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

Gene ID: 6875, updated on 3-Apr-2024

Summary

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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; AllianceGenome:HGNC:11538
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
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Genomic context

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See TAF4B in Genome Data Viewer
Location:
18q11.2
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (26226445..26391685)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (26421246..26585805)
105.20220307 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 ATAC-STARR-seq lymphoblastoid active region 13179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13180 Neighboring gene dihydrofolate reductase pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:23787469-23787645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9371 Neighboring gene nucleophosmin 1 pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:23812073-23812268 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:23824799-23825157 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:23841243-23841743 Neighboring gene SINHCAF pseudogene 1 Neighboring gene MPRA-validated peak3086 silencer Neighboring gene uncharacterized LOC124904383 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:23918413-23918607 Neighboring gene zinc finger protein 347 pseudogene Neighboring gene RNA, U6 small nuclear 1289, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr18:23973056-23973249 Neighboring gene uncharacterized LOC107985142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13183 Neighboring gene long intergenic non-protein coding RNA 1543

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Analysis of TATA-box binding protein associated factor 4b gene mutations in a Chinese population with nonobstructive azoospermia. Xi Q, et al. Medicine (Baltimore), 2020 Jun 5. PMID 32502024, Free PMC Article
  2. Targeting TBP-Associated Factors in Ovarian Cancer. Ribeiro JR, et al. Front Oncol, 2014. PMID 24653979, Free PMC Article
  3. Cyclic AMP-dependent modification of gonad-selective TAF(II)105 in a human ovarian granulosa cell line. Wu Y, et al. J Cell Biochem, 2005 Nov 1. PMID 16088961
  4. A composite nuclear export signal in the TBP-associated factor TAFII105. Rashevsky-Finkel A, et al. J Biol Chem, 2001 Nov 30. PMID 11567023
  5. Specific interaction of TAFII105 with OCA-B is involved in activation of octamer-dependent transcription. Wolstein O, et al. J Biol Chem, 2000 Jun 2. PMID 10828057

See all (51) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The c.11G>T mutation of the TAF4B gene may be associated with NOA in a Chinese population.
    Title: Analysis of TATA-box binding protein associated factor 4b gene mutations in a Chinese population with nonobstructive azoospermia.
  2. Nonobstructive Azoospermia variants included MTRR c.537T>C (rs161870), odds ratios (OR), 3.686, 95% confidence interval (CI), 1.228-11.066; MTRR, c.1049A>G (rs162036), OR, 3.686, 95% CI, 1.228-11.066; PIWIL1, c.1580G>A (rs1106042), OR, 4.737, 95% CI, 1.314-17.072; TAF4B, c.1815T>C (rs1677016), OR, 3.599, 95% CI, 1.255-10.327; and SOX10 c.927T>C (rs139884), OR, 3.192, 95% CI, 1.220-8.353.
    Title: Targeted Next-Generation Sequencing Identifies Novel Sequence Variations of Genes Associated with Nonobstructive Azoospermia in the Han Population of Northeast China.
  3. The methionine synthase reductase (MTRR), TAF4B protein, PIWI protein (PIWIL1) four single nucleotide polymorphisms (SNPs) are not shown to be significantly related with non-obstructive azoospermia (NOA).
    Title: Association Study Between MTRR, TAF4B, PIWIL1 Variants and Non-Obstructive Azoospermia in Northeast Chinese Han Population.
  4. The existence of a highly conserved TAF4b-dependent gene regulatory network.
    Title: TAF4b Regulates Oocyte-Specific Genes Essential for Meiosis.
  5. Two candidate loci in each family and homozygous truncating mutations p.R611X in TAF4B in family 1 and p.K507Sfs*3 in ZMYND15 in family 2, were identified.
    Title: Truncating mutations in TAF4B and ZMYND15 causing recessive azoospermia.
  6. We show evidence for the first time of an interdependence of TAF4b and AP-1 family members in cell type-specific promoter recognition and initiation of transcription in the context of cancer progression and EMT.
    Title: TAF4b and Jun/activating protein-1 collaborate to regulate the expression of integrin alpha6 and cancer cell migration properties.
  7. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Genome-wide association study in premature ovarian failure patients suggests ADAMTS19 as a possible candidate gene.
  8. Findings suggest that DNA binding by TAF4/4b-TAF12 facilitates the association of TFIID with the core promoter of a subset of genes.
    Title: TAF4/4b x TAF12 displays a unique mode of DNA binding and is required for core promoter function of a subset of genes.
  9. Expression of the TAF4b gene is induced by MYC through a non-canonical, but not canonical, E-box which contributes to its specific response to MYC.
    Title: Expression of the TAF4b gene is induced by MYC through a non-canonical, but not canonical, E-box which contributes to its specific response to MYC.
  10. TAF4b incorporation into TFIID induces an open conformation at the lobe involved in TFIIA & putative activator interactions, correlating with differential activator-dependent transcription & promoter recognition by 4b/4-IID.
    Title: Structural changes in TAF4b-TFIID correlate with promoter selectivity.
Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

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

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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 PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables NF-kappaB binding IPI
Inferred from Physical Interaction
more info
 PubMed 
contributes_to RNA polymerase II general transcription initiation factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II general transcription initiation factor activity IC
Inferred by Curator
more info
 PubMed 
enables protein heterodimerization activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in RNA polymerase II preinitiation complex assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in mRNA transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in oogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription initiation by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in spermatogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription initiation at RNA polymerase II promoter IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in fibrillar center IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of transcription factor TFIID complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription factor TFIID complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of transcription factor TFIID complex ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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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)

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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_001293725.2 → NP_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/TrEMBL
    A4PBF7, J3KTH2
    Related
    ENSP00000462980.1, ENST00000578121.5
    Conserved Domains (2) summary
    pfam05236
    Location:621 → 862
    TAF4; Transcription initiation factor TFIID component TAF4 family
    pfam07531
    Location:258 → 346
    TAFH; NHR1 homology to TAF

  2. NM_005640.3 → NP_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
    Q29YA4, Q29YA5, Q92750
    UniProtKB/TrEMBL
    A4PBF7
    Related
    ENSP00000269142.6, ENST00000269142.10
    Conserved Domains (2) summary
    pfam05236
    Location:616 → 857
    TAF4; Transcription initiation factor TFIID component TAF4 family
    pfam07531
    Location:258 → 346
    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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_024451239.2 → XP_024307007.1  transcription initiation factor TFIID subunit 4B isoform X1

    UniProtKB/TrEMBL
    A4PBF7
    Conserved Domains (3) summary
    pfam05236
    Location:616 → 801
    TAF4; Transcription initiation factor TFIID component TAF4 family
    pfam07531
    Location:258 → 346
    TAFH; NHR1 homology to TAF
    cl26464
    Location:14 → 154
    Atrophin-1; Atrophin-1 family

  2. XM_011526153.3 → XP_011524455.1  transcription initiation factor TFIID subunit 4B isoform X4

    Conserved Domains (1) summary
    pfam07531
    Location:258 → 346
    TAFH; NHR1 homology to TAF

  3. XM_017025932.2 → XP_016881421.1  transcription initiation factor TFIID subunit 4B isoform X3

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

    Conserved Domains (1) summary
    pfam07531
    Location:258 → 346
    TAFH; NHR1 homology to TAF

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    26421246..26585805
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054319037.1 → XP_054175012.1  transcription initiation factor TFIID subunit 4B isoform X1

  2. XM_054319041.1 → XP_054175016.1  transcription initiation factor TFIID subunit 4B isoform X5

    UniProtKB/TrEMBL
    B4DYT3

  3. XM_054319040.1 → XP_054175015.1  transcription initiation factor TFIID subunit 4B isoform X4

  4. XM_054319039.1 → XP_054175014.1  transcription initiation factor TFIID subunit 4B isoform X3

  5. XM_054319038.1 → XP_054175013.1  transcription initiation factor TFIID subunit 4B isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92750.2 GenPept UniProtKB/Swiss-Prot:Q92750

Gene LinkOut

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