Hoxd9 homeo box D9 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hoxd9provided by RGD
Official Full Name: homeo box D9provided by RGD
Primary source: RGD:1582908
See related: EnsemblRapid:ENSRNOG00000001580 AllianceGenome:RGD:1582908
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in embryonic skeletal system morphogenesis; negative regulation of transcription by RNA polymerase II; and regionalization. Predicted to act upstream of or within several processes, including embryonic skeletal system development; limb morphogenesis; and peripheral nervous system neuron development. Predicted to be located in nucleolus and nucleoplasm. Predicted to be active in nucleus. Orthologous to human HOXD9 (homeobox D9). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 75.3), Uterus (RPKM 36.4) and 3 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q23

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (80008006..80010186)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (59600575..59602755)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (61620192..61622360)

Chromosome 3 - NC_086021.1 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?

All-trans-retinoic acid suppresses rat embryo hindlimb bud mesenchymal chondrogenesis by modulating HoxD9 expression.
Title: All-trans-retinoic acid suppresses rat embryo hindlimb bud mesenchymal chondrogenesis by modulating HoxD9 expression.

Submit: New GeneRIF Correction

General gene information

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Markers

RH129262 (e-PCR)
- UniSTS:212569

Hoxd9 (e-PCR), detects polymorphism
- UniSTS:536674

RH139211 (e-PCR)
- UniSTS:221297

Hoxd9 (e-PCR), detects polymorphism
- UniSTS:474753

D2Mit38 (e-PCR), detects polymorphism
- UniSTS:129277

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology 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 transcription regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region 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 DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in adult locomotory behavior	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within adult locomotory behavior	ISO Inferred from Sequence Orthology more info
involved_in anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
involved_in anterior/posterior pattern specification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
involved_in embryonic forelimb morphogenesis	IEA Inferred from Electronic Annotation 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 embryonic skeletal system morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within embryonic skeletal system morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forelimb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in hindlimb morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within hindlimb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in mammary gland development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mammary gland development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in peripheral nervous system neuron development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within peripheral nervous system neuron development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in proximal/distal pattern formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in proximal/distal pattern formation	IEA Inferred from Electronic Annotation 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 single fertilization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within single fertilization	ISO Inferred from Sequence Orthology more info
involved_in skeletal muscle tissue development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within skeletal muscle tissue development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	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
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: homeobox protein Hox-D9

Names: homeobox Hox-D9

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.