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HOXC9 homeobox C9 [ Homo sapiens (human) ]

Gene ID: 3225, updated on 13-Mar-2020

Summary

Official Symbol
HOXC9provided by HGNC
Official Full Name
homeobox C9provided by HGNC
Primary source
HGNC:HGNC:5130
See related
Ensembl:ENSG00000180806 MIM:142971
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

Genomic context

See HOXC9 in Genome Data Viewer
Location:
12q13.13
Exon count:
2
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (54000161..54003337)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54393877..54397121)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene HOXC cluster antisense RNA 2 Neighboring gene HOXC cluster antisense RNA 1 Neighboring gene uncharacterized LOC107984512 Neighboring gene homeobox C8

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
anterior/posterior pattern specification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
embryonic skeletal system morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proximal/distal pattern formation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
aggresome IDA
Inferred from Direct Assay
more info
 
nuclear chromatin ISA
Inferred from Sequence Alignment
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-C9
Names
homeo box C9
homeobox protein Hox-3B

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.

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
    P31274
    UniProtKB/TrEMBL
    A0A024RAZ6
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

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