HOXC5 homeobox C5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HOXC5provided by HGNC
Official Full Name: homeobox C5provided by HGNC
Primary source: HGNC:HGNC:5127
See related: Ensembl:ENSG00000172789 MIM:142973; AllianceGenome:HGNC:5127
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: CP11; HOX3; HOX3D
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, HOXC5, 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 have been described for HOXC5. The transcript variant which includes the shared exon apparently doesn't encode a protein. The protein-coding transcript variant contains gene-specific exons only. [provided by RefSeq, Jul 2008]
Expression: Biased expression in ovary (RPKM 1.6), kidney (RPKM 1.3) and 12 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..54035361)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (53982461..54000926)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (54410672..54429145)

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?

Both mir-615-3p and HOXC5 are activated upon differentiation, which constitute a feed-forward loop that coordinates transcriptional and post-transcriptional repression of hTERT during cellular differentiation. Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.
Title: HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis.
The A17860G located in 3'flanking sequence of HOXC5 gene is associated with simple congenital heart disease; the haplotype of 3 SNPs may be linked with the susceptible gene of simple CHD.
Title: Analysis of single nucleotide polymorphisms and haplotypes in HOXC gene cluster within susceptible region 12q13 of simple congenital heart disease.
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.

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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

D12S1961 (e-PCR)
- UniSTS:9524

RH65687 (e-PCR)
- UniSTS:71486

Hoxc5 (e-PCR), detects polymorphism
- UniSTS:536662

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

STS-X61755 (e-PCR)
- UniSTS:67709

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

GDB:384845 (e-PCR)
- UniSTS:157106

HOXC5_135.2 (e-PCR)
- UniSTS:280761

G64243 (e-PCR)
- UniSTS:166640

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	TAS Traceable Author Statement 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 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

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 cell junction	IDA Inferred from Direct Assay more info
part_of 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

General protein information

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Preferred Names: homeobox protein Hox-C5

Names: homeo box C5; homeobox protein CP11; homeobox protein Hox-3D

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..23504

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_018953.4 → NP_061826.1 homeobox protein Hox-C5

See identical proteins and their annotated locations for NP_061826.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the shorter transcript and is protein coding.

Source sequence(s)

AC012531, AC023794

Consensus CDS

CCDS8872.1

UniProtKB/Swiss-Prot

Q00444

Related

ENSP00000309336.2, ENST00000312492.3

Conserved Domains (1) summary

pfam00046
Location:158 → 211

Homeobox; Homeobox domain

RNA

NR_003084.3 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate 5'-most exon, compared to variant 1. Three genes, HOXC4, HOXC5 and HOXC6, share this 5' non-coding exon. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.

Source sequence(s)

BC034922, BE255323, DA747240