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    HOXC4 homeobox C4 [ Homo sapiens (human) ]

    Gene ID: 3221, updated on 2-Nov-2024

    Summary

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    Official Symbol
    HOXC4provided by HGNC
    Official Full Name
    homeobox C4provided by HGNC
    Primary source
    HGNC:HGNC:5126
    See related
    Ensembl:ENSG00000198353 MIM:142974; AllianceGenome:HGNC:5126
    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; cp19; HOX3E
    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, HOXC4, is one of several homeobox 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. Two alternatively spliced variants that encode the same protein have been described for HOXC4. Transcript variant one includes the shared exon, and transcript variant two includes only gene-specific exons. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in kidney (RPKM 4.9), ovary (RPKM 2.4) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HOXC4 in Genome Data Viewer
    Location:
    12q13.13
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (54016888..54056030)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (53982461..54021597)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (54410672..54449814)

    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 C6 Neighboring gene homeobox C5 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 Neighboring gene uncharacterized LOC100240734

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. A likely HOXC4 predisposition variant for Chiari malformations. Brockmeyer DL, et al. J Neurosurg, 2023 Jul 1. PMID 36433874, Free PMC Article
    2. Homeobox C4 promotes hepatocellular carcinoma progression by the transactivation of Snail. Yang T, et al. Neoplasma, 2021 Jan. PMID 32977722
    3. HOXC4, HOXC5, and HOXC6 expression in primary cutaneous lymphoid lesions. High expression of HOXC5 in anaplastic large-cell lymphomas. Bijl JJ, et al. Am J Pathol, 1997 Oct. PMID 9327740, Free PMC Article
    4. Expression of the homeobox gene HOXC4 in keratinocytes of normal skin and epithelial skin tumors is correlated with differentiation. Rieger E, et al. J Invest Dermatol, 1994 Sep. PMID 7915745
    5. Expression of HOXC4 homeoprotein in the nucleus of activated human lymphocytes. Meazza R, et al. Blood, 1995 Apr 15. PMID 7718879

    See all (50) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HOXC4 promotes proliferation of pancreatic cancer cells by increasing LDHA-mediated glycolysis.
      Title: HOXC4 promotes proliferation of pancreatic cancer cells by increasing LDHA-mediated glycolysis.
    2. A likely HOXC4 predisposition variant for Chiari malformations.
      Title: A likely HOXC4 predisposition variant for Chiari malformations.
    3. Homeobox C4 promotes hepatocellular carcinoma progression by the transactivation of Snail.
      Title: Homeobox C4 promotes hepatocellular carcinoma progression by the transactivation of Snail.
    4. he upregulation of miR-608 reduced the expression of HOXC4 in the uveal melanoma cells, which was rescued by overexpression of MALAT1. Hence, MALAT1 could upregulate the HOXC4 by binding to miR-608.
      Title: Suppression of long noncoding RNA MALAT1 inhibits the development of uveal melanoma via microRNA-608-mediated inhibition of HOXC4.
    5. HOXC4 homeoprotein expands human hematopoietic immature cells by 3 to 6 times ex vivo and significantly improves the level of in vivo engraftment.
      Title: HOXC4 homeoprotein efficiently expands human hematopoietic stem cells and triggers similar molecular alterations as HOXB4.
    6. Human cytomegalovirus downregulates while all-trans retinoic acid upregulates expression of hoxc4 and hoxc6 in lymphocytic progenitor cells.
      Title: [Effect of human cytomegalovirus infection on the expression of hoxc4 and hoxc6 genes in the proliferation of lymphocytic progenitor cells].
    7. Esr1 bind to and activate the HOXC4 promoter to potentiate HoxC4-mediated AID induction, immunoglobulin class switch and somatic hypermutation.
      Title: Estrogen receptors bind to and activate the HOXC4/HoxC4 promoter to potentiate HoxC4-mediated activation-induced cytosine deaminase induction, immunoglobulin class switch DNA recombination, and somatic hypermutation.
    8. HoxC4 directly activates the Aicda promoter
      Title: HoxC4 binds to the promoter of the cytidine deaminase AID gene to induce AID expression, class-switch DNA recombination and somatic hypermutation.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Analysis of single nucleotide polymorphisms and haplotypes in HOXC gene cluster within susceptible region 12q13 of simple congenital heart disease.
    10. Selective inhibition of class switching to IgG and IgE by recruitment of this and Oct-1 proteins and Ku70/Ku86 to newly identified ATTT cis-elements.
      Title: Selective inhibition of class switching to IgG and IgE by recruitment of the HoxC4 and Oct-1 homeodomain proteins and Ku70/Ku86 to newly identified ATTT cis-elements.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables HMG box domain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in anterior/posterior pattern specification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cartilage development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in embryonic skeletal system morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    homeobox protein Hox-C4
    Names
    homeo box 3E
    homeobox protein CP19
    homeobox protein Hox-3E

    NCBI Reference Sequences (RefSeq)

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    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..44173
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014620.6 → NP_055435.2  homeobox protein Hox-C4

      See identical proteins and their annotated locations for NP_055435.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AA805317, AI200419, BC050442, CA432146, DA905719, X07495
      Consensus CDS
      CCDS8873.1
      UniProtKB/Swiss-Prot
      P09017
      UniProtKB/TrEMBL
      Q86TF7
      Related
      ENSP00000305973.4, ENST00000303406.4
      Conserved Domains (1) summary
      pfam00046
      Location:159 → 213
      Homeobox; Homeobox domain

    2. NM_153633.3 → NP_705897.1  homeobox protein Hox-C4

      See identical proteins and their annotated locations for NP_705897.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AC023794, BC050442
      Consensus CDS
      CCDS8873.1
      UniProtKB/Swiss-Prot
      P09017
      UniProtKB/TrEMBL
      Q86TF7
      Related
      ENSP00000399808.2, ENST00000430889.3
      Conserved Domains (1) summary
      pfam00046
      Location:159 → 213
      Homeobox; Homeobox domain

    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
      54016888..54056030
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      53982461..54021597
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P09017.2 GenPept UniProtKB/Swiss-Prot:P09017

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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