4B isoform X2

    Conserved Domains (1) summary
    pfam07531
    Location:258346
    TAFH; NHR1 homology to TAF
  5. XM_017025933.1XP_016881422.1  transcription initiation factor TFIID subunit 4B isoform X5

    UniProtKB/TrEMBL
    B4DYT3
    Conserved Domains (2) summary
    pfam05236
    Location:362603
    TAF4; Transcription initiation factor TFIID component TAF4 family
    pfam07531
    Location:492
    TAFH; NHR1 homology to TAF
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