Hoxd13 homeo box D13 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hoxd13provided by RGD
Official Full Name: homeo box D13provided by RGD
Primary source: RGD:1308417
See related: EnsemblRapid:ENSRNOG00000001588 AllianceGenome:RGD:1308417
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: Enables sequence-specific double-stranded DNA binding activity. Involved in embryonic hindgut morphogenesis; prostate gland development; and response to testosterone. Predicted to be located in nucleoplasm. Biomarker of hypospadias. Human ortholog(s) of this gene implicated in brachydactyly-syndactyly syndrome; clubfoot; cryptorchidism; and dysostosis (multiple). Orthologous to human HOXD13 (homeobox D13). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Low expression observed in reference dataset 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 (79978077..79981393)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (59570647..59573963)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (61590376..61593692)

Chromosome 3 - NC_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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 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?

Hoxd13 expression was decreased in rat embryos with congenital malformations. The administration of exogenous Hoxd13 alleviated fetal malformation probably through stimulation of Slim1 expression and Wnt/beta-catenin signaling pathway.
Title: Molecular mechanism of Hoxd13-mediated congenital malformations in rat embryos.
The expression of Gli3, regulated by HOXD13, may play a role in idiopathic congenital talipes equinovarus.
Title: The expression of Gli3, regulated by HOXD13, may play a role in idiopathic congenital talipes equinovarus.

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General gene information

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Markers

Hoxd13 (e-PCR), detects polymorphism
- UniSTS:225863

Hoxd13 (e-PCR), detects polymorphism
- UniSTS:265598

Hoxd13 (e-PCR), detects polymorphism
- UniSTS:547820

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within anterior/posterior pattern specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within branch elongation of an epithelium	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic digit morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic hindgut morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic limb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gland morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within limb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within male genitalia development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within morphogenesis of an epithelial fold	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pattern specification process	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
acts_upstream_of_or_within prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in prostate gland development	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within regulation of branching involved in prostate gland morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in response to testosterone	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within skeletal system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of transcription by RNA polymerase II	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
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: homeobox protein Hox-D13

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_001105886.1 → NP_001099356.1 homeobox protein Hox-D13

See identical proteins and their annotated locations for NP_001099356.1

Status: PROVISIONAL

Source sequence(s)

CH473949

UniProtKB/TrEMBL

A6HMC7

Related

ENSRNOP00000002155.4, ENSRNOT00000002155.6

Conserved Domains (2) summary

cd00086
Location:265 → 321

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam12284
Location:113 → 162

HoxA13_N; Hox protein A13 N terminal