HOXC4 homeobox C4 [Homo sapiens (human)] - Gene

Summary

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

Location:: 12q13.13

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (54016888..54056030)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (53982461..54021597)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (54410672..54449814)

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?

A likely HOXC4 predisposition variant for Chiari malformations.
Title: A likely HOXC4 predisposition variant for Chiari malformations.
Homeobox C4 promotes hepatocellular carcinoma progression by the transactivation of Snail.
Title: Homeobox C4 promotes hepatocellular carcinoma progression by the transactivation of Snail.
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.
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.
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].
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.
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.
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.
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.
The hs1,2mediated enhancement of V(H) and C(H) promoter-driven transcription as induced by HoxC4 and Oct-1/Oct-2 suggests an important role of these homeodomain proteins in the overall regulation of the IgH locus expression.
Title: The HoxC4 homeodomain protein mediates activation of the immunoglobulin heavy chain 3' hs1,2 enhancer in human B cells. Relevance to class switch DNA recombination.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

Hoxc4 (e-PCR), detects polymorphism
- UniSTS:143389

HOX3A (e-PCR)
- UniSTS:266290

D12S1961 (e-PCR)
- UniSTS:9524

RH65687 (e-PCR)
- UniSTS:71486

D12S103 (e-PCR)
- UniSTS:13906

Hoxc4 (e-PCR), detects polymorphism
- UniSTS:536661

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

D12S103 (e-PCR)
- UniSTS:91893

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
part_of 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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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..44173

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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