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GTF2H2 general transcription factor IIH subunit 2 [ Homo sapiens (human) ]

Gene ID: 2966, updated on 8-Dec-2018

Summary

Official Symbol
GTF2H2provided by HGNC
Official Full Name
general transcription factor IIH subunit 2provided by HGNC
Primary source
HGNC:HGNC:4656
See related
Ensembl:ENSG00000145736 MIM:601748
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
p44; BTF2; TFIIH; BTF2P44; T-BTF2P44
Summary
This gene is part of a 500 kb inverted duplication on chromosome 5q13. This duplicated region contains at least four genes and repetitive elements which make it prone to rearrangements and deletions. The repetitiveness and complexity of the sequence have also caused difficulty in determining the organization of this genomic region. This gene is within the telomeric copy of the duplication. Deletion of this gene sometimes accompanies deletion of the neighboring SMN1 gene in spinal muscular atrophy (SMA) patients but it is unclear if deletion of this gene contributes to the SMA phenotype. This gene encodes the 44 kDa subunit of RNA polymerase II transcription initiation factor IIH which is involved in basal transcription and nucleotide excision repair. Transcript variants for this gene have been described, but their full length nature has not been determined. A second copy of this gene within the centromeric copy of the duplication has been described in the literature. It is reported to be different by either two or four base pairs; however, no sequence data is currently available for the centromeric copy of the gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in appendix (RPKM 16.9), testis (RPKM 15.9) and 25 other tissues See more
Orthologs

Genomic context

See GTF2H2 in Genome Data Viewer
Location:
5q13.2
Exon count:
19
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (71035124..71109113, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (70330951..70363516, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112267942 Neighboring gene NLR family apoptosis inhibitory protein Neighboring gene NAIP promoter region Neighboring gene OCLN pseudogene 1 Neighboring gene small nucleolar RNA, C/D box 13B-2 Neighboring gene NLR family apoptosis inhibitory protein pseudogene Neighboring gene cadherin 12 pseudogene 4 Neighboring gene uncharacterized LOC107986352 Neighboring gene POM121 membrane glycoprotein (rat) pseudogene

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of general transcription factor IIH, polypeptide 2 (GTF2H2, 44kDa) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Tat tat TFIIH synergizes with HIV-1 Tat to induce transcription elongation from the HIV-1 LTR promoter PubMed
tat Interaction of HIV-1 Tat with TFIIH stimulates phosphorylation of Ser-5 of the RNA polymerase II C-terminal domain (CTD), which in turn also stimulates co-transcriptional capping of HIV-1 mRNA PubMed
tat TFIIH interacts with HIV-1 Tat as a component of the HIV-1 transcription preinitiation complex, but is released from the elongation complex which includes P-TEFb PubMed
tat CAK/TFIIH is required for HIV-1 Tat-mediated transactivation of the HIV-1 LTR promoter PubMed
tat Amino acids 1-48 of HIV-1 Tat, which includes the Tat activation domain, mediate the binding of Tat to CAK and the TFIIH complex through a direct interaction with CDK7 and possibly other TFIIH subunits, including p62 and ERCC3 PubMed
tat HIV-1 Tat interacts with the RNA polymerase II holoenzyme and transcription preinitiation complexes, which include TFIIH, during Tat-mediated transactivation of the HIV-1 LTR 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

Clone Names

  • MGC102806

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity NAS
Non-traceable Author Statement
more info
PubMed 
contributes_to DNA-dependent ATPase activity IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to RNA polymerase II CTD heptapeptide repeat kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
nucleic acid binding TAS
Traceable Author Statement
more info
PubMed 
protein N-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
contributes_to protein kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
translation factor activity, RNA binding TAS
Traceable Author Statement
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
7-methylguanosine mRNA capping TAS
Traceable Author Statement
more info
 
G protein-coupled receptor internalization IMP
Inferred from Mutant Phenotype
more info
PubMed 
global genome nucleotide-excision repair TAS
Traceable Author Statement
more info
 
nucleotide-excision repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleotide-excision repair, DNA incision TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, DNA incision, 5'-to lesion TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, preincision complex assembly TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, preincision complex stabilization TAS
Traceable Author Statement
more info
 
positive regulation of DNA helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein phosphorylation IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to UV TAS
Traceable Author Statement
more info
PubMed 
termination of RNA polymerase I transcription TAS
Traceable Author Statement
more info
 
transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 
transcription elongation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
transcription initiation from RNA polymerase I promoter TAS
Traceable Author Statement
more info
 
transcription initiation from RNA polymerase II promoter TAS
Traceable Author Statement
more info
 
transcription-coupled nucleotide-excision repair TAS
Traceable Author Statement
more info
 
translation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
core TFIIH complex portion of holo TFIIH complex IDA
Inferred from Direct Assay
more info
PubMed 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor TFIID complex IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor TFIIH core complex IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor TFIIH holo complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription factor TFIIH holo complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
general transcription factor IIH subunit 2
Names
BTF2 p44
TFIIH basal transcription factor complex p44 subunit
basic transcription factor 2 44 kDa subunit
general transcription factor IIH polypeptide 2
general transcription factor IIH, polypeptide 2, 44kD subunit
general transcription factor IIH, polypeptide 2, 44kDa

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.

mRNA and Protein(s)

  1. NM_001364567.1NP_001351496.1  general transcription factor IIH subunit 2 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), as well as variant 1, encodes isoform a.
    Source sequence(s)
    AC044797
    Conserved Domains (2) summary
    cd01453
    Location:56236
    vWA_transcription_factor_IIH_type; Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins ...
    cl06838
    Location:11385
    C1_4; TFIIH C1-like domain
  2. NM_001364568.1NP_001351497.1  general transcription factor IIH subunit 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), as well as variants 4, 5, and 6, encodes isoform b.
    Source sequence(s)
    AC044797
    Conserved Domains (2) summary
    cd01453
    Location:56236
    vWA_transcription_factor_IIH_type; Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins ...
    cl06838
    Location:288346
    C1_4; TFIIH C1-like domain
  3. NM_001364569.1NP_001351498.1  general transcription factor IIH subunit 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4), as well as variants 3, 5, and 6, encodes isoform b.
    Source sequence(s)
    AC044797
    Conserved Domains (2) summary
    cd01453
    Location:56236
    vWA_transcription_factor_IIH_type; Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins ...
    cl06838
    Location:288346
    C1_4; TFIIH C1-like domain
  4. NM_001364570.1NP_001351499.1  general transcription factor IIH subunit 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5), as well as variants 3, 4, and 6, encodes isoform b.
    Source sequence(s)
    AC044797
    Conserved Domains (2) summary
    cd01453
    Location:56236
    vWA_transcription_factor_IIH_type; Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins ...
    cl06838
    Location:288346
    C1_4; TFIIH C1-like domain
  5. NM_001364571.1NP_001351500.1  general transcription factor IIH subunit 2 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6), as well as variants 3, 4, and 5, encodes isoform b.
    Source sequence(s)
    AC044797
    Conserved Domains (2) summary
    cd01453
    Location:56236
    vWA_transcription_factor_IIH_type; Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins ...
    cl06838
    Location:288346
    C1_4; TFIIH C1-like domain
  6. NM_001364572.1NP_001351501.1  general transcription factor IIH subunit 2 isoform c

    Status: REVIEWED

    Source sequence(s)
    AC044797
    Conserved Domains (2) summary
    pfam04056
    Location:7179
    Ssl1; Ssl1-like
    cl06838
    Location:231289
    C1_4; TFIIH C1-like domain
  7. NM_001364573.1NP_001351502.1  general transcription factor IIH subunit 2 isoform d

    Status: REVIEWED

    Source sequence(s)
    AC044797
    Conserved Domains (2) summary
    cd01453
    Location:1180
    vWA_transcription_factor_IIH_type; Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins ...
    cl06838
    Location:232290
    C1_4; TFIIH C1-like domain
  8. NM_001515.3NP_001506.1  general transcription factor IIH subunit 2 isoform a

    See identical proteins and their annotated locations for NP_001506.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AC044797, AF078847, BG283896, BM083743
    Consensus CDS
    CCDS34183.1
    UniProtKB/Swiss-Prot
    Q13888
    Related
    ENSP00000274400.5, ENST00000274400.9
    Conserved Domains (2) summary
    cd01453
    Location:56236
    vWA_transcription_factor_IIH_type; Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins ...
    cl06838
    Location:11385
    C1_4; TFIIH C1-like domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    71035124..71109113 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017009403.2XP_016864892.1  general transcription factor IIH subunit 2 isoform X1

    UniProtKB/Swiss-Prot
    Q13888
    Conserved Domains (2) summary
    cd01453
    Location:56236
    vWA_transcription_factor_IIH_type; Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins ...
    cl06838
    Location:11385
    C1_4; TFIIH C1-like domain
  2. XM_017009406.2XP_016864895.1  general transcription factor IIH subunit 2 isoform X1

    UniProtKB/Swiss-Prot
    Q13888
    Conserved Domains (2) summary
    cd01453
    Location:56236
    vWA_transcription_factor_IIH_type; Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins ...
    cl06838
    Location:11385
    C1_4; TFIIH C1-like domain
  3. XM_017009404.1XP_016864893.1  general transcription factor IIH subunit 2 isoform X1

    UniProtKB/Swiss-Prot
    Q13888
    Related
    ENSP00000328901.6, ENST00000330280.11
    Conserved Domains (2) summary
    cd01453
    Location:56236
    vWA_transcription_factor_IIH_type; Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins ...
    cl06838
    Location:11385
    C1_4; TFIIH C1-like domain
  4. XM_024446037.1XP_024301805.1  general transcription factor IIH subunit 2 isoform X2

    Conserved Domains (2) summary
    cd01453
    Location:1179
    vWA_transcription_factor_IIH_type; Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins ...
    cl06838
    Location:231331
    C1_4; TFIIH C1-like domain

Reference GRCh38.p12 ALT_REF_LOCI_2

Genomic

  1. NT_187651.1 Reference GRCh38.p12 ALT_REF_LOCI_2

    Range
    583510..616049 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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