Hoxd3 homeo box D3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hoxd3provided by RGD
Official Full Name: homeo box D3provided by RGD
Primary source: RGD:1588601
See related: Ensembl:ENSRNOG00000001577 AllianceGenome:RGD:1588601
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: Hox4r6
Summary: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including Notch signaling pathway; embryonic skeletal system morphogenesis; and positive regulation of macromolecule metabolic process. Predicted to act upstream of or within several processes, including glossopharyngeal nerve morphogenesis; positive regulation of neuron differentiation; and thyroid gland development. Predicted to be located in aggresome and nuclear body. Predicted to be active in nucleus. Orthologous to human HOXD3 (homeobox D3). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 13.4), Kidney (RPKM 13.0) and 5 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 (80041598..80057700)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (59638708..59650282)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (61650569..61670285)

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?

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General gene information

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Markers

Hoxd3 (e-PCR), detects polymorphism
- UniSTS:158733

NoName (e-PCR)
- UniSTS:491330

UniSTS:467540 (e-PCR)
- UniSTS:467540

Hoxd3 (e-PCR), detects polymorphism
- UniSTS:467540

BB104313 (e-PCR)
- UniSTS:207345

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology 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 DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in Notch signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in Notch signaling pathway	ISO Inferred from Sequence Orthology 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 cartilage development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cartilage development	ISO Inferred from Sequence Orthology more info
involved_in cell-matrix adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell-matrix adhesion	ISO Inferred from Sequence Orthology 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
involved_in glossopharyngeal nerve morphogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within glossopharyngeal nerve morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of neuron differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in thyroid gland development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within thyroid gland development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in aggresome	IEA Inferred from Electronic Annotation more info
located_in aggresome	ISO Inferred from Sequence Orthology more info
located_in nuclear body	IEA Inferred from Electronic Annotation more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: homeobox protein Hox-D3

Names: Homeobox gene D3; homeobox protein R6

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_001271038.1 → NP_001257967.1 homeobox protein Hox-D3

See identical proteins and their annotated locations for NP_001257967.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/TrEMBL

D3Z957

Related

ENSRNOP00000034938.4, ENSRNOT00000033511.6

Conserved Domains (2) summary

pfam00046
Location:198 → 251

Homeobox; Homeobox domain

pfam13293
Location:369 → 430

DUF4074; Domain of unknown function (DUF4074)

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_086021.1 Reference GRCr8

Range

80041598..80057700

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039104414.2 → XP_038960342.1 homeobox protein Hox-D3 isoform X1

UniProtKB/TrEMBL

D3Z957

Conserved Domains (2) summary

pfam00046
Location:198 → 251

Homeobox; Homeobox domain

pfam13293
Location:369 → 430

DUF4074; Domain of unknown function (DUF4074)