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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
    mouse all
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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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