HOXC9 homeobox C9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: HOXC9provided by HGNC
Official Full Name: homeobox C9provided by HGNC
Primary source: HGNC:HGNC:5130
See related: Ensembl:ENSG00000180806 MIM:142971; AllianceGenome:HGNC:5130
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; HOX3B
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 is one of several homeobox HOXC genes located in a cluster on chromosome 12. [provided by RefSeq, Jul 2008]
Expression: Biased expression in kidney (RPKM 2.8), fat (RPKM 2.6) and 10 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q13.13

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (54000161..54003337)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (53965683..53968859)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (54393945..54397121)

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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HOXC9 characterizes a suppressive tumor immune microenvironment and integration with multiple immune biomarkers predicts response to PD-1 blockade plus chemotherapy in lung adenocarcinoma.
Title: HOXC9 characterizes a suppressive tumor immune microenvironment and integration with multiple immune biomarkers predicts response to PD-1 blockade plus chemotherapy in lung adenocarcinoma.
circRNA-mediated upregulation of HOXC9 is correlated with poor outcome and immune microenvironment infiltrates in LUAD.
Title: circRNA-mediated upregulation of HOXC9 is correlated with poor outcome and immune microenvironment infiltrates in LUAD.
Upregulation of HOXC9 generates interferon-gamma resistance in gastric cancer by inhibiting the DAPK1/RIG1/STAT1 axis.
Title: Upregulation of HOXC9 generates interferon-gamma resistance in gastric cancer by inhibiting the DAPK1/RIG1/STAT1 axis.
HOXC9 overexpression is associated with gastric cancer progression and a prognostic marker for poor survival in gastric cancer patients.
Title: HOXC9 overexpression is associated with gastric cancer progression and a prognostic marker for poor survival in gastric cancer patients.
Transcription factor homeobox C9 (HOXC9) may play a critical role in colorectal cancer (CRC) progression and serve as a potential marker of poor prognosis in CRC.
Title: Clinical Prognostic Significance of HOXC9 Expression in Patients with Colorectal Cancer.
HOXC9 knockdown inhibited the metastasis and stem cell-like phenotype of GC cells without significant effects on cell proliferation as a direct target of miR-26a.
Title: miR-26a/HOXC9 Dysregulation Promotes Metastasis and Stem Cell-Like Phenotype of Gastric Cancer.
downregulation of HOXC9 releases its transcriptional inhibition of DAPK1, resulting in the activation of the DAPK1-Beclin1 pathway, which induces autophagy in glioblastoma cells
Title: Homeobox C9 suppresses Beclin1-mediated autophagy in glioblastoma by directly inhibiting the transcription of death-associated protein kinase 1.
HOXC9 and HOXC10 may play an important role in the development of obesity, adverse fat distribution, and subsequent alterations in whole-body metabolism and adipose tissue function.
Title: Fat depot-specific expression of HOXC9 and HOXC10 may contribute to adverse fat distribution and related metabolic traits.
Results provide a set of the essential genes in the miR-193a-3p/HOXC9/DNA damage response/oxidative stress pathway axis as the diagnostic targets for the guided anti-bladder cancer chemotherapy.
Title: MiR-193a-3p promotes the multi-chemoresistance of bladder cancer by targeting the HOXC9 gene.
HOXC9 coordinates diverse cellular processes associated with differentiation by directly activating and repressing the transcription of distinct sets of genes.
Title: HOXC9 directly regulates distinct sets of genes to coordinate diverse cellular processes during neuronal differentiation.

Submit: New GeneRIF Correction See all GeneRIFs (16)

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

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

RH68776 (e-PCR)
- UniSTS:66349

MARC_44775-44776:1100041323:1 (e-PCR)
- UniSTS:471623

Hoxc9 (e-PCR), detects polymorphism
- UniSTS:468838

SGC35159 (e-PCR)
- UniSTS:34723

HOXC9_2416 (e-PCR)
- UniSTS:280763

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation 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
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within anterior/posterior pattern specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic skeletal system development	IEA Inferred from Electronic Annotation more info
involved_in embryonic skeletal system morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within embryonic skeletal system morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell cycle	NAS Non-traceable Author Statement more info	PubMed
involved_in proximal/distal pattern formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of DNA-templated transcription	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 aggresome	IDA Inferred from Direct Assay more info
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of transcription repressor complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: homeobox protein Hox-C9

Names: homeo box C9; homeobox protein Hox-3B

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.