Hoxd4 homeobox D4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Hoxd4provided by MGI
Official Full Name: homeobox D4provided by MGI
Primary source: MGI:MGI:96208
See related: Ensembl:ENSMUSG00000101174 AllianceGenome:MGI:96208
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-4.2; Hox-5.1; 6030436D05Rik
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. Acts upstream of or within anterior/posterior pattern specification; embryonic skeletal system morphogenesis; and stem cell differentiation. Predicted to be located in cell junction. Predicted to be active in nucleoplasm. Is expressed in several structures, including embryo ectoderm; embryo mesenchyme; genitourinary system; gut; and nervous system. Orthologous to human HOXD4 (homeobox D4). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in genital fat pad adult (RPKM 27.5), ovary adult (RPKM 18.8) and 9 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 C3; 2 44.13 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (74552322..74559504)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (74721978..74729160)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

The expression profiles of Hoxd4 and miR-10b transcripts during neural differentiation of mouse embryonal carcinoma (EC) P19 cells are co-ordinately regulated and generated by Drosha cleavage.
Title: Nuclear accumulation of an uncapped RNA produced by Drosha cleavage of a transcript encoding miR-10b and HOXD4.
Data provide the basis for future studies in pathogenesis of cartilage defects in Hoxc8- and Hoxd4-transgenic mice.
Title: Expression of cartilage developmental genes in Hoxc8- and Hoxd4-transgenic mice.
detected chromatin changes at the Hoxd4 locus during neurogenesis in P19 cells and embryonic day 8.0 (E8.0) and E10.5 embryos
Title: Sequential histone modifications at Hoxd4 regulatory regions distinguish anterior from posterior embryonic compartments.
a new molecular link, completing a feedback circuit between retinoic acid receptor beta, Hoxb4 and Hoxd4
Title: Direct crossregulation between retinoic acid receptor {beta} and Hox genes during hindbrain segmentation.
results reveal an evolutionarily conserved role for Pax6 in AP-restricted expression of vertebrate Hoxd4 orthologs
Title: Stereospecificity and PAX6 function direct Hoxd4 neural enhancer activity along the antero-posterior axis.
Af9 null mutation affects Hoxd-4 gene expression
Title: Mouse Af9 is a controller of embryo patterning, like Mll, whose human homologue fuses with Af9 after chromosomal translocation in leukemia.
The sequence of regulatory elements, including a DR5 type retinoic acid response element (RARE) required for Hoxd4 neural enhancer activity, are highly conserved, zebrafish and mouse neural enhancers function identically in transgenic mouse embryos.
Title: The role of a retinoic acid response element in establishing the anterior neural expression border of Hoxd4 transgenes.
Results identify components of the Hoxd4 P1 promoter directing expression in neurally differentiating retinoic acid-treated P19 cells.
Title: Interplay between chromatin and trans-acting factors regulating the Hoxd4 promoter during neural differentiation.

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Variation

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Alleles

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

Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D2Tfv12 (e-PCR), detects polymorphism
- UniSTS:142336

UniSTS:480790 (e-PCR)
- UniSTS:480790

Hoxd4 (e-PCR), detects polymorphism
- UniSTS:143397

Hoxd4 (e-PCR), detects polymorphism
- UniSTS:536672

Hoxd4 (e-PCR), detects polymorphism
- UniSTS:547244

Gene Ontology Provided by MGI

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 DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor 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 anterior/posterior pattern specification	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within anterior/posterior pattern specification	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within anterior/posterior pattern specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryonic skeletal system morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within embryonic skeletal system morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic skeletal system morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor 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
acts_upstream_of_or_within stem cell differentiation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cell junction	IEA Inferred from Electronic Annotation more info
located_in cell junction	ISO Inferred from Sequence Orthology more info
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: homeobox protein Hox-D4

Names: homeo box D4; homeobox protein Hox-4.2; homeobox protein Hox-5.1

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.