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

gene page
Transcription Start Sites

6 TSS

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

18
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	MGP_129S1SvImJ_G0025849	protein coding gene	Chr2:75011903-75014384 (+)
A/J	MGP_AJ_G0025827	protein coding gene	Chr2:72079029-72081509 (+)
AKR/J	MGP_AKRJ_G0025795	protein coding gene	Chr2:74032245-74034726 (+)
BALB/cJ	MGP_BALBcJ_G0025821	protein coding gene	Chr2:72265654-72268135 (+)
C3H/HeJ	MGP_C3HHeJ_G0025581	protein coding gene	Chr2:74220083-74222564 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0026268	protein coding gene	Chr2:77247668-77250149 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023671	protein coding gene	Chr2:69502265-69504729 (+)
CAST/EiJ	MGP_CASTEiJ_G0025045	protein coding gene	Chr2:74537069-74539546 (+)
CBA/J	MGP_CBAJ_G0025562	protein coding gene	Chr2:80067191-80069672 (+)
DBA/2J	MGP_DBA2J_G0025693	protein coding gene	Chr2:71685574-71688055 (+)
FVB/NJ	MGP_FVBNJ_G0025655	protein coding gene	Chr2:71075735-71078216 (+)
LP/J	MGP_LPJ_G0025781	protein coding gene	Chr2:74876034-74878515 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0025686	protein coding gene	Chr2:81980813-81983294 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0026325	protein coding gene	Chr2:74147780-74150261 (+)
PWK/PhJ	MGP_PWKPhJ_G0024786	protein coding gene	Chr2:71616499-71618975 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0024594	protein coding gene	Chr2:74381596-74384070 (+)
WSB/EiJ	MGP_WSBEiJ_G0025113	protein coding gene	Chr2:74583715-74586196 (+)

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

neXtProt AC: NX_P28356

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
55 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

36
Chemically induced (other)

1
Endonuclease-mediated

1
Radiation induced

1
Spontaneous

1
Targeted

32
Genomic Mutations

30 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

48
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.

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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

1246
Tissues

225
cDNA Data

20
Literature Summary

81

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

29
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

IPR050803 Abd-B homeobox transcription factor

IPR017970 Homeobox, conserved site

IPR001356 Homeobox domain

IPR020479 Homeobox domain, metazoa

IPR009057 Homeobox-like domain superfamily

IPR006711 Hox9, N-terminal activation domain

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All nucleic 65

Genomic 14

cDNA 24

Primer pair 13

Other 14

Microarray probesets 2

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

Summaries

All 155

Developmental Gene Expression 81

Gene Ontology 11

Phenotypes 55
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:354194 Oikonomakos I, et al., In vitro differentiation of mouse pluripotent stem cells into corticosteroid-producing adrenocortical cells. Stem Cell Reports. 2024 Sep 10;19(9):1289-1303

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)
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