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GTF2A1 general transcription factor IIA subunit 1 [ Homo sapiens (human) ]

Gene ID: 2957, updated on 5-Mar-2024

Summary

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Official Symbol
GTF2A1provided by HGNC
Official Full Name
general transcription factor IIA subunit 1provided by HGNC
Primary source
HGNC:HGNC:4646
See related
Ensembl:ENSG00000165417 MIM:600520; AllianceGenome:HGNC:4646
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TF2A1; TFIIA; TFIIAL; TFIIA-42
Summary
Accurate transcription initiation on TATA-containing class II genes involves the ordered assembly of RNA polymerase II (POLR2A; MIM 180660) and several general initiation factors (summarized by DeJong and Roeder, 1993 [PubMed 8224848]). One of these factors is TFIIA, which when purified from HeLa extracts consists of 35-, 19-, and 12-kD subunits.[supplied by OMIM, Jul 2010]
Expression
Ubiquitous expression in thyroid (RPKM 15.3), testis (RPKM 12.9) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
14q31.1
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (81175452..81221390, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (75387683..75433560, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (81641796..81687734, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene thyroid stimulating hormone receptor Neighboring gene uncharacterized LOC101928462 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:81507651-81507772 Neighboring gene NMNAT1 pseudogene 1 Neighboring gene uncharacterized LOC105370594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8824 Neighboring gene GTF2A1 intron CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5984 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5986 Neighboring gene small nucleolar RNA, H/ACA box 79 Neighboring gene GTF2A1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8828 Neighboring gene dynein light chain LC8-type 1 pseudogene 1 Neighboring gene uracil-DNA glycosylase pseudogene 3

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. Cleavage and proteasome-mediated degradation of the basal transcription factor TFIIA. Høiby T, et al. EMBO J, 2004 Aug 4. PMID 15257296, Free PMC Article
  2. Human genome search in celiac disease: mutated gliadin T-cell-like epitope in two human proteins promotes T-cell activation. Kumar R, et al. J Mol Biol, 2002 Jun 7. PMID 12054857
  3. Disease-relevant signalling-pathways in head and neck cancer: Taspase1's proteolytic activity fine-tunes TFIIA function. Gribko A, et al. Sci Rep, 2017 Nov 2. PMID 29097782, Free PMC Article
  4. Ubiquitin-proteasome-dependent degradation of TBP-like protein is prevented by direct binding of TFIIA. Isogai M, et al. Genes Cells, 2016 Nov. PMID 27696626
  5. Activity of the upstream TATA-less promoter of the p21(Waf1/Cip1) gene depends on transcription factor IIA (TFIIA) in addition to TFIIA-reactive TBP-like protein. Suzuki H, et al. FEBS J, 2014 Jul. PMID 24835508, Free PMC Article

See all (101) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. De novo produced TFIIA is rapidly confined to the cytoplasm via an evolutionary conserved nuclear export signal (NES, amino acids 21VINDVRDIFL30), interacting with the nuclear export receptor Exportin-1/chromosomal region maintenance 1 (Crm1).
    Title: TFIIA transcriptional activity is controlled by a 'cleave-and-run' Exportin-1/Taspase 1-switch.
  2. Proteolytic processing of TFIIA by Taspase1 was found to mask evolutionary conserved nuclear export signal, thereby promoting nuclear localization and transcriptional activation of TFIIA target genes, such as CDKN2A.
    Title: Disease-relevant signalling-pathways in head and neck cancer: Taspase1's proteolytic activity fine-tunes TFIIA function.
  3. In a cohort of youth at risk for bipolar disorder, pathway analysis showed an enrichment of the glucocorticoid receptor (GR) pathway with the genes MED1, HSPA1L, GTF2A1 and TAF15, which might underlie the previously reported role of stress response in the risk for bipolar disorder in vulnerable populations.
    Title: Integrated transcriptome and methylome analysis in youth at high risk for bipolar disorder: a preliminary analysis.
  4. Data suggest that many TATA-box-containing promoters contain a TFIIA recognition element (IIARE) that activates transcription by increasing the recruitment of RNA polymerase II, TFIIA (TF2A1/TF2A2 subunits), TAF4, and P300. (TAF4 = TATA box binding protein (TBP)-associated factor, RNA polymerase II, C1; P300 = E1A binding protein p300)
    Title: A transcription factor IIA-binding site differentially regulates RNA polymerase II-mediated transcription in a promoter context-dependent manner.
  5. The interaction of TBP-like protein with TFIIA is essential to suppress proteasome-dependent turnover of TBP-like protein
    Title: Ubiquitin-proteasome-dependent degradation of TBP-like protein is prevented by direct binding of TFIIA.
  6. Our results provide first evidence that Taspase1 processing affects TFIIA regulation of TFIID and suggest that Taspase1 processing of TFIIA is required to establish INR-selective core promoter activity in the presence of NC2.
    Title: Taspase1 processing alters TFIIA cofactor properties in the regulation of TFIID.
  7. GTF2A1 alone, or GTF2A1 plus HAAO are excellent candidate biomarkers for detecting Ovarian cancer
    Title: Identification of candidate epigenetic biomarkers for ovarian cancer detection.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Evaluating new candidate SNPs as low penetrance risk factors in sporadic breast cancer: a two-stage Spanish case-control study.
  9. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Interaction of polymorphisms in the interleukin 1B-31 and general transcription factor 2A1 genes on the susceptibility to gastric cancer.
  10. TFIIA induces a conformational change within the TBP/TATA complex that enhances its stability under both in vitro and physiological salt conditions.
    Title: TFIIA changes the conformation of the DNA in TBP/TATA complexes and increases their kinetic stability.
Submit: New GeneRIF Correction See all GeneRIFs (15)

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

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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Replication interactions

Interaction Pubs
Knockdown of general transcription factor IIA, 1, 19/37kDa (GTF2A1) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Tat 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

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

Clone Names

  • FLJ21525, MGC129969, MGC129970

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II general transcription initiation factor activity TAS
Traceable Author Statement
more info
 PubMed 
enables RNA polymerase II general transcription initiation factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables RNA polymerase II-specific DNA-binding transcription factor binding IEA
Inferred from Electronic Annotation
more info
  
enables TBP-class protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA polymerase II preinitiation complex assembly NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of 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 transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cytosol 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 IDA
Inferred from Direct Assay
more info
 PubMed 
part_of transcription factor TFIIA complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transcription factor TFIIA complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of transcription factor TFIIA complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of transcription factor TFIID complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of transcription preinitiation complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
transcription initiation factor IIA subunit 1
Names
TFIIA alpha/beta subunits
general transcription factor IIA 1
general transcription factor IIA, 1, 19/37kDa
glucose regulated protein, 58kD pseudogene
transcription initiation factor TFIIA 42 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.

mRNA and Protein(s)

  1. NM_001278940.2 → NP_001265869.1  transcription initiation factor IIA subunit 1 isoform 3

    See identical proteins and their annotated locations for NP_001265869.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) includes an alternate exon and uses a downstream start codon compared to variant 1. It encodes isoform 3 which has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AL136040, BC050703, BC107156
    UniProtKB/Swiss-Prot
    P52655
    Conserved Domains (1) summary
    pfam03153
    Location:126 → 326
    TFIIA; Transcription factor IIA, alpha/beta subunit

  2. NM_015859.4 → NP_056943.1  transcription initiation factor IIA subunit 1 isoform 1

    See identical proteins and their annotated locations for NP_056943.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL136040, BC050703, D14887
    Consensus CDS
    CCDS9873.1
    UniProtKB/Swiss-Prot
    P52655, Q3KNQ9
    Related
    ENSP00000452454.1, ENST00000553612.6
    Conserved Domains (1) summary
    pfam03153
    Location:13 → 376
    TFIIA; Transcription factor IIA, alpha/beta subunit

  3. NM_201595.3 → NP_963889.1  transcription initiation factor IIA subunit 1 isoform 2

    See identical proteins and their annotated locations for NP_963889.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AL136040, D14886
    Consensus CDS
    CCDS9874.1
    UniProtKB/Swiss-Prot
    P52655
    Related
    ENSP00000409492.2, ENST00000434192.2
    Conserved Domains (1) summary
    pfam03153
    Location:1 → 337
    TFIIA; Transcription factor IIA, alpha/beta subunit

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    81175452..81221390 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    75387683..75433560 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P52655.1 GenPept UniProtKB/Swiss-Prot:P52655

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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