Hoxd11 homeobox D11 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Hoxd11provided by MGI
Official Full Name: homeobox D11provided by MGI
Primary source: MGI:MGI:96203
See related: Ensembl:ENSMUSG00000042499 AllianceGenome:MGI:96203
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Hox-4.6; Hox-5.4; Hox-5.5; E230017H14Rik
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within several processes, including embryonic morphogenesis; kidney development; and regionalization. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including embryo mesenchyme; genitourinary system; limb; nervous system; and skin. Orthologous to human HOXD11 (homeobox D11). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in limb E14.5 (RPKM 8.5), subcutaneous fat pad adult (RPKM 4.6) and 5 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 C3; 2 44.13 cM

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (74509902..74517360)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (74679558..74687016)

Chromosome 2 - NC_000068.8 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

expressed adjacent to the pisiform in late-stage embryonic limbs, supporting a role for Hox genes in growth plate specification
Title: The pisiform growth plate is lost in humans and supports a role for Hox in growth plate formation.
Hoxa11 and Hoxd11 regulate chondrocyte differentiation upstream of Runx2 and Shox2 in mice.
Title: Hoxa11 and Hoxd11 regulate chondrocyte differentiation upstream of Runx2 and Shox2 in mice.
Hox11 genes (Hoxa11, Hoxc11 and Hoxd11) co-regulate and coordinate the development of zeugopod skeletal elements and adjacent elbow and knee joints, and dictate joint identity, morphogenesis and anatomical and functional organization.
Title: Hox11 genes establish synovial joint organization and phylogenetic characteristics in developing mouse zeugopod skeletal elements.
Mice lacking all Hox11 activity fail to form metanephric kidney structures; when Hoxd11 is ectopically activated in the anterior mesonephros, we observe a partial transformation to a metanephric program of development.
Title: Hoxd11 specifies a program of metanephric kidney development within the intermediate mesoderm of the mouse embryo.
mice individually mutant for Hoxa11 or Hoxd11 show no discernible kidney abnormalities. Hoxa11/Hoxd11 double mutants, however, demonstrate hypoplasia of the kidneys
Title: Hox11 paralogous genes are essential for metanephric kidney induction.
analysis of the Hoxd11 duplication demonstrated that the Hoxd11 can perform some functions supplied by its paralogue Hoxa11, the defects in forelimb bones are corrected when extra copies of Hoxd11 are present in the Hoxa11 homozygous mutant background
Title: Duplication of the Hoxd11 gene causes alterations in the axial and appendicular skeleton of the mouse.
early posterior restriction of Hox gene products sets up an anterior-posterior prepattern, which determines the localized activation of Shh; this signal is then translated into digit morphological asymmetry by promoting the late expression of Hoxd genes
Title: A dual role for Hox genes in limb anterior-posterior asymmetry.
malformation of the forelimb zeugopod in Hoxa11/Hoxd11 double mutants is a consequence of interruption at multiple steps during the formation of the radius and ulna
Title: Multiple roles of Hoxa11 and Hoxd11 in the formation of the mammalian forelimb zeugopod.
identify the multiple molecular pathways downstream of Hoxa11/Hoxd11 function in the developing kidney
Title: Comprehensive microarray analysis of Hoxa11/Hoxd11 mutant kidney development.
genes compete for a remote enhancer that recognizes the locus in a polar fashion, with a preference for 5' extremity; modifications in either number or topography of Hoxd loci induced regulatory reallocations affecting both number and morphology of digits
Title: Serial deletions and duplications suggest a mechanism for the collinearity of Hoxd genes in limbs.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)
Targeted (6) 1 citation

General gene information

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Markers

D2Tfv9 (e-PCR), detects polymorphism
- UniSTS:142345

NoName (e-PCR)
- UniSTS:494133

Hoxd11 (e-PCR), detects polymorphism
- UniSTS:536668

UniSTS:489068 (e-PCR)
- UniSTS:489068

Hoxd11 (e-PCR), detects polymorphism
- UniSTS:474752

D2Mit271 (e-PCR), detects polymorphism
- UniSTS:129154

Hoxd11 (e-PCR), detects polymorphism
- UniSTS:547243

Hoxd11 (e-PCR), detects polymorphism
- UniSTS:547819

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	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 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	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within branching involved in ureteric bud morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cartilage development involved in endochondral bone morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of cell development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of chondrocyte development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of chondrocyte differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within developmental growth	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within dorsal/ventral pattern formation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic digit morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic forelimb morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic limb morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in embryonic skeletal joint morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within embryonic skeletal joint morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within metanephros development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within organ induction	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pattern specification process	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of chondrocyte development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of chondrocyte differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within proximal/distal pattern formation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of chondrocyte differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of gene expression	IGI Inferred from Genetic Interaction more info	PubMed
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 single fertilization	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within skeletal system development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: homeobox protein Hox-D11

Names: homeo box D11; homeobox protein Hox-4.6; homeobox protein Hox-5.5

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_008273.2 → NP_032299.1 homeobox protein Hox-D11

See identical proteins and their annotated locations for NP_032299.1

Status: VALIDATED

Description

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

Source sequence(s)

AK054090, AL928644, BC138115

Consensus CDS

CCDS16140.1

UniProtKB/Swiss-Prot

P23813

UniProtKB/TrEMBL

A2ASM7

Related

ENSMUSP00000122582.2, ENSMUST00000142312.3

Conserved Domains (2) summary

pfam00046
Location:267 → 320

Homeobox; Homeobox domain

pfam12045
Location:26 → 187

DUF3528; Protein of unknown function (DUF3528)

RNA

NR_073086.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains an alternate 5' exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.

Source sequence(s)

AK054090, AL928644

Related

ENSMUST00000048086.9