TBP TATA-box binding protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: TBPprovided by HGNC
Official Full Name: TATA-box binding proteinprovided by HGNC
Primary source: HGNC:HGNC:11588
See related: Ensembl:ENSG00000112592 MIM:600075; AllianceGenome:HGNC:11588
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: HDL4; TBP1; GTF2D; SCA17; TFIID; GTF2D1
Summary: Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes TBP, the TATA-binding protein. A distinctive feature of TBP is a long string of glutamines in the N-terminus. This region of the protein modulates the DNA binding activity of the C terminus, and modulation of DNA binding affects the rate of transcription complex formation and initiation of transcription. The number of CAG repeats encoding the polyglutamine tract is usually 25-42, and expansion of the number of repeats to 45-66 increases the length of the polyglutamine string and is associated with spinocerebellar ataxia 17, a neurodegenerative disorder classified as a polyglutamine disease. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2016]
Expression: Broad expression in testis (RPKM 21.7), lymph node (RPKM 7.6) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q27

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (170554369..170572859)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (171927920..171946405)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (170863457..170881947)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

A New Case Series Suggests That SCA48 (ATX/STUB1) Is Primarily a Monogenic Disorder.
Title: A New Case Series Suggests That SCA48 (ATX/STUB1) Is Primarily a Monogenic Disorder.
The New Face of Dynamic Mutation-The CAA [CAG]n CAA CAG Motif as a Mutable Unit in the TBP Gene Causative for Spino-Cerebellar Ataxia Type 17.
Title: The New Face of Dynamic Mutation-The CAA [CAG]n CAA CAG Motif as a Mutable Unit in the TBP Gene Causative for Spino-Cerebellar Ataxia Type 17.
Taf1 N-terminal domain 2 (TAND2) of TFIID promotes formation of stable and mobile unstable TBP-TATA complexes.
Title: Taf1 N-terminal domain 2 (TAND2) of TFIID promotes formation of stable and mobile unstable TBP-TATA complexes.
Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID.
Title: Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID.
TATA-box-binding protein promotes hepatocellular carcinoma metastasis through epithelial-mesenchymal transition.
Title: TATA-box-binding protein promotes hepatocellular carcinoma metastasis through epithelial-mesenchymal transition.
Complex Ataxia-Dementia Phenotype in Patients with Digenic TBP/STUB1 Spinocerebellar Ataxia.
Title: Complex Ataxia-Dementia Phenotype in Patients with Digenic TBP/STUB1 Spinocerebellar Ataxia.
Genotype-Phenotype Correlations for ATX-TBP (SCA17): MDSGene Systematic Review.
Title: Genotype-Phenotype Correlations for ATX-TBP (SCA17): MDSGene Systematic Review.
Intermediate repeat expansions of TBP and STUB1: Genetic modifier or pure digenic inheritance in spinocerebellar ataxias?
Title: Intermediate repeat expansions of TBP and STUB1: Genetic modifier or pure digenic inheritance in spinocerebellar ataxias?
Differential dependencies of human RNA polymerase II promoters on TBP, TAF1, TFIIB and XPB.
Title: Differential dependencies of human RNA polymerase II promoters on TBP, TAF1, TFIIB and XPB.
Mutation analysis of the TATA box-binding protein (TBP) gene in Russian patients with spinocerebellar ataxia and Huntington disease-like phenotype.
Title: Mutation analysis of the TATA box-binding protein (TBP) gene in Russian patients with spinocerebellar ataxia and Huntington disease-like phenotype.

Submit: New GeneRIF Correction See all GeneRIFs (108)

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
Parkinson disease, late-onset MedGen: C3160718 OMIM: 168600 GeneReviews: Parkinson Disease Overview, Gaucher Disease	not available
Spinocerebellar ataxia type 17 MedGen: C1846707 OMIM: 607136 GeneReviews: Hereditary Ataxia Overview, Spinocerebellar Ataxia Type 17	not available

EBI GWAS Catalog

Description
A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci. 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
Envelope surface glycoprotein gp120	env	The transcription factors and kinases c-Jun, JNK, MEK, p38 MAPK, STAT-3, JAK-1, TFII D, TFII F, eIF-4E, and RNA polymerase II are induced by HIV-1 gp120	PubMed
Tat	tat	Recruitment of TBP to the HIV-1 LTR promoter is a limiting step for HIV-1 Tat transactivation, however interaction of Tat with TBP/TFIID occurs after this recruitment	PubMed
	tat	TBP is required for HIV-1 Tat-mediated transactivation of the HIV-1 LTR promoter	PubMed
	tat	TBP interacts with HIV-1 Tat as part of the HIV-1 transcription preinitiation complex (PIC) and is necessary for Tat association with the PIC	PubMed
	tat	Inhibition of HIV-1 Tat by p53 is mediated through the Sp1 and TATA box of the HIV-1 LTR, suggesting p53 interferes with the interaction between Tat and TBP during LTR transactivation	PubMed
	tat	Interaction of TBP/TFIID with the HIV-1 LTR, and therefore presumably HIV-1 Tat, 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	HIV-1 Tat competes for Dr1 interaction with TBP	PubMed
	tat	Binding of HIV-1 Tat to the TBP subunit of TFIID stabilizes the interaction of TFIID with TFIIA	PubMed
	tat	HIV-1 Tat interacts with the RNA polymerase II holoenzyme complex that supports Tat-mediated transactivation of the HIV-1 LTR in vitro upon addition of TBP and TFIIB	PubMed
	tat	TBP synergizes with HIV-1 Tat during Tat-mediated transactivation of the HIV-1 LTR promoter	PubMed
	tat	Binding of HIV-1 Tat to TBP has been mapped to the cysteine rich and core domains (amino acids 20-50) of Tat and the H1 alpha helical and S2 domains (amino acids 163-220) of TBP	PubMed
	tat	HIV-1 Tat directly interacts with TBP as demonstrated by Tat-affinity column purification	PubMed
	tat	HIV-1 Tat binds directly to the basal transcription factor TFIID through the TBP subunit of TFIID	PubMed
	tat	Binding of HIV-1 Tat to p300 induces a conformational change in the CBP/p300 complex such that it can acquire and bind better to basal transcription factors such as TBP, indicating Tat helps CBP/p300 recruit new partners to the transcription machinery	PubMed
Vpr	vpr	HIV-1 Vpr (amino acids 1-35) binds to TFIID, an interaction that is associated with the ability of Vpr to stimulate transcription through the glucocorticoid receptor pathway	PubMed

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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

NoName (e-PCR)
- UniSTS:489739

STS-M55654 (e-PCR)
- UniSTS:17484

AGC001b (e-PCR)
- UniSTS:498587

GDB:262118 (e-PCR)
- UniSTS:156333

WI-18913 (e-PCR)
- UniSTS:20411

GDB:180309 (e-PCR)
- UniSTS:155074

RH18157 (e-PCR)
- UniSTS:209609

G64292 (e-PCR)
- UniSTS:158671

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA polymerase I core promoter sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II core promoter sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables 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	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II general transcription initiation factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA polymerase III general transcription initiation factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables TFIIB-class transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables aryl hydrocarbon receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables core promoter sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA-templated transcription initiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in RNA polymerase I preinitiation complex assembly	IEA Inferred from Electronic Annotation more info
involved_in RNA polymerase II preinitiation complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA polymerase II preinitiation complex assembly	IPI Inferred from Physical Interaction more info	PubMed
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 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 by RNA polymerase II	IC Inferred by Curator more info	PubMed
involved_in transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within transcription by RNA polymerase III	IDA Inferred from Direct Assay more info	PubMed
involved_in transcription by RNA polymerase III	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription initiation at RNA polymerase II promoter	IC Inferred by Curator more info	PubMed

Component	Evidence Code	Pubs
part_of RNA polymerase transcription factor SL1 complex	IDA Inferred from Direct Assay more info	PubMed
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in euchromatin	IDA Inferred from Direct Assay more info	PubMed
located_in female germ cell nucleus	IEA Inferred from Electronic Annotation more info
located_in female pronucleus	IEA Inferred from Electronic Annotation more info
located_in male germ cell nucleus	IEA Inferred from Electronic Annotation more info
located_in male pronucleus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	EXP Inferred from Experiment more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-containing complex	IMP Inferred from Mutant Phenotype more info	PubMed
part_of transcription factor TFIIA complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription factor TFIID complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription factor TFIID complex	IPI Inferred from Physical Interaction 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: TATA-box-binding protein

Names: TATA sequence-binding protein; TATA-box binding protein N-terminal domain; TATA-box factor; transcription initiation factor TFIID TBP 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_008165.1 RefSeqGene

Range

4987..23477

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001172085.2 → NP_001165556.1 TATA-box-binding protein isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

AK304648, AL031259, CA422572

Consensus CDS

CCDS55077.1

UniProtKB/TrEMBL

Q32MN7

Related

ENSP00000442132.1, ENST00000540980.5

Conserved Domains (2) summary

PLN00062
Location:142 → 318

PLN00062; TATA-box-binding protein; Provisional

cd04516
Location:142 → 315

TBP_eukaryotes; eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation ...
NM_003194.5 → NP_003185.1 TATA-box-binding protein isoform 1

See identical proteins and their annotated locations for NP_003185.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AL031259, BC109053, BM720195, CA422572

Consensus CDS

CCDS5315.1

UniProtKB/Swiss-Prot

B4E3B3, F5H869, P20226, Q16845, Q6IBM6, Q9UC02

UniProtKB/TrEMBL

Q32MN7

Related

ENSP00000375942.2, ENST00000392092.7

Conserved Domains (1) summary

PLN00062
Location:162 → 338

PLN00062; TATA-box-binding protein; Provisional