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HOXC4 homeobox C4 [ Homo sapiens (human) ]

Gene ID: 3221, updated on 7-Dec-2018

Summary

Official Symbol
HOXC4provided by HGNC
Official Full Name
homeobox C4provided by HGNC
Primary source
HGNC:HGNC:5126
See related
Ensembl:ENSG00000198353 MIM:142974
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
HOX3; cp19; HOX3E
Summary
This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, which are located on different chromosomes and consist of 9 to 11 genes arranged in tandem. This gene, HOXC4, is one of several homeobox HOXC genes located in a cluster on chromosome 12. Three genes, HOXC5, HOXC4 and HOXC6, share a 5' non-coding exon. Transcripts may include the shared exon spliced to the gene-specific exons, or they may include only the gene-specific exons. Two alternatively spliced variants that encode the same protein have been described for HOXC4. Transcript variant one includes the shared exon, and transcript variant two includes only gene-specific exons. [provided by RefSeq, Jul 2008]
Expression
Broad expression in kidney (RPKM 4.9), ovary (RPKM 2.4) and 16 other tissues See more
Orthologs

Genomic context

See HOXC4 in Genome Data Viewer
Location:
12q13.13
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (54016852..54056030)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54388716..54449814)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984512 Neighboring gene VISTA enhancer hs2078 Neighboring gene homeobox C8 Neighboring gene homeobox C6 Neighboring gene homeobox C5 Neighboring gene VISTA enhancer hs1875 Neighboring gene microRNA 615 Neighboring gene uncharacterized LOC440101 Neighboring gene uncharacterized LOC100240735 Neighboring gene uncharacterized LOC100240734

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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
anterior/posterior pattern specification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cartilage development IEA
Inferred from Electronic Annotation
more info
 
embryonic skeletal system morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
skeletal system development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
homeobox protein Hox-C4
Names
homeo box 3E
homeobox protein CP19
homeobox protein Hox-3E

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_029818.1 RefSeqGene

    Range
    4995..44173
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014620.5NP_055435.2  homeobox protein Hox-C4

    See identical proteins and their annotated locations for NP_055435.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AA805317, AC012531, AI200419, BC050442, CA432146, DA905719, X07495
    Consensus CDS
    CCDS8873.1
    UniProtKB/Swiss-Prot
    P09017
    UniProtKB/TrEMBL
    A0A024RB51, Q86TF7
    Related
    ENSP00000305973.4, ENST00000303406.4
    Conserved Domains (1) summary
    pfam00046
    Location:159212
    Homeobox; Homeobox domain
  2. NM_153633.3NP_705897.1  homeobox protein Hox-C4

    See identical proteins and their annotated locations for NP_705897.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AC023794, BC050442
    Consensus CDS
    CCDS8873.1
    UniProtKB/Swiss-Prot
    P09017
    UniProtKB/TrEMBL
    A0A024RB51, Q86TF7
    Related
    ENSP00000399808.2, ENST00000430889.2
    Conserved Domains (1) summary
    pfam00046
    Location:159212
    Homeobox; Homeobox domain

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.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    54016852..54056030
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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