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HOXC5 homeobox C5 [ Homo sapiens (human) ]

Gene ID: 3222, updated on 18-Nov-2018

Summary

Official Symbol
HOXC5provided by HGNC
Official Full Name
homeobox C5provided by HGNC
Primary source
HGNC:HGNC:5127
See related
Ensembl:ENSG00000172789 Ensembl:ENSG00000273046 MIM:142973; Vega:OTTHUMG00000160028
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
CP11; HOX3; HOX3D
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, HOXC5, 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 have been described for HOXC5. The transcript variant which includes the shared exon apparently doesn't encode a protein. The protein-coding transcript variant contains gene-specific exons only. [provided by RefSeq, Jul 2008]
Expression
Biased expression in ovary (RPKM 1.6), kidney (RPKM 1.3) and 12 other tissues See more
Orthologs

Genomic context

See HOXC5 in Genome Data Viewer
Location:
12q13.13
Exon count:
3
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (54016852..54035361)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54410642..54429145)

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 C4 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 Jun 15 11:32:44 2016

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

General gene information

Markers

Potential readthrough

Included gene: HOXC10

Homology

Gene Ontology Provided by GOA

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

General protein information

Preferred Names
homeobox protein Hox-C5
Names
homeo box C5
homeobox protein CP11
homeobox protein Hox-3D

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..23504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_018953.3NP_061826.1  homeobox protein Hox-C5

    See identical proteins and their annotated locations for NP_061826.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and is protein coding.
    Source sequence(s)
    AC012531, BC034922, BE255323, BM786543, CN309383
    Consensus CDS
    CCDS8872.1
    UniProtKB/Swiss-Prot
    Q00444
    Related
    ENSP00000309336.2, OTTHUMP00000217386, ENST00000312492.2, OTTHUMT00000358947
    Conserved Domains (1) summary
    pfam00046
    Location:158211
    Homeobox; Homeobox domain

RNA

  1. NR_003084.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5'-most exon, compared to variant 1. Three genes, HOXC4, HOXC5 and HOXC6, share this 5' non-coding exon. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    BC034922, BE255323, DA747240
    Related
    ENST00000512206.1

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_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    54016852..54035361
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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