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

    Gene ID: 205717, updated on 17-Jun-2019

    Summary

    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
    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

    Genomic context

    See USF3 in Genome Data Viewer
    Location:
    3q13.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (113648385..113696657, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (113367232..113415493, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SID1 transmembrane family member 1 Neighboring gene microRNA 4446 Neighboring gene RNA, 7SL, cytoplasmic 767, pseudogene Neighboring gene N(alpha)-acetyltransferase 50, NatE catalytic subunit Neighboring gene ATPase H+ transporting V1 subunit A

    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 Apr 4 07:08:55 2018

    Bibliography

    Phenotypes

    NHGRI GWAS Catalog

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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • DKFZp781O0144

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    DNA-binding transcription factor activity, RNA polymerase II-specific ISM
    Inferred from Sequence Model
    more info
    PubMed 
    protein dimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    negative regulation of epithelial to mesenchymal transition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    nucleus IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

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

    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.

    Genomic

    1. NG_055006.1 RefSeqGene

      Range
      5012..53273
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001009899.4NP_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
      Related
      ENSP00000320794.4, ENST00000316407.9
      Conserved Domains (1) summary
      pfam00010
      Location:2070
      HLH; Helix-loop-helix DNA-binding domain

    RNA

    1. NR_111981.1 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: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

      Range
      113648385..113696657 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

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

      Related
      ENSP00000420721.1, ENST00000478658.1
      Conserved Domains (1) summary
      pfam00010
      Location:2070
      HLH; Helix-loop-helix DNA-binding domain
    3. XM_005247208.4XP_005247265.2  basic helix-loop-helix domain-containing protein USF3 isoform X2

    4. XM_024453392.1XP_024309160.1  basic helix-loop-helix domain-containing protein USF3 isoform X2

    5. XM_024453391.1XP_024309159.1  basic helix-loop-helix domain-containing protein USF3 isoform X1

      Conserved Domains (1) summary
      pfam00010
      Location:2070
      HLH; Helix-loop-helix DNA-binding domain
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