Hoxd3 MGI Mouse Gene Detail - MGI:96207

Symbol

Hoxd3
Name

homeobox D3
Synonyms

Hox-4.1, Hox-5.5

Feature Type

protein coding gene
IDs

MGI:96207
NCBI Gene: 15434
Member of

Hoxd cluster
Alliance

genome feature page
Transcription Start Sites

6 TSS

Sequence Map

Chr2:74542337-74578615 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 44.13 cM, cytoband C2
Mapping Data

11 experiments

SNPs within 2kb

582 from dbSNP Build 142
Strain Annotations

19
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_96207	protein coding gene	Chr2:74542271-74578786 (+)
129S1/SvImJ	ENSMUSG00200002777	protein coding gene	Chr2:71622904-71627247 (+)
A/J	ENSMUSG00195019261	protein coding gene	Chr2:71769630-71773973 (+)
AKR/J	ENSMUSG00220002235	protein coding gene	Chr2:71734257-71738600 (+)
BALB/cJ	ENSMUSG00180006027	protein coding gene	Chr2:71723284-71727628 (+)
C3H/HeJ	ENSMUSG00175010490	protein coding gene	Chr2:71849154-71853497 (+)
C57BL/6NJ	ENSMUSG00215013284	protein coding gene	Chr2:71686113-71690459 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023673	protein coding gene	Chr2:69516325-69553117 (+)
CAST/EiJ	ENSTCUG00005028101	protein coding gene	Chr2:71163071-71167416 (+)
CBA/J	ENSMUSG00210002035	protein coding gene	Chr2:71891817-71896160 (+)
DBA/2J	ENSMUSG00185010388	protein coding gene	Chr2:71727659-71732002 (+)
FVB/NJ	ENSMUSG00205013631	protein coding gene	Chr2:71179666-71184009 (+)
JF1/MsJ	ENSUMUG00000024494	protein coding gene	Chr2:71404539-71408887 (+)
LP/J	ENSMUSG00230024124	protein coding gene	Chr2:73522500-73526843 (+)
NOD/ShiLtJ	ENSMUSG00190009660	protein coding gene	Chr2:71802361-71806704 (+)
NZO/HlLtJ	ENSMUSG00225014220	protein coding gene	Chr2:81286564-81290908 (+)
PWK/PhJ	ENSLUMG00010030527	protein coding gene	Chr2:71642900-71647245 (+)
SPRET/EiJ	ENSMSPG00010019200	protein coding gene	Chr2:73043262-73047585 (+)
WSB/EiJ	ENSIUOG00005011351	protein coding gene	Chr2:71845641-71849983 (+)

Human Ortholog

HOXD3, homeobox D3

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

HOXD3, homeobox D3
Synonyms

HOX1D, HOX4, Hox-4.1, HOX4A
Links

HGNC:5137

NCBI Gene ID: 3232

UniProt: P31249
Chr Location

2q31.1; chr2:176136545-176174227 (+) GRCh38

MGI Vertebrate Homology

Hoxd3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: HOXD3
Gene Tree

Hoxd3

less

Phenotype Summary

14 phenotypes from 3 alleles in 2 genetic backgrounds
21 phenotypes from multigenic genotypes
51 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

26
Chemically induced (other)

1
Endonuclease-mediated

3
Radiation induced

1
Targeted

21
Genomic Mutations

18 involving Hoxd3
Incidental Mutations

CvDC
Find Mice (IMSR)

13 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele show partial postnatal lethality, asymmetric rib-sternum attachment, and anterior transformations of the cervical vertebrae I (atlas) and II (axis). Mice homozygous for a different knock-out allele lack the anteriorarch of the atlas and the dens of the axis.

less

All GO Annotations

47
GO References

11

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

985
Tissues

188
cDNA Data

17
Literature Summary

59

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA HOXD3

Xenbase hoxd3

ZFIN hoxd3a

less

All Sequences

49
RefSeq

2
UniProt

4
CCDS

CCDS38149.1

Ensembl

ENSMUSG00000079277 (Evidence)
NCBI Gene

15434

			Length	Strain/Species	Flank
genomic	15434	NCBI Gene Model \| MGI Sequence Detail	36279	C57BL/6J	± kb
transcript	NM_010468	RefSeq \| MGI Sequence Detail	2902	ZRU/MplStud
polypeptide	P09027	UniProt \| EBI \| MGI Sequence Detail	433	Not Applicable

less

UniProt

4 Sequences
Protein Ontology

PR:000008721 homeobox protein Hox-D3

(term hierarchy)
InterPro Domains

IPR025281 Domain of unknown function DUF4074

IPR017970 Homeobox, conserved site

IPR001827 Homeobox protein, antennapedia type, conserved site

IPR001356 Homeodomain

IPR009057 Homeodomain-like superfamily

IPR020479 Homeodomain, metazoa

less

All nucleic 45

Genomic 10

cDNA 18

Primer pair 8

Other 9

Microarray probesets 3

less

MGD-MRK-10848, MGD-MRK-10862, MGD-MRK-10908

Summaries

All 134

Developmental Gene Expression 59

Gene Ontology 11

Phenotypes 51
Earliest

J:8920 Lonai P, et al., New murine homeoboxes: structure, chromosomal assignment, and differential expression in adult erythropoiesis. DNA. 1987 Oct;6(5):409-18
Latest

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

TSS for Hoxd3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr18432	Chr2:74542202-74542217 (+)	-127 bp
Tssr18433	Chr2:74542232-74542252 (+)	-95 bp
Tssr18434	Chr2:74542255-74542283 (+)	-68 bp
Tssr18435	Chr2:74542302-74542344 (+)	-14 bp
Tssr18436	Chr2:74542465-74542501 (+)	146 bp
Tssr18437	Chr2:74547332-74547339 (+)	4,999 bp

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 09/08/2026 MGI 6.24