Hoxd9 MGI Mouse Gene Detail - MGI:96210

Symbol

Hoxd9
Name

homeobox D9
Synonyms

Hox-4.4, Hox-5.2

Feature Type

protein coding gene
IDs

MGI:96210
NCBI Gene: 15438
Member of

Hoxd cluster
Alliance

genome feature page
Transcription Start Sites

6 TSS
Regulated by

Rr31 (1 regulatory region)

Sequence Map

Chr2:74528107-74530552 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

13 experiments

SNPs within 2kb

59 from dbSNP Build 142
Strain Annotations

19
PCR

2

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_96210	protein coding gene	Chr2:74528071-74530552 (+)
129S1/SvImJ	ENSMUSG00200002592	protein coding gene	Chr2:71576703-71579184 (+)
A/J	ENSMUSG00195019454	protein coding gene	Chr2:71723407-71725888 (+)
AKR/J	ENSMUSG00220002339	protein coding gene	Chr2:71688040-71690521 (+)
BALB/cJ	ENSMUSG00180006860	protein coding gene	Chr2:71677062-71679543 (+)
C3H/HeJ	ENSMUSG00175010680	protein coding gene	Chr2:71802957-71805438 (+)
C57BL/6NJ	ENSMUSG00215012722	protein coding gene	Chr2:71639904-71642385 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023671	protein coding gene	Chr2:69502265-69504729 (+)
CAST/EiJ	ENSTCUG00005027417	protein coding gene	Chr2:71116817-71119294 (+)
CBA/J	ENSMUSG00210002000	protein coding gene	Chr2:71845613-71848094 (+)
DBA/2J	ENSMUSG00185011443	protein coding gene	Chr2:71681458-71683939 (+)
FVB/NJ	ENSMUSG00205013003	protein coding gene	Chr2:71133438-71135919 (+)
JF1/MsJ	ENSUMUG00000025511	protein coding gene	Chr2:71358642-71361121 (+)
LP/J	ENSMUSG00230023747	protein coding gene	Chr2:73476291-73478772 (+)
NOD/ShiLtJ	ENSMUSG00190010753	protein coding gene	Chr2:71756166-71758647 (+)
NZO/HlLtJ	ENSMUSG00225014184	protein coding gene	Chr2:81240358-81242839 (+)
PWK/PhJ	ENSLUMG00010030313	protein coding gene	Chr2:71596969-71599445 (+)
SPRET/EiJ	ENSMSPG00010018948	protein coding gene	Chr2:72996935-72999409 (+)
WSB/EiJ	ENSIUOG00005011257	protein coding gene	Chr2:71799439-71801920 (+)

Human Ortholog

HOXD9, homeobox D9

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

HOXD9, homeobox D9
Synonyms

HOX4, Hox-4.3, HOX4C, Hox-5.2
Links

HGNC:5140

NCBI Gene ID: 3235

UniProt: P28356
Chr Location

2q31.1; chr2:176122719-176124937 (+) GRCh38

MGI Vertebrate Homology

Hoxd9 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: HOXD9
Gene Tree

Hoxd9

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Phenotype Summary

7 phenotypes from 1 allele in 1 genetic background
48 phenotypes from multigenic genotypes
58 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

37
Chemically induced (other)

1
Endonuclease-mediated

1
Radiation induced

1
Spontaneous

1
Targeted

33
Genomic Mutations

31 involving Hoxd9
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

16 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a targeted mutation exhibit anterior transformation of lumbar, sacral, and caudal vertebrae with abnormal humerus morphology.

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All GO Annotations

56
GO References

13

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.

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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

1160
Tissues

230
cDNA Data

20
Literature Summary

86

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA HOXD9

Xenbase hoxd9

ZFIN hoxd9a

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All Sequences

30
RefSeq

2
UniProt

1
CCDS

CCDS16142.1

Ensembl

ENSMUSG00000043342 (Evidence)
NCBI Gene

15438

			Length	Strain/Species	Flank
genomic	15438	NCBI Gene Model \| MGI Sequence Detail	2446	C57BL/6J	± kb
transcript	NM_013555	RefSeq \| MGI Sequence Detail	2100	ZRU/MplStud
polypeptide	P28357	UniProt \| EBI \| MGI Sequence Detail	339	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000008724 homeobox protein Hox-D9

(term hierarchy)
InterPro Domains

IPR017970 Homeobox, conserved site

IPR017112 Homeobox protein HXA9/HXB9/HXC9

IPR001356 Homeodomain

IPR009057 Homeodomain-like superfamily

IPR020479 Homeodomain, metazoa

IPR006711 Hox9, N-terminal activation domain

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All nucleic 69

Genomic 14

cDNA 24

Primer pair 15

Other 16

Microarray probesets 2

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MGD-MRK-10851, MGD-MRK-10859, MGD-MRK-10911

Summaries

All 165

Developmental Gene Expression 86

Gene Ontology 13

Phenotypes 58
Earliest

J:9875 Oliver G, et al., Complementary homeo protein gradients in developing limb buds. Genes Dev. 1989 May;3(5):641-50
Latest

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

Hoxd9 expression regulated by:

Feature	Feature Type	Location	Reference
Rr31, regulatory region 31	enhancer	Chr2:75269157-75271345	J:199174

TSS for Hoxd9:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr18414	Chr2:74528007-74528018 (+)	-94 bp
Tssr18415	Chr2:74528083-74528095 (+)	-18 bp
Tssr18416	Chr2:74528290-74528295 (+)	186 bp
Tssr18417	Chr2:74528313-74528326 (+)	213 bp
Tssr18418	Chr2:74528337-74528352 (+)	238 bp
Tssr18419	Chr2:74528358-74528370 (+)	257 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 09/01/2026 MGI 6.24