U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

HOXC6 homeobox C6 [ Homo sapiens (human) ]

Gene ID: 3223, updated on 17-Jun-2024

Summary

Official Symbol
HOXC6provided by HGNC
Official Full Name
homeobox C6provided by HGNC
Primary source
HGNC:HGNC:5128
See related
Ensembl:ENSG00000197757 MIM:142972; AllianceGenome:HGNC:5128
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See HOXC6 in Genome Data Viewer
Location:
12q13.13
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (54016888..54030823)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (53982461..53996388)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54410672..54424607)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6431 Neighboring gene homeobox C9 Neighboring gene uncharacterized LOC124902939 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4522 Neighboring gene VISTA enhancer hs2078 Neighboring gene homeobox C8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6433 Neighboring gene homeobox C5 Neighboring gene homeobox C4 Neighboring gene Sharpr-MPRA regulatory region 5451 Neighboring gene VISTA enhancer hs1875 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4523 Neighboring gene microRNA 615 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:54440225-54441124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54445415-54446396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54446397-54447378 Neighboring gene CRISPRi-FlowFISH-validated NFE2 regulatory element 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54451435-54451936 Neighboring gene uncharacterized LOC440101 Neighboring gene uncharacterized LOC100240735 Neighboring gene Sharpr-MPRA regulatory region 1856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6435

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 Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in anterior/posterior pattern specification IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in embryonic skeletal system development IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 

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)

NEW Try the new Transcript table

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
    5031..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
    B2RBV2, P09630, Q6DK09
    UniProtKB/TrEMBL
    Q6IB50
    Related
    ENSP00000243108.4, ENST00000243108.5
    Conserved Domains (1) summary
    pfam00046
    Location:145198
    Homeobox; Homeobox domain
  2. NM_153693.5NP_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:63116
    Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    54016888..54030823
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    53982461..53996388
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)