HOXC6 homeobox C6 [Homo sapiens (human)] - Gene

Summary

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

Location:: 12q13.13

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (54016888..54030823)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (53982461..53996388)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (54410672..54424607)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
MicroRNA-495 confers inhibitory effects on cancer stem cells in oral squamous cell carcinoma through the HOXC6-mediated TGF-beta signaling pathway.
Title: MicroRNA-495 confers inhibitory effects on cancer stem cells in oral squamous cell carcinoma through the HOXC6-mediated TGF-β signaling pathway.

Submit: New GeneRIF Correction See all GeneRIFs (33)

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:482059

RH65687 (e-PCR)
- UniSTS:71486

MARC_44017-44022:1098368610:3 (e-PCR)
- UniSTS:471619

STS-M16938 (e-PCR)
- UniSTS:20596

STS-S82986 (e-PCR)
- UniSTS:9088

Hoxc6 (e-PCR), detects polymorphism
- UniSTS:547241

G64243 (e-PCR)
- UniSTS:166640

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
part_of 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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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

NG_029818.1 RefSeqGene

Range

5031..18966

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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