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HOXC6 homeobox C6 [ Homo sapiens (human) ]

Gene ID: 3223, updated on 23-Dec-2018

Summary

Official Symbol
HOXC6provided by HGNC
Official Full Name
homeobox C6provided by HGNC
Primary source
HGNC:HGNC:5128
See related
Ensembl:ENSG00000197757 MIM:142972
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
CP25; HOX3; HOX3C; HHO.C8
Summary
This gene belongs to the homeobox family, members of which 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, HOXC6, is one of several 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. Alternatively spliced transcript variants encoding different isoforms have been identified for HOXC6. Transcript variant two includes the shared exon, and transcript variant one includes only gene-specific exons. [provided by RefSeq, Jul 2008]
Expression
Biased expression in ovary (RPKM 7.2), adrenal (RPKM 6.2) and 11 other tissues See more
Orthologs

Genomic context

See HOXC6 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..54030823)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54410642..54424607)

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 C5 Neighboring gene homeobox C4 Neighboring gene VISTA enhancer hs1875 Neighboring gene microRNA 615 Neighboring gene uncharacterized LOC440101 Neighboring gene uncharacterized LOC100240735

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

Related articles in PubMed

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

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 
embryonic skeletal system development IEA
Inferred from Electronic Annotation
more info
 
multicellular organism development TAS
Traceable Author Statement
more info
PubMed 
negative regulation of nucleic acid-templated transcription 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
cytosol 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-C6
Names
homeo box 3C
homeo box C8 protein
homeobox protein CP25
homeobox protein HHO.C8
homeobox protein Hox-3C

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..18966
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_004503.4NP_004494.1  homeobox protein Hox-C6 isoform 1

    See identical proteins and their annotated locations for NP_004494.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC012531, S82986
    Consensus CDS
    CCDS8871.1
    UniProtKB/Swiss-Prot
    P09630
    Related
    ENSP00000243108.4, ENST00000243108.4
    Conserved Domains (1) summary
    pfam00046
    Location:145197
    Homeobox; Homeobox domain
  2. NM_153693.4NP_710160.1  homeobox protein Hox-C6 isoform 2

    See identical proteins and their annotated locations for NP_710160.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate 5' exon structure and thus differs in the 5' UTR 5' coding region. These difference cause translation initiation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AC012531, BF058345, BF108967, BF434131, DA996894, M16938
    Consensus CDS
    CCDS41792.1
    UniProtKB/Swiss-Prot
    P09630
    Related
    ENSP00000377864.3, ENST00000394331.3
    Conserved Domains (1) summary
    pfam00046
    Location:63115
    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..54030823
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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