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    HOXC9 homeobox C9 [ Homo sapiens (human) ]

    Gene ID: 3225, updated on 10-Dec-2024

    Summary

    Official Symbol
    HOXC9provided by HGNC
    Official Full Name
    homeobox C9provided by HGNC
    Primary source
    HGNC:HGNC:5130
    See related
    Ensembl:ENSG00000180806 MIM:142971; AllianceGenome:HGNC:5130
    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; HOX3B
    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 is one of several homeobox HOXC genes located in a cluster on chromosome 12. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in kidney (RPKM 2.8), fat (RPKM 2.6) and 10 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See HOXC9 in Genome Data Viewer
    Location:
    12q13.13
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (54000161..54003337)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (53965683..53968859)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54393945..54397121)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:54389001-54389569 Neighboring gene HOXC cluster antisense RNA 2 Neighboring gene HOXC cluster antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6431 Neighboring gene homeobox C8 Neighboring gene uncharacterized LOC124902939 Neighboring gene homeobox C6 Neighboring gene homeobox C5 Neighboring gene homeobox C4

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in anterior/posterior pattern specification IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in embryonic skeletal system morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of cell cycle NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in proximal/distal pattern formation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in aggresome IDA
    Inferred from Direct Assay
    more info
     
    located_in chromatin ISA
    Inferred from Sequence Alignment
    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
     
    part_of transcription repressor complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 

    General protein information

    Preferred Names
    homeobox protein Hox-C9
    Names
    homeo box C9
    homeobox protein Hox-3B

    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.

    mRNA and Protein(s)

    1. NM_006897.3NP_008828.1  homeobox protein Hox-C9

      See identical proteins and their annotated locations for NP_008828.1

      Status: REVIEWED

      Source sequence(s)
      AC012531, BC053894
      Consensus CDS
      CCDS8869.1
      UniProtKB/Swiss-Prot
      B2RCN7, P31274, Q9H1I0
      UniProtKB/TrEMBL
      Q8N561
      Related
      ENSP00000302836.4, ENST00000303450.5
      Conserved Domains (2) summary
      smart00389
      Location:192241
      HOX; Homeodomain
      pfam04617
      Location:1179
      Hox9_act; Hox9 activation region

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      54000161..54003337
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      53965683..53968859
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)