Hoxd1 MGI Mouse Gene Detail - MGI:96201

Symbol

Hoxd1
Name

homeobox D1
Synonyms

Hox-4.9

Feature Type

protein coding gene
IDs

MGI:96201
NCBI Gene: 15429
Member of

Hoxd cluster
Alliance

genome feature page
Regulated by

Rr57 (1 regulatory region)

Sequence Map

Chr2:74593324-74595486 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 44.13 cM
Mapping Data

4 experiments

SNPs within 2kb

117 from dbSNP Build 142
Strain Annotations

19
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_96201	protein coding gene	Chr2:74593324-74595486 (+)
129S1/SvImJ	ENSMUSG00200002645	protein coding gene	Chr2:71641943-71644104 (+)
A/J	ENSMUSG00195019366	protein coding gene	Chr2:71788671-71790833 (+)
AKR/J	ENSMUSG00220002254	protein coding gene	Chr2:71753295-71755457 (+)
BALB/cJ	ENSMUSG00180005998	protein coding gene	Chr2:71742323-71744484 (+)
C3H/HeJ	ENSMUSG00175010692	protein coding gene	Chr2:71868249-71870409 (+)
C57BL/6NJ	ENSMUSG00215019459	protein coding gene	Chr2:71705171-71707333 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023676	protein coding gene	Chr2:69567477-69569636 (+)
CAST/EiJ	ENSTCUG00005028074	protein coding gene	Chr2:71182157-71184297 (+)
CBA/J	ENSMUSG00210002028	protein coding gene	Chr2:71910916-71913075 (+)
DBA/2J	ENSMUSG00185010507	protein coding gene	Chr2:71746751-71748911 (+)
FVB/NJ	ENSMUSG00205018218	protein coding gene	Chr2:71198702-71200864 (+)
JF1/MsJ	ENSUMUG00000024931	protein coding gene	Chr2:71423659-71425801 (+)
LP/J	ENSMUSG00230024276	protein coding gene	Chr2:73541541-73543702 (+)
NOD/ShiLtJ	ENSMUSG00190009797	protein coding gene	Chr2:71821399-71823560 (+)
NZO/HlLtJ	ENSMUSG00225014243	protein coding gene	Chr2:81305622-81307786 (+)
PWK/PhJ	ENSLUMG00010028364	protein coding gene	Chr2:71661946-71664088 (+)
SPRET/EiJ	ENSMSPG00010019267	protein coding gene	Chr2:73062345-73064425 (+)
WSB/EiJ	ENSIUOG00005010963	protein coding gene	Chr2:71864658-71866818 (+)

Human Ortholog

HOXD1, homeobox D1

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

HOXD1, homeobox D1
Synonyms

HOX4, Hox-4.7, HOX4G
Links

HGNC:5132

NCBI Gene ID: 3231

UniProt: Q9GZZ0
Chr Location

2q31.1; chr2:176188667-176190907 (+) GRCh38

MGI Vertebrate Homology

Hoxd1 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: HOXD1
Gene Tree

Hoxd1

less

Phenotype Summary

10 phenotypes from 2 alleles in 2 genetic backgrounds
39 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

21
Chemically induced (other)

1
Endonuclease-mediated

4
Radiation induced

1
Targeted

15
Genomic Mutations

16 involving Hoxd1
Find Mice (IMSR)

16 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a reporter allele display abnormal cervical vertebrae. Mice homozygous for a knock-out allele exhibit abnormal nociceptor innervation of the skin, aberrant nociceptor axonal projections in the spinal cord, and deficits in pain sensitivity.

less

All GO Annotations

19
GO References

8

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

less

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

844
Tissues

145
cDNA Data

14
Literature Summary

35

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase hoxd1

less

All Sequences

32
RefSeq

2
UniProt

1
CCDS

CCDS16147.1

Ensembl

ENSMUSG00000042448 (Evidence)
NCBI Gene

15429

			Length	Strain/Species	Flank
genomic	15429	NCBI Gene Model \| MGI Sequence Detail	2163	C57BL/6J	± kb
transcript	NM_010467	RefSeq \| MGI Sequence Detail	1878	ZRU/MplStud
polypeptide	Q01822	UniProt \| EBI \| MGI Sequence Detail	328	Not Applicable

less

UniProt

1 Sequence
Protein Ontology

PR:000008716 homeobox protein Hox-D1

(term hierarchy)
InterPro Domains

IPR017970 Homeobox, conserved site

IPR046327 Homeobox protein Hox-A1/B1/D1

IPR001356 Homeodomain

IPR009057 Homeodomain-like superfamily

IPR020479 Homeodomain, metazoa
GlyGen

Q01822 1 site

less

All nucleic 41

Genomic 9

cDNA 15

Primer pair 11

Other 6

Antibodies 1

Microarray probesets 4

less

MGD-MRK-10856, MGD-MRK-10902

Summaries

All 104

Developmental Gene Expression 35

Gene Ontology 8

Phenotypes 39
Earliest

J:9607 Ferguson-Smith AC, et al., The genomics of human homeobox-containing loci. Pathol Immunopathol Res. 1988;7(1-2):119-26
Latest

J:373797 Hintermann A, et al., Co-option of an ancestral cloacal regulatory landscape during digit evolution. Nature. 2025 Sep 17;

Hoxd1 expression regulated by:

Feature	Feature Type	Location	Reference
Rr57, regulatory region 57	CpG island	Chr2:74593034-74594216	J:252916

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 09/01/2026 MGI 6.24