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

Gene ID: 205717, updated on 12-Aug-2018

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; Vega:OTTHUMG00000159322
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 current GRCh38.p12 (GCF_000001405.38) 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 Jun 15 11:32:44 2016

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_001009899.3NP_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, ENST00000316407.8
    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, OTTHUMT00000354588

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_000003.12 Reference GRCh38.p12 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, OTTHUMP00000214838, ENST00000478658.1, OTTHUMT00000354591
    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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