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    HOXC6 homeobox C6 [ Homo sapiens (human) ]

    Gene ID: 3223, updated on 2-Nov-2024

    Summary

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    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
    mouse all
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    Genomic context

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    See HOXC6 in Genome Data Viewer
    Location:
    12q13.13
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (54016888..54030823)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (53982461..53996388)
    RS_2024_09 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

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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. HOXC6 predicts invasion and poor survival in hepatocellular carcinoma by driving epithelial-mesenchymal transition. Li PD, et al. Aging (Albany NY), 2018 Jan 15. PMID 29348394, Free PMC Article
    2. HOXC6 in the prognosis of prostate cancer. Zhou J, et al. Artif Cells Nanomed Biotechnol, 2019 Dec. PMID 31271305
    3. HoxC6 Functions as an Oncogene and Isoform HoxC6-2 May Play the Primary Role in Gastric Carcinogenesis. Lin J, et al. Dig Dis Sci, 2020 Oct. PMID 31900716
    4. Downregulation of HOXC6 in Serous Ovarian Cancer. Tait DL, et al. Cancer Invest, 2015. PMID 26046583
    5. Upregulated Hoxc6 expression is associated with poor survival in gastric cancer patients. Zhang Q, et al. Neoplasma, 2013. PMID 23581417

    See all (61) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. [Mechanism of HOXC6 promoting the progression of prostate cancer by activating the SFRP1/Wnt/beta-catenin signaling pathway].
      Title: [Mechanism of HOXC6 promoting the progression of prostate cancer by activating the SFRP1/Wnt/β-catenin signaling pathway].
    2. High expression of HOXC6 predicts a poor prognosis and induces proliferation and inflammation in multiple myeloma cells.
      Title: High expression of HOXC6 predicts a poor prognosis and induces proliferation and inflammation in multiple myeloma cells.
    3. LINC01857 promotes the proliferation, migration, and invasion of gastric cancer cells via regulating miR-4731-5p/HOXC6.
      Title: LINC01857 promotes the proliferation, migration, and invasion of gastric cancer cells via regulating miR-4731-5p/HOXC6.
    4. HOXC6/8/10/13 predict poor prognosis and associate with immune infiltrations in glioblastoma.
      Title: HOXC6/8/10/13 predict poor prognosis and associate with immune infiltrations in glioblastoma.
    5. The Effects of Differentially-Expressed Homeobox Family Genes on the Prognosis and HOXC6 on Immune Microenvironment Orchestration in Colorectal Cancer.
      Title: The Effects of Differentially-Expressed Homeobox Family Genes on the Prognosis and HOXC6 on Immune Microenvironment Orchestration in Colorectal Cancer.
    6. HOXC6-Mediated miR-188-5p Expression Induces Cell Migration through the Inhibition of the Tumor Suppressor FOXN2.
      Title: HOXC6-Mediated miR-188-5p Expression Induces Cell Migration through the Inhibition of the Tumor Suppressor FOXN2.
    7. TrkB/C-induced HOXC6 activation enhances the ADAM8-mediated metastasis of chemoresistant colon cancer cells.
      Title: TrkB/C-induced HOXC6 activation enhances the ADAM8-mediated metastasis of chemoresistant colon cancer cells.
    8. Prospective assessment of two-gene urinary test with multiparametric magnetic resonance imaging of the prostate for men undergoing primary prostate biopsy.
      Title: Prospective assessment of two-gene urinary test with multiparametric magnetic resonance imaging of the prostate for men undergoing primary prostate biopsy.
    9. HomeoboxC6 promotes metastasis by orchestrating the DKK1/Wnt/beta-catenin axis in right-sided colon cancer.
      Title: HomeoboxC6 promotes metastasis by orchestrating the DKK1/Wnt/β-catenin axis in right-sided colon cancer.
    10. HomeoboxC6 affects the apoptosis of human vascular endothelial cells and is involved in atherosclerosis.
      Title: HomeoboxC6 affects the apoptosis of human vascular endothelial cells and is involved in atherosclerosis.
    Submit: New GeneRIF Correction See all GeneRIFs (34)

    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)

    Genotypes

    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 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 RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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
    located_in 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

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    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)

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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..18966
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_004503.4 → NP_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:145 → 198
      Homeobox; Homeobox domain

    2. NM_153693.5 → NP_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:63 → 116
      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..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)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P09630.3 GenPept UniProtKB/Swiss-Prot:P09630

    Gene LinkOut

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