Hoxd1 homeobox D1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Hoxd1provided by MGI
Official Full Name: homeobox D1provided by MGI
Primary source: MGI:MGI:96201
See related: Ensembl:ENSMUSG00000042448 AllianceGenome:MGI:96201
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-4.9
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 embryonic skeletal system development; neuron differentiation; and sensory perception of pain. Located in nucleus. Is expressed in several structures, including early embryo; embryo mesenchyme; genitourinary system; intestine epithelium; and nervous system. Orthologous to human HOXD1 (homeobox D1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Low expression observed in reference dataset See more
Orthologs: human all
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Genomic context

Location:: 2 C3; 2 44.13 cM

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (74593324..74595486)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (74762980..74765142)

Chromosome 2 - NC_000068.8 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: 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?

Mice lacking Hoxd1 displayed altered nociceptor circuitry that resembles that normally found in chicks.
Title: An evolving NGF-Hoxd1 signaling pathway mediates development of divergent neural circuits in vertebrates.
Hox1b contains the cis-acting elements sufficient to initiate ectopic local nuclear reorganisation and chromatin decondensation and to break Hoxd colinearity in the primitive streak region of the early embryo.
Title: Ectopic nuclear reorganisation driven by a Hoxb1 transgene transposed into Hoxd.
myelin oligodendrocyte glycoprotein may be a target of Hoxd1
Title: Hoxd1 is expressed by oligodendroglial cells and binds to a region of the human myelin oligodendrocyte glycoprotein promoter in vitro.
HOXD and Gli3 gene interactions control the limb apical ectodermal ridge via Fgf10
Title: Interactions between HOXD and Gli3 genes control the limb apical ectodermal ridge via Fgf10.

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Variation

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Alleles

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

Endonuclease-mediated (2)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D2Tfv13 (e-PCR), detects polymorphism
- UniSTS:142337

D2Tfv14 (e-PCR), detects polymorphism
- UniSTS:142338

Hoxd1 (e-PCR), detects polymorphism
- UniSTS:536666

X60034 (e-PCR)
- UniSTS:125815

X60034 (e-PCR)
- UniSTS:163287

NoName (e-PCR)
- UniSTS:492511

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
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	IEA Inferred from Electronic Annotation 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 embryonic skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron differentiation	IMP Inferred from Mutant Phenotype 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 sensory perception of pain	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
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: homeobox protein Hox-D1

Names: homeo box D1; homeobox protein Hox-4.9

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.