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USF3 upstream transcription factor family member 3 [ Homo sapiens (human) ]

Gene ID: 205717, updated on 5-Mar-2024

Summary

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Official Symbol
USF3provided by HGNC
Official Full Name
upstream transcription factor family member 3provided by HGNC
Primary source
HGNC:HGNC:30494
See related
Ensembl:ENSG00000176542 MIM:617568; AllianceGenome:HGNC:30494
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
KIAA2018
Summary
This gene encodes a large protein that contains a helix-loop-helix domain and a polyglutamine region. A deletion in the polyglutamine region was associated with risk for thyroid carcinoma. [provided by RefSeq, May 2017]
Expression
Ubiquitous expression in bone marrow (RPKM 3.4), kidney (RPKM 3.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
3q13.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (113648385..113696642, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (116369551..116417840, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (113367232..113415489, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SID1 transmembrane family member 1 Neighboring gene uncharacterized LOC124909410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14607 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:113356851-113357351 Neighboring gene RNA, 7SL, cytoplasmic 767, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14609 Neighboring gene N-alpha-acetyltransferase 50, NatE catalytic subunit Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:113463940-113464676 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:113464677-113465412 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:113465413-113466148 Neighboring gene ATPase H+ transporting V1 subunit A

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. USF3 modulates osteoporosis risk by targeting WNT16, RANKL, RUNX2, and two GWAS lead SNPs rs2908007 and rs4531631. Ye W, et al. Hum Mutat, 2021 Jan. PMID 33058301
  2. Osteoporosis genome-wide association study variant c.3781 C>A is regulated by a novel anti-osteogenic factor miR-345-5p. Wang Y, et al. Hum Mutat, 2020 Mar. PMID 31883164
  3. Germline compound heterozygous poly-glutamine deletion in USF3 may be involved in predisposition to heritable and sporadic epithelial thyroid carcinoma. Ni Y, et al. Hum Mol Genet, 2017 Jan 15. PMID 28011713, Free PMC Article
  4. Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Estrada K, et al. Nat Genet, 2012 Apr 15. PMID 22504420, Free PMC Article
  5. Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. Eeles RA, et al. Nat Genet, 2013 Apr. PMID 23535732, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. USF3 modulates osteoporosis risk by targeting WNT16, RANKL, RUNX2, and two GWAS lead SNPs rs2908007 and rs4531631.
    Title: USF3 modulates osteoporosis risk by targeting WNT16, RANKL, RUNX2, and two GWAS lead SNPs rs2908007 and rs4531631.
  2. Osteoporosis genome-wide association study variant c.3781 C>A is regulated by a novel anti-osteogenic factor miR-345-5p.
    Title: Osteoporosis genome-wide association study variant c.3781 C>A is regulated by a novel anti-osteogenic factor miR-345-5p.
  3. Therefore, USF3 may be involved in the predisposition of thyroid cancer. Importantly, the results that glutamine-dependent survival and sensitivity to ER stress in USF3-deficient cells provide avenues for therapeutic and adjunct preventive interventions for both sporadic cancer as well as cancer predisposition syndromes with similar mechanisms.
    Title: Germline compound heterozygous poly-glutamine deletion in USF3 may be involved in predisposition to heritable and sporadic epithelial thyroid carcinoma.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
EBI GWAS Catalog
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp781O0144

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in negative regulation of epithelial to mesenchymal transition IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of epithelial to mesenchymal transition IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
basic helix-loop-helix domain-containing protein USF3

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_055006.1 RefSeqGene

    Range
    5016..53273
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001009899.4 → NP_001009899.3  basic helix-loop-helix domain-containing protein USF3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represent the longer transcript and encodes the protein.
    Source sequence(s)
    AC055740, AC108693, KF457673
    Consensus CDS
    CCDS43133.1
    UniProtKB/Swiss-Prot
    Q68DE3, Q7Z3L9, Q8IVF3, Q9H8T4
    Related
    ENSP00000320794.4, ENST00000316407.9
    Conserved Domains (1) summary
    cd18910
    Location:15 → 79
    bHLHzip_USF3; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in basic helix-loop-helix domain-containing protein USF3 and similar proteins

RNA

  1. NR_111981.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' terminal exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.
    Source sequence(s)
    AC055740, BC043383
    Related
    ENST00000491165.5

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    113648385..113696642 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017005872.2 → XP_016861361.1  basic helix-loop-helix domain-containing protein USF3 isoform X2

  2. XM_017005871.2 → XP_016861360.1  basic helix-loop-helix domain-containing protein USF3 isoform X1

    UniProtKB/Swiss-Prot
    Q68DE3, Q7Z3L9, Q8IVF3, Q9H8T4
    Related
    ENSP00000420721.1, ENST00000478658.1
    Conserved Domains (1) summary
    cd18910
    Location:15 → 79
    bHLHzip_USF3; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in basic helix-loop-helix domain-containing protein USF3 and similar proteins

  3. XM_005247208.5 → XP_005247265.2  basic helix-loop-helix domain-containing protein USF3 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    116369551..116417840 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345664.1 → XP_054201639.1  basic helix-loop-helix domain-containing protein USF3 isoform X2

  2. XM_054345662.1 → XP_054201637.1  basic helix-loop-helix domain-containing protein USF3 isoform X1

  3. XM_054345663.1 → XP_054201638.1  basic helix-loop-helix domain-containing protein USF3 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q68DE3.4 GenPept UniProtKB/Swiss-Prot:Q68DE3

Gene LinkOut

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

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