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    HOXC6 homeobox C6 [ Homo sapiens (human) ]

    Gene ID: 3223, updated on 4-Feb-2018
    Official Symbol
    HOXC6provided by HGNC
    Official Full Name
    homeobox C6provided by HGNC
    Primary source
    HGNC:HGNC:5128
    See related
    Ensembl:ENSG00000197757 MIM:142972; Vega:OTTHUMG00000160027
    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
    Location:
    12q13.13
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 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 homeobox C8 Neighboring gene homeobox C5 Neighboring gene homeobox C4 Neighboring gene microRNA 615 Neighboring gene uncharacterized LOC440101 Neighboring gene uncharacterized LOC100240735

    • 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

    Related articles in PubMed

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    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
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    transcription corepressor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    anterior/posterior pattern specification IEA
    Inferred from Electronic Annotation
    more info
     
    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
     
    regulation of transcription by RNA polymerase II TAS
    Traceable Author Statement
    more info
    PubMed 
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    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

    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_004503.3NP_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, OTTHUMP00000217382, ENST00000243108.4, OTTHUMT00000358943
      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, OTTHUMP00000217383, ENST00000394331.3, OTTHUMT00000358944
      Conserved Domains (1) summary
      pfam00046
      Location:63115
      Homeobox; Homeobox domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p7 Primary Assembly

      Range
      54016852..54030823
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018923.2 Alternate CHM1_1.1

      Range
      54377340..54391295
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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