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GTF2IRD1 GTF2I repeat domain containing 1 [ Homo sapiens (human) ]

Gene ID: 9569, updated on 29-Mar-2023

Summary

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Official Symbol
GTF2IRD1provided by HGNC
Official Full Name
GTF2I repeat domain containing 1provided by HGNC
Primary source
HGNC:HGNC:4661
See related
Ensembl:ENSG00000006704 MIM:604318; AllianceGenome:HGNC:4661
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
BEN; WBS; GTF3; RBAP2; CREAM1; MUSTRD1; WBSCR11; WBSCR12; hMusTRD1alpha1
Summary
The protein encoded by this gene contains five GTF2I-like repeats and each repeat possesses a potential helix-loop-helix (HLH) motif. It may have the ability to interact with other HLH-proteins and function as a transcription factor or as a positive transcriptional regulator under the control of Retinoblastoma protein. This gene plays a role in craniofacial and cognitive development and mutations have been associated with Williams-Beuren syndrome, a multisystem developmental disorder caused by deletion of multiple genes at 7q11.23. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2010]
Expression
Ubiquitous expression in thyroid (RPKM 6.1), esophagus (RPKM 4.7) and 23 other tissues See more
Orthologs
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Genomic context

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See GTF2IRD1 in Genome Data Viewer
Location:
7q11.23
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (74453906..74602605)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (75656184..75805371)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (73868236..74016931)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73849734-73850353 Neighboring gene CAGE-defined high expression enhancer upstream of GTF2IRD1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73892244-73892825 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73892826-73893408 Neighboring gene RNA, 5S ribosomal pseudogene 233 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73909445-73910043 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73919312-73919812 Neighboring gene Williams-Beuren syndrome chromosome region 23 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73995345-73995846 Neighboring gene Sharpr-MPRA regulatory region 2459 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74001529-74002116 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74002117-74002703 Neighboring gene microRNA 10525 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74031162-74031727 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:74031728-74032292

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. GTF2IRD1 overexpression promotes tumor progression and correlates with less CD8+ T cells infiltration in pancreatic cancer. Zhuang H, et al. Biosci Rep, 2020 Sep 30. PMID 32936232, Free PMC Article
  2. Williams Syndrome neuroanatomical score associates with GTF2IRD1 in large-scale magnetic resonance imaging cohorts: a proof of concept for multivariate endophenotypes. Fan CC, et al. Transl Psychiatry, 2018 Jun 8. PMID 29884845, Free PMC Article
  3. GTF2IRD1 regulates transcription by binding an evolutionarily conserved DNA motif 'GUCE'. Thompson PD, et al. FEBS Lett, 2007 Mar 20. PMID 17346708
  4. Characterization and gene structure of a novel retinoblastoma-protein-associated protein similar to the transcription regulator TFII-I. Yan X, et al. Biochem J, 2000 Feb 1. PMID 10642537, Free PMC Article
  5. A transcription factor involved in skeletal muscle gene expression is deleted in patients with Williams syndrome. Tassabehji M, et al. Eur J Hum Genet, 1999 Oct-Nov. PMID 10573005

See all (59) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. GTF2IRD1 overexpression promotes tumor progression and correlates with less CD8+ T cells infiltration in pancreatic cancer.
    Title: GTF2IRD1 overexpression promotes tumor progression and correlates with less CD8+ T cells infiltration in pancreatic cancer.
  2. Study showed that GTF2IRD1 was overexpressed due to copy number amplification at Ch.7q in colorectal cancer (CRC). The expression of GTF2IRD1 was positively associated with the malignant pathological phenotype. Furthermore, high expression of GTF2IRD1 was an independent poor prognostic factor in CRC. Mechanistically, GTF2IRD1 promoted cell cycle progression by downregulation of TGFbetaR2 in CRC.
    Title: GTF2IRD1 on chromosome 7 is a novel oncogene regulating the tumor-suppressor gene TGFβR2 in colorectal cancer.
  3. Among 110 SNPs within the 7q11.23 William's Syndrome (WS) chromosomal region, we found one associated locus located at GTF2IRD1, which has been implicated in animal models of WS.
    Title: Williams Syndrome neuroanatomical score associates with GTF2IRD1 in large-scale magnetic resonance imaging cohorts: a proof of concept for multivariate endophenotypes.
  4. The mis-regulation of genes downstream of GTF2IRD1, including TbetaR2 and BMPR1b, also individually promoted mammary cancer development, and silencing of TbetaR2 suppressed GTF2IRD1-driven tumor promotion.
    Title: An In Vivo Gain-of-Function Screen Identifies the Williams-Beuren Syndrome Gene GTF2IRD1 as a Mammary Tumor Promoter.
  5. Study demonstrates a significant association between SLE in Chinese Han population and the GTF2I rs117026326 T allele/GTF2IRD1 rs4717901 C allele.
    Title: Association of GTF2I and GTF2IRD1 polymorphisms with systemic lupus erythematosus in a Chinese Han population.
  6. GTF2IRD1 binding partners are mostly involved in chromatin modification and transcriptional regulation, whilst others indicate an unexpected role in connection with the primary cilium.
    Title: The nuclear localization pattern and interaction partners of GTF2IRD1 demonstrate a role in chromatin regulation.
  7. GTF2IRD1 is SUMOylated by the SUMO E2 ligase UBC9 and the level of SUMOylation is enhanced by PIASxbeta.
    Title: SUMOylation of GTF2IRD1 regulates protein partner interactions and ubiquitin-mediated degradation.
  8. CLIP2 haploinsufficiency by itself does not lead to the physical or cognitive characteristics of the Williams-Beuren syndrome; GTF2IRD1 and GTF2I are the main genes causing the cognitive defects
    Title: The contribution of CLIP2 haploinsufficiency to the clinical manifestations of the Williams-Beuren syndrome.
  9. This study provided evidences that insufficiency of GTF2IRD1 protein contributes to abnormalities of facial development, motor function and specific behavioural disorders that accompany Williams-Beuren syndrome.
    Title: Mutation of Gtf2ird1 from the Williams-Beuren syndrome critical region results in facial dysplasia, motor dysfunction, and altered vocalisations.
  10. functional hemizygosity for the GTF2I and GTF2IRD1 genes is the main cause of the neurocognitive profile and some aspects of the gestalt phenotype of Williams-Beuren syndrome
    Title: Partial 7q11.23 deletions further implicate GTF2I and GTF2IRD1 as the main genes responsible for the Williams-Beuren syndrome neurocognitive profile.
Submit: New GeneRIF Correction See all GeneRIFs (21)

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

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated 2012-10-10)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated 2012-10-10)

ClinGen Genome Curation Page

EBI GWAS Catalog

Description
A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögren's syndrome at 7q11.23.
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

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 transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables DNA-binding transcription factor activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific NAS
Non-traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in transition between slow and fast fiber IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
general transcription factor II-I repeat domain-containing protein 1
Names
USE B1-binding protein
Williams-Beuren syndrome chromosome region 11
binding factor for early enhancer
general transcription factor 3
general transcription factor III
muscle TFII-I repeat domain-containing protein 1 alpha 1
slow-muscle-fiber enhancer-binding protein
williams-Beuren syndrome chromosomal region 12 protein

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_027954.2 RefSeqGene

    Range
    5002..153701
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001199207.2 → NP_001186136.1  general transcription factor II-I repeat domain-containing protein 1 isoform 3

    See identical proteins and their annotated locations for NP_001186136.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
    Source sequence(s)
    AF151354, AY648295
    Consensus CDS
    CCDS56492.1
    UniProtKB/Swiss-Prot
    Q9UHL9
    Related
    ENSP00000397566.2, ENST00000455841.6
    Conserved Domains (1) summary
    pfam02946
    Location:597 → 669
    GTF2I; GTF2I-like repeat

  2. NM_001410888.1 → NP_001397817.1  general transcription factor II-I repeat domain-containing protein 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC004851, AC005015, AC211433
    Consensus CDS
    CCDS94121.1
    UniProtKB/TrEMBL
    E9PFE2

  3. NM_005685.4 → NP_005676.3  general transcription factor II-I repeat domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_005676.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the coding region, compared to variant 3. The encoded isoform (2) is shorter compared to isoform 3.
    Source sequence(s)
    AF118270, AF151354, AF156489, AY648295
    Consensus CDS
    CCDS47613.1
    UniProtKB/Swiss-Prot
    Q9UHL9
    Related
    ENSP00000408477.2, ENST00000424337.7
    Conserved Domains (1) summary
    pfam02946
    Location:565 → 637
    GTF2I; GTF2I-like repeat

  4. NM_016328.3 → NP_057412.1  general transcription factor II-I repeat domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_057412.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) uses alternate splice sites in the coding region, compared to variant 3. The encoded isoform (1) is shorter compared to isoform 3.
    Source sequence(s)
    AF151354, AY648295, BC018136
    Consensus CDS
    CCDS5571.1
    UniProtKB/Swiss-Prot
    Q9UHL9, Q9UI91
    Related
    ENSP00000265755.3, ENST00000265755.7
    Conserved Domains (1) summary
    pfam02946
    Location:565 → 637
    GTF2I; GTF2I-like repeat

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    74453906..74602605
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047421058.1 → XP_047277014.1  general transcription factor II-I repeat domain-containing protein 1 isoform X3

  2. XM_047421064.1 → XP_047277020.1  general transcription factor II-I repeat domain-containing protein 1 isoform X8

  3. XM_011516713.2 → XP_011515015.1  general transcription factor II-I repeat domain-containing protein 1 isoform X11

    Conserved Domains (1) summary
    pfam02946
    Location:565 → 637
    GTF2I; GTF2I-like repeat

  4. XM_047421056.1 → XP_047277012.1  general transcription factor II-I repeat domain-containing protein 1 isoform X1

  5. XM_047421057.1 → XP_047277013.1  general transcription factor II-I repeat domain-containing protein 1 isoform X2

  6. XM_047421061.1 → XP_047277017.1  general transcription factor II-I repeat domain-containing protein 1 isoform X5

  7. XM_017012802.2 → XP_016868291.1  general transcription factor II-I repeat domain-containing protein 1 isoform X4

    Conserved Domains (1) summary
    pfam02946
    Location:565 → 637
    GTF2I; GTF2I-like repeat

  8. XM_006716182.4 → XP_006716245.1  general transcription factor II-I repeat domain-containing protein 1 isoform X6

    See identical proteins and their annotated locations for XP_006716245.1

    UniProtKB/TrEMBL
    E9PFE2
    Conserved Domains (1) summary
    pfam02946
    Location:565 → 637
    GTF2I; GTF2I-like repeat

  9. XM_017012805.2 → XP_016868294.1  general transcription factor II-I repeat domain-containing protein 1 isoform X10

  10. XM_047421059.1 → XP_047277015.1  general transcription factor II-I repeat domain-containing protein 1 isoform X3

  11. XM_047421062.1 → XP_047277018.1  general transcription factor II-I repeat domain-containing protein 1 isoform X7

    UniProtKB/Swiss-Prot
    Q9UI91

  12. XM_017012804.2 → XP_016868293.1  general transcription factor II-I repeat domain-containing protein 1 isoform X9

    UniProtKB/Swiss-Prot
    Q9UHL9
    Conserved Domains (1) summary
    pfam02946
    Location:565 → 637
    GTF2I; GTF2I-like repeat

  13. XM_047421060.1 → XP_047277016.1  general transcription factor II-I repeat domain-containing protein 1 isoform X4

  14. XM_047421066.1 → XP_047277022.1  general transcription factor II-I repeat domain-containing protein 1 isoform X10

  15. XM_047421063.1 → XP_047277019.1  general transcription factor II-I repeat domain-containing protein 1 isoform X7

    UniProtKB/Swiss-Prot
    Q9UI91

  16. XM_047421065.1 → XP_047277021.1  general transcription factor II-I repeat domain-containing protein 1 isoform X9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    75656184..75805371
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054359379.1 → XP_054215354.1  general transcription factor II-I repeat domain-containing protein 1 isoform X1

  2. XM_054359385.1 → XP_054215360.1  general transcription factor II-I repeat domain-containing protein 1 isoform X5

  3. XM_054359380.1 → XP_054215355.1  general transcription factor II-I repeat domain-containing protein 1 isoform X2

  4. XM_054359392.1 → XP_054215367.1  general transcription factor II-I repeat domain-containing protein 1 isoform X10

  5. XM_054359383.1 → XP_054215358.1  general transcription factor II-I repeat domain-containing protein 1 isoform X4

  6. XM_054359386.1 → XP_054215361.1  general transcription factor II-I repeat domain-containing protein 1 isoform X6

  7. XM_054359381.1 → XP_054215356.1  general transcription factor II-I repeat domain-containing protein 1 isoform X3

  8. XM_054359389.1 → XP_054215364.1  general transcription factor II-I repeat domain-containing protein 1 isoform X8

  9. XM_054359394.1 → XP_054215369.1  general transcription factor II-I repeat domain-containing protein 1 isoform X11

  10. XM_054359390.1 → XP_054215365.1  general transcription factor II-I repeat domain-containing protein 1 isoform X9

  11. XM_054359387.1 → XP_054215362.1  general transcription factor II-I repeat domain-containing protein 1 isoform X7

  12. XM_054359393.1 → XP_054215368.1  general transcription factor II-I repeat domain-containing protein 1 isoform X10

  13. XM_054359384.1 → XP_054215359.1  general transcription factor II-I repeat domain-containing protein 1 isoform X4

  14. XM_054359382.1 → XP_054215357.1  general transcription factor II-I repeat domain-containing protein 1 isoform X3

  15. XM_054359388.1 → XP_054215363.1  general transcription factor II-I repeat domain-containing protein 1 isoform X7

  16. XM_054359391.1 → XP_054215366.1  general transcription factor II-I repeat domain-containing protein 1 isoform X9

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UHL9.1 GenPept UniProtKB/Swiss-Prot:Q9UHL9

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