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

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; 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: mouse all
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Genomic context

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_000018.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
The existence of a highly conserved TAF4b-dependent gene regulatory network.
Title: TAF4b Regulates Oocyte-Specific Genes Essential for Meiosis.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies genetic risk underlying primary rhegmatogenous retinal detachment. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-53854 (e-PCR)
- UniSTS:35108

SHGC-64852 (e-PCR)
- UniSTS:67252

RH70966 (e-PCR)
- UniSTS:5088

g01503rbk (e-PCR)
- UniSTS:96242

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

NG_034162.1 RefSeqGene

Range

4563..169803

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

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

NC_000018.10 Reference GRCh38.p14 Primary Assembly

Range

26226445..26391685

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_060942.1 Alternate T2T-CHM13v2.0

Range

26421246..26585805

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054319037.1 → XP_054175012.1 transcription initiation factor TFIID subunit 4B isoform X1
XM_054319041.1 → XP_054175016.1 transcription initiation factor TFIID subunit 4B isoform X5

UniProtKB/TrEMBL

B4DYT3
XM_054319040.1 → XP_054175015.1 transcription initiation factor TFIID subunit 4B isoform X4
XM_054319039.1 → XP_054175014.1 transcription initiation factor TFIID subunit 4B isoform X3
XM_054319038.1 → XP_054175013.1 transcription initiation factor TFIID subunit 4B isoform X2