Hoxc9 homeobox C9 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Hoxc9provided by MGI
Official Full Name: homeobox C9provided by MGI
Primary source: MGI:MGI:96199
See related: Ensembl:ENSMUSG00000036139 AllianceGenome:MGI:96199
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Hox-3.2
Summary: Predicted to enable DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within anterior/posterior pattern specification and embryonic skeletal system morphogenesis. Predicted to be located in aggresome and nucleoplasm. Predicted to be part of transcription repressor complex. Predicted to be active in nucleus. Is expressed in several structures, including embryo mesenchyme; extraembryonic component; genitourinary system; limb; and nervous system. Orthologous to human HOXC9 (homeobox C9). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in ovary adult (RPKM 7.9), mammary gland adult (RPKM 7.9) and 7 other tissues See more
Orthologs: human all
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Genomic context

Location:: 15 F3; 15 58.04 cM

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	15	NC_000081.7 (102885467..102893324)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	15	NC_000081.6 (102977032..102984444)

Chromosome 15 - NC_000081.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

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.
Differential abilities to engage inaccessible chromatin diversify vertebrate Hox binding patterns.
Title: Differential abilities to engage inaccessible chromatin diversify vertebrate Hox binding patterns.
Hoxc9, has an essential role in organizing the motor system through global repressive activities. Hoxc9 is required for the generation of thoracic motor columns, and in its absence, neurons acquire the fates of limb-innervating populations
Title: Global control of motor neuron topography mediated by the repressive actions of a single hox gene.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Hoxc9 (e-PCR), detects polymorphism
- UniSTS:143392

PMC15172P2 (e-PCR)
- UniSTS:271172

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

Hoxc9 (e-PCR), detects polymorphism
- UniSTS:536665

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

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
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 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific double-stranded DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology 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	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic skeletal system development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in embryonic skeletal system morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within embryonic skeletal system morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proximal/distal pattern formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in aggresome	IEA Inferred from Electronic Annotation more info
located_in aggresome	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of transcription repressor complex	IEA Inferred from Electronic Annotation more info
part_of transcription repressor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: homeobox protein Hox-C9

Names: homeo box C9; homeobox protein Hox-3.2

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.

mRNA and Protein(s)

NM_008272.3 → NP_032298.1 homeobox protein Hox-C9

See identical proteins and their annotated locations for NP_032298.1

Status: PROVISIONAL

Source sequence(s)

AC021667

Consensus CDS

CCDS27893.1

UniProtKB/Swiss-Prot

P09633

Related

ENSMUSP00000001706.7, ENSMUST00000001706.7

Conserved Domains (2) summary

smart00389
Location:192 → 241

HOX; Homeodomain

pfam04617
Location:1 → 179

Hox9_act; Hox9 activation region

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000081.7 Reference GRCm39 C57BL/6J

Range

102885467..102893324

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036159164.1 → XP_036015057.1 homeobox protein Hox-C9 isoform X1

UniProtKB/Swiss-Prot

P09633

Conserved Domains (2) summary

smart00389
Location:192 → 241

HOX; Homeodomain

pfam04617
Location:1 → 179

Hox9_act; Hox9 activation region