Hoxa9 homeobox A9 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Hoxa9provided by RGD
Full Name: homeobox A9provided by RGD
Primary source: RGD:1310001
See related: AllianceGenome:RGD:1310001
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Hoxa9l; RGD1310001
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and enzyme binding activity. Involved in prostate gland development and response to testosterone. Predicted to be located in nucleoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human HOXA9 (homeobox A9). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 119.9), Uterus (RPKM 73.6) and 2 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 4q24

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (82653847..82659958, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (81323235..81329344, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4 Unlocalized Scaffold	NW_007906169.1 (93210..100431, complement)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HOXA9-induced chemerin signals through CMKLR1/AMPK/TXNIP/NLRP3 pathway to induce pyroptosis of trophoblasts and aggravate preeclampsia.
Title: HOXA9-induced chemerin signals through CMKLR1/AMPK/TXNIP/NLRP3 pathway to induce pyroptosis of trophoblasts and aggravate preeclampsia.
HOXA9 inhibited myogenic differentiation, affected the best known atrophic signaling pathways, and promoted apoptosis but did not eliminate the differentiation potential of primary satellite cells. HOXA9 may promote denervated muscle atrophy by regulating the activity of satellite cells.
Title: Modulation of HOXA9 after skeletal muscle denervation and reinnervation.

Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Markers

Hoxa7 (e-PCR), detects polymorphism
- UniSTS:143371

Hoxa7 (e-PCR), detects polymorphism
- UniSTS:143372

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

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

Hoxa7 (e-PCR), detects polymorphism
- UniSTS:536645

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

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

RH135228 (e-PCR)
- UniSTS:218505

REN100580 (e-PCR)
- UniSTS:425377

stSG609369 (e-PCR)
- UniSTS:449458

REN100619 (e-PCR)
- UniSTS:425416

REN100620 (e-PCR)
- UniSTS:425417

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

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor 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	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within definitive hemopoiesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic forelimb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic skeletal system development	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mammary gland development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of myeloid cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in prostate gland development	IEP Inferred from Expression Pattern 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to testosterone	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within single fertilization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spermatogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within uterus development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
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
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

Go to the top of the page Help

Preferred Names: homeobox protein Hox-A9

Names: homeo box A9; homeobox protein Hox-A9-like

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001401868.1 → NP_001388797.1 homeobox protein Hox-A9

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

A6K0R2, D3ZSU5

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

82653847..82659958 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039108678.1 → XP_038964606.1 homeobox protein Hox-A9 isoform X1

UniProtKB/TrEMBL

A6K0R3

Conserved Domains (1) summary

pfam00046
Location:75 → 129

Homeobox; Homeobox domain