Hoxa1 homeobox A1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hoxa1provided by RGD
Official Full Name: homeobox A1provided by RGD
Primary source: RGD:11414885
See related: Ensembl:ENSRNOG00000005628 AllianceGenome:RGD:11414885
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: Hoxa1l
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 identical protein binding activity. Predicted to be involved in several processes, including abducens nerve formation; embryonic organ morphogenesis; and optokinetic behavior. Predicted to act upstream of or within several processes, including cellular response to ethanol; cellular response to retinoic acid; and nervous system development. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Athabaskan brainstem dysgenesis syndrome and autistic disorder. Orthologous to human HOXA1 (homeobox A1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 7.7), Kidney (RPKM 3.0) and 6 other tissues See more
Orthologs: human mouse all
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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 (82586505..82589209, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (81255814..81258587, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4 Unlocalized Scaffold	NW_007906169.1 (26653..28471, complement)

Chromosome 4 - NC_086022.1 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

MiR-30b-5p Influences Chronic Exercise Arthritic Injury by Targeting Hoxa1.
Title: MiR-30b-5p Influences Chronic Exercise Arthritic Injury by Targeting Hoxa1.
results report a role for HoxA1 in linking TGFbeta-mediated signaling to gene expression in pancreatic epithelial cell populations
Title: Conservation of the TGFbeta/Labial homeobox signaling loop in endoderm-derived cells between Drosophila and mammals.

Submit: New GeneRIF Correction

General gene information

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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	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	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 identical protein binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA 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 abducens nerve formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within anatomical structure formation involved in morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within anatomical structure morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in anatomical structure morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
involved_in artery development	ISO Inferred from Sequence Orthology more info
involved_in artery morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within cellular response to ethanol	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to retinoic acid	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within central nervous system neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in cochlea development	ISO Inferred from Sequence Orthology more info
involved_in cochlea morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cognition	ISO Inferred from Sequence Orthology more info
involved_in embryonic neurocranium morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within facial nerve structural organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within facial nucleus development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within hindbrain development	ISO Inferred from Sequence Orthology more info
involved_in inner ear development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within motor neuron axon guidance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system development	ISO Inferred from Sequence Orthology more info
involved_in neuromuscular process	ISO Inferred from Sequence Orthology more info
involved_in optokinetic behavior	ISO Inferred from Sequence Orthology more info
involved_in outer ear morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	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 regulation of behavior	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 regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within rhombomere 3 development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within rhombomere 4 development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within rhombomere 5 development	ISO Inferred from Sequence Orthology more info
involved_in semicircular canal formation	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of sound	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: homeobox protein Hox-A1

Names: homeo box A1

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_001309364.2 → NP_001296293.1 homeobox protein Hox-A1 isoform 2

See identical proteins and their annotated locations for NP_001296293.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region, which results in a frameshift, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

A0A0G2K0H5, A6K0Q0, O08657

Related

ENSRNOP00000071447.1, ENSRNOT00000083658.2
NM_013075.3 → NP_037207.2 homeobox protein Hox-A1 isoform 1

See identical proteins and their annotated locations for NP_037207.2

Status: VALIDATED

Description

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

Source sequence(s)

JAXUCZ010000004

UniProtKB/Swiss-Prot

O08656

UniProtKB/TrEMBL

A6K0P9, G3V6R3

Related

ENSRNOP00000007807.1, ENSRNOT00000007807.3

Conserved Domains (2) summary

COG5576
Location:175 → 285

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:232 → 284

Homeobox; Homeobox domain