Emx2 MGI Mouse Gene Detail - MGI:95388 - empty spiracles homeobox 2

Symbol

Emx2
Name

empty spiracles homeobox 2
Synonyms

Pdo

Feature Type

protein coding gene
IDs

MGI:95388
NCBI Gene: 13797
Alliance

genome feature page
Transcription Start Sites

10 TSS
Regulated by

Rr1295, Rr103 (2 regulatory regions)

Sequence Map

Chr19:59447122-59453789 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 19, 56.28 cM
Mapping Data

7 experiments

SNPs within 2kb

126 from dbSNP Build 142
Strain Annotations

19
PCR

1
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_95388	protein coding gene	Chr19:59446804-59453789 (+)
129S1/SvImJ	ENSMUSG00200013793	protein coding gene	Chr19:56154378-56161328 (+)
A/J	ENSMUSG00195002521	protein coding gene	Chr19:56327334-56334272 (+)
AKR/J	ENSMUSG00220017884	protein coding gene	Chr19:56063359-56070296 (+)
BALB/cJ	ENSMUSG00180017240	protein coding gene	Chr19:56552937-56559889 (+)
C3H/HeJ	ENSMUSG00175021012	protein coding gene	Chr19:56096477-56103442 (+)
C57BL/6NJ	ENSMUSG00215021809	protein coding gene	Chr19:56190169-56197201 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023115	protein coding gene	Chr19:55944101-55951141 (+)
CAST/EiJ	ENSTCUG00005015216	protein coding gene	Chr19:55746431-55753401 (+)
CBA/J	ENSMUSG00210020073	protein coding gene	Chr19:56176518-56183486 (+)
DBA/2J	ENSMUSG00185027295	protein coding gene	Chr19:56672396-56679362 (+)
FVB/NJ	ENSMUSG00205003433	protein coding gene	Chr19:55584945-55591893 (+)
JF1/MsJ	ENSUMUG00000021221	protein coding gene	Chr19:56883263-56890279 (+)
LP/J	ENSMUSG00230024366	protein coding gene	Chr19:57436764-57443712 (+)
NOD/ShiLtJ	ENSMUSG00190012672	protein coding gene	Chr19:56120927-56127875 (+)
NZO/HlLtJ	ENSMUSG00225020751	protein coding gene	Chr19:61061964-61068912 (+)
PWK/PhJ	ENSLUMG00010018255	protein coding gene	Chr19:55938337-55945321 (+)
SPRET/EiJ	ENSMSPG00010002977	protein coding gene	Chr19:55782546-55789570 (+)
WSB/EiJ	ENSIUOG00005022431	protein coding gene	Chr19:55541737-55548685 (+)

Human Ortholog

EMX2, empty spiracles homeobox 2

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

EMX2, empty spiracles homeobox 2
Links

HGNC:3341

NCBI Gene ID: 2018

UniProt: Q04743
Chr Location

10q26.11; chr10:117542445-117549546 (+) GRCh38

MGI Vertebrate Homology

Emx2 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: EMX2
Gene Tree

Emx2

Diseases

2 with human EMX2 associations

				Human Disease	Mouse Models
				colorectal cancer IDs colorectal cancer DOID:9256 ICD10CM:C18.9 KEGG:05210 MESH:D015179 NCI:C2956 NCI:C4978 OMIM:114500 UMLS_CUI:C0009404 UMLS_CUI:C0346629
				stomach cancer IDs stomach cancer DOID:10534 DOID:10539 DOID:10542 DOID:10543 DOID:4713 ICD10CM:C16 ICD10CM:C16.2 ICD10CM:C16.5 ICD10CM:C16.6 ICD9CM:151 ICD9CM:151.4 ICD9CM:151.5 ICD9CM:151.6 ICD9CM:151.9 MESH:D013274 NCI:C194067 NCI:C194069 NCI:C194070 NCI:C3387 NCI:C9331 OMIM:613659 UMLS_CUI:C0024623 UMLS_CUI:C0038356 UMLS_CUI:C0153421 UMLS_CUI:C0153422 UMLS_CUI:C0153423

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

64 phenotypes from 5 alleles in 7 genetic backgrounds
48 phenotypes from multigenic genotypes
98 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

17
Chemically induced (ENU)

2
Endonuclease-mediated

8
Targeted

7
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

25 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Homozygous disruption of this gene causes neonatal death, impaired urogenital development and malformation of several forebrain regions. Heterozygotes for a null allele show middle and inner ear defects. Homozygotes for an ENU-induced allele die neonatally with middle ear defects and small kidneys.

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All GO Annotations

40
GO References

20

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

1675
Tissues

482
cDNA Data

18
Literature Summary

230

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

GEISHA EMX2

Xenbase emx2

ZFIN emx2

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All Sequences

37
RefSeq

4
UniProt

2
CCDS

CCDS29937.1

Ensembl

ENSMUSG00000043969 (Evidence)
NCBI Gene

13797

			Length	Strain/Species	Flank
genomic	13797	NCBI Gene Model \| MGI Sequence Detail	6668	C57BL/6J	± kb
transcript	NM_010132	RefSeq \| MGI Sequence Detail	2598	Not Specified
polypeptide	Q04744	UniProt \| EBI \| MGI Sequence Detail	253	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000007069 homeobox protein EMX2

(term hierarchy)
InterPro Domains

IPR050877 EMX/VAX/Noto Homeobox Transcription Factors

IPR000047 Helix-turn-helix motif

IPR017970 Homeobox, conserved site

IPR001356 Homeodomain

IPR009057 Homeodomain-like superfamily

IPR020479 Homeodomain, metazoa

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All nucleic 79

Genomic 2

cDNA 22

Primer pair 20

Other 35

Antibodies 3

Microarray probesets 2

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MGD-MRK-9496, MGI:1890590

Summaries

All 337

Developmental Gene Expression 230

Gene Ontology 20

Phenotypes 98
Earliest

J:1461 Simeone A, et al., Two vertebrate homeobox genes related to the Drosophila empty spiracles gene are expressed in the embryonic cerebral cortex. EMBO J. 1992 Jul;11(7):2541-50
Latest

J:390120 Trowe MO, et al., Mesenchymal WNT signaling coordinates epithelial and mesenchymal differentiation in the developing murine ureter. Cell Commun Signal. 2026 Jul 21;24(1)

Emx2 expression regulated by:

Feature	Feature Type	Location	Reference
Rr1295, regulatory region 1295	enhancer	Chr19:60003878-60005269	J:333416
Rr103, regulatory region 103	enhancer	Chr19, Syntenic	J:163926

TSS for Emx2:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr157342	Chr19:59446553-59446565 (+)	-563 bp
Tssr157343	Chr19:59446857-59446882 (+)	-252 bp
Tssr157344	Chr19:59447081-59447094 (+)	-34 bp
Tssr157345	Chr19:59447105-59447127 (+)	-6 bp
Tssr157346	Chr19:59447148-59447159 (+)	32 bp
Tssr157347	Chr19:59447163-59447213 (+)	66 bp
Tssr157348	Chr19:59447371-59447412 (+)	270 bp
Tssr157349	Chr19:59447537-59447570 (+)	432 bp
Tssr157350	Chr19:59447950-59447988 (+)	847 bp
Tssr157351	Chr19:59447994-59448025 (+)	888 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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