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Hoxa9 homeobox A9 [ Mus musculus (house mouse) ]

Gene ID: 15405, updated on 9-May-2024

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
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Genomic context

Location:
6 B3; 6 25.4 cM
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (52200077..52203169, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (52223097..52227370, complement)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene homeobox A3 Neighboring gene Hoxa cluster antisense RNA 3 Neighboring gene homeobox A6 Neighboring gene homeobox A7 Neighboring gene mistral long non-coding RNA Neighboring gene predicted gene, 57855 Neighboring gene predicted gene, 52902 Neighboring gene microRNA 196b Neighboring gene homeobox A10

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

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 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
 
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
 
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
 
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
 
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

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)

  1. NM_001277238.2NP_001264167.2  homeobox protein Hox-A9 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC015583
  2. NM_001419377.1NP_001406306.1  homeobox protein Hox-A9 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC015583
  3. NM_001419378.1NP_001406307.1  homeobox protein Hox-A9 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC015583
  4. NM_001419379.1NP_001406308.1  homeobox protein Hox-A9 isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC015583
  5. NM_001419380.1NP_001406309.1  homeobox protein Hox-A9 isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC015583
  6. NM_010456.4NP_034586.1  homeobox protein Hox-A9 isoform 1

    See identical proteins and their annotated locations for NP_034586.1

    Status: REVIEWED

    Source sequence(s)
    AC015583
    Consensus CDS
    CCDS20146.1
    UniProtKB/Swiss-Prot
    O70154, O70155, P09631
    Related
    ENSMUSP00000046939.6, ENSMUST00000048680.8
    Conserved Domains (2) summary
    pfam00046
    Location:208261
    Homeobox; Homeobox domain
    pfam04617
    Location:1192
    Hox9_act; Hox9 activation region

RNA

  1. NR_185066.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC015583
  2. NR_185067.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC015583

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

  1. NC_000072.7 Reference GRCm39 C57BL/6J

    Range
    52200077..52203169 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)