Hoxa9 homeobox A9 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Hoxa9provided by MGI
Official Full Name: homeobox A9provided by MGI
Primary source: MGI:MGI:96180
See related: Ensembl:ENSMUSG00000038227 AllianceGenome:MGI:96180
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: D6a9; Hox-1.7
Summary: This gene is located in a cluster of developmentally and temporally regulated genes on chromosome 6 encoding proteins involved in pattern formation. These proteins contain a characteristic DNA-binding motif called a homeodomain and function in transcriptional regulation. There are four distinct clusters of similar genes on chromosomes 2, 6, 11, and 15. The protein encoded by this gene is important for hematopoeisis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]
Expression: Biased expression in limb E14.5 (RPKM 22.0), colon adult (RPKM 13.7) and 6 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 B3; 6 25.4 cM

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (52200077..52204350, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (52223097..52227370, complement)

Chromosome 6 - NC_000072.7 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: 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?

A pro B cell population forms the apex of the leukemic hierarchy in Hoxa9/Meis1-dependent AML.
Title: A pro B cell population forms the apex of the leukemic hierarchy in Hoxa9/Meis1-dependent AML.
HOXA9 promotes MYC-mediated leukemogenesis by maintaining gene expression for multiple anti-apoptotic pathways.
Title: HOXA9 promotes MYC-mediated leukemogenesis by maintaining gene expression for multiple anti-apoptotic pathways.
CircRNA FUT10 regulates the regenerative potential of aged skeletal muscle stem cells by targeting HOXA9.
Title: CircRNA FUT10 regulates the regenerative potential of aged skeletal muscle stem cells by targeting HOXA9.
LncRNA PEG10 aggravates cardiac hypertrophy through regulating HOXA9.
Title: LncRNA PEG10 aggravates cardiac hypertrophy through regulating HOXA9.
A novel, so far overlooked, protein encoded by HoxA9 in humans and mice, has been described.
Title: A predicted novel protein isoform of HOXA9.
these data support the conclusion that HoxA9 represses Cebpa expression, at least in part via inhibition of its +8 kb enhancer, potentially allowing normal myeloid progenitors to maintain immaturity and contributing to the pathogenesis of acute myeloid leukemia associated with increased HOXA9.
Title: HoxA9 binds and represses the Cebpa +8 kb enhancer.
DOT1L, LSD1, and HDAC Class I Inhibitors Reduce HOXA9 Expression in MLL-AF9 Rearranged Leukemia Cells, But Dysregulate the Expression of Many Histone-Modifying Enzymes
Title: Selective DOT1L, LSD1, and HDAC Class I Inhibitors Reduce HOXA9 Expression in MLL-AF9 Rearranged Leukemia Cells, But Dysregulate the Expression of Many Histone-Modifying Enzymes.
HOXA9 inhibits HIF1A-mediated glycolysis through interacting with CRIP2 to repress cutaneous squamous cell carcinoma development.
Title: HOXA9 inhibits HIF-1α-mediated glycolysis through interacting with CRIP2 to repress cutaneous squamous cell carcinoma development.
Beta-catenin regulates expression of downstream targets of a key transcriptional memory gene, Hoxa9 that is highly enriched in myeloid leukemia cancer stem cells and helps sustain leukemic self-renewal.
Title: Transcriptional memory of cells of origin overrides β-catenin requirement of MLL cancer stem cells.
The analysis points to a critical role for Hoxa9 and PU.1 in distal regulation of c-myb expression in murine myeloid cells during iL-6-induced cell differentiation.
Title: Distal regulation of c-myb expression during IL-6-induced differentiation in murine myeloid progenitor M1 cells.

Submit: New GeneRIF Correction See all GeneRIFs (47)

Variation

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Alleles

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

Targeted (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:274178

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:143375

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:143376

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:143377

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:265256

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:265257

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:265258

PMC15172P1 (e-PCR)
- UniSTS:271171

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:536646

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:467538

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:468837

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:506985

stSG609369 (e-PCR)
- UniSTS:449458

REN100619 (e-PCR)
- UniSTS:425416

REN100620 (e-PCR)
- UniSTS:425417

AA987181 (e-PCR)
- UniSTS:208345

HOX1 (e-PCR)
- UniSTS:71932

Hoxa9 (e-PCR), detects polymorphism
- UniSTS:516607

Homology

Homologs of the Hoxa9 gene: The Hoxa9 gene is conserved in human, chimpanzee, Rhesus monkey, dog, cow, rat, chicken, and frog.
Orthologs from Annotation Pipeline: 317 organisms have orthologs with human gene Hoxa9
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
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	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
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	PubMed
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 definitive hemopoiesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic forelimb morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic skeletal system development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryonic skeletal system morphogenesis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in endothelial cell activation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within male gonad development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within mammary gland development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of myeloid cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in proximal/distal pattern formation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within proximal/distal pattern formation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within single fertilization	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within spermatogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within uterus development	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: homeobox protein Hox-A9

Names: homeo box A9; homeobox protein Hox-1.7

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_001277238.1 → NP_001264167.1 homeobox protein Hox-A9 isoform 2

See identical proteins and their annotated locations for NP_001264167.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an internal segment in the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is longer than isoform 1. The exon structure of this variant is similar to Hoxa9T (PMID: 9524228).

Source sequence(s)

AC015583

Conserved Domains (2) summary

pfam00046
Location:232 → 285

Homeobox; Homeobox domain

pfam04617
Location:190 → 216

Hox9_act; Hox9 activation region
NM_010456.3 → NP_034586.1 homeobox protein Hox-A9 isoform 1

See identical proteins and their annotated locations for NP_034586.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the shorter isoform (1).

Source sequence(s)

AC015583

Consensus CDS

CCDS20146.1

UniProtKB/Swiss-Prot

O70155, P09631

UniProtKB/TrEMBL

A0A6P5PW60

Related

ENSMUSP00000046939.6, ENSMUST00000048680.8

Conserved Domains (2) summary

pfam00046
Location:208 → 261

Homeobox; Homeobox domain

pfam04617
Location:1 → 192

Hox9_act; Hox9 activation region