Lhx2 MGI Mouse Gene Detail - MGI:96785

Symbol

Lhx2
Name

LIM homeobox protein 2
Synonyms

ap, apterous, Lh-2, LH2A

Feature Type

protein coding gene
IDs

MGI:96785
NCBI Gene: 16870
Alliance

genome feature page
Transcription Start Sites

10 TSS
Regulated by

Rr555999, Rr556004 (2 regulatory regions)

Sequence Map

Chr2:38229293-38259745 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 24.31 cM, cytoband B
Mapping Data

1 experiment

SNPs within 2kb

534 from dbSNP Build 142
Strain Annotations

26

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_96785	protein coding gene	Chr2:38229282-38259747 (+)
129S1/SvImJ	ENSMUSG00200044545	protein coding gene	Chr2:35223671-35225185 (+)
129S1/SvImJ	ENSMUSGG00200054950	protein coding gene	Chr2:35222128-35222333 (+)
A/J	ENSMUSGG00195055168	protein coding gene	Chr2:35333694-35333899 (+)
A/J	ENSMUSG00195036812	protein coding gene	Chr2:35335237-35336751 (+)
AKR/J	ENSMUSG00220041682	protein coding gene	Chr2:35450221-35451735 (+)
AKR/J	ENSMUSGG00220054588	protein coding gene	Chr2:35448678-35448883 (+)
BALB/cJ	ENSMUSG00180045076	protein coding gene	Chr2:35346871-35348385 (+)
BALB/cJ	ENSMUSGG00180055265	protein coding gene	Chr2:35345328-35345533 (+)
C3H/HeJ	ENSMUSGG00175054780	protein coding gene	Chr2:35332168-35332373 (+)
C3H/HeJ	ENSMUSG00175041595	protein coding gene	Chr2:35333711-35335225 (+)
C57BL/6NJ	ENSMUSGG00215055457	protein coding gene	Chr2:35386445-35386650 (+)
C57BL/6NJ	ENSMUSG00215044690	protein coding gene	Chr2:35387988-35389502 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023524	protein coding gene	Chr2:34216444-34246697 (+)
CAST/EiJ	no annotation
CBA/J	ENSMUSG00210049657	protein coding gene	Chr2:35388106-35389620 (+)
CBA/J	ENSMUSGG00210055030	protein coding gene	Chr2:35386563-35386768 (+)
DBA/2J	ENSMUSG00185046851	protein coding gene	Chr2:35247879-35249393 (+)
DBA/2J	ENSMUSGG00185057633	protein coding gene	Chr2:35246336-35246541 (+)
FVB/NJ	ENSMUSG00205022585	protein coding gene	Chr2:35052949-35054463 (+)
FVB/NJ	ENSMUSGG00205054269	protein coding gene	Chr2:35051406-35051611 (+)
JF1/MsJ	no annotation
LP/J	ENSMUSG00230039861	protein coding gene	Chr2:37168118-37169632 (+)
LP/J	ENSMUSGG00230055413	protein coding gene	Chr2:37166575-37166780 (+)
NOD/ShiLtJ	ENSMUSGG00190054764	protein coding gene	Chr2:35247547-35247752 (+)
NOD/ShiLtJ	ENSMUSG00190039702	protein coding gene	Chr2:35249090-35250604 (+)
NZO/HlLtJ	ENSMUSG00225048102	protein coding gene	Chr2:44931698-44933212 (+)
NZO/HlLtJ	ENSMUSGG00225055364	protein coding gene	Chr2:44930155-44930360 (+)
PWK/PhJ	no annotation
SPRET/EiJ	no annotation
WSB/EiJ	no annotation

Human Ortholog

LHX2, LIM homeobox 2

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LHX2, LIM homeobox 2
Synonyms

hLhx2, LH2
Links

HGNC:6594

NCBI Gene ID: 9355

UniProt: P50458
Chr Location

9q33.3; chr9:124001670-124033301 (+) GRCh38

MGI Vertebrate Homology

Lhx2 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: LHX2
Gene Tree

Lhx2

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Phenotype Summary

34 phenotypes from 8 alleles in 14 genetic backgrounds
3 phenotypes from multigenic genotypes
3 images
84 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

15
Endonuclease-mediated

3
Gene trapped

1
Targeted

10
Transgenic

1
Find Mice (IMSR)

12 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit lethality during fetal development and the perinatal period with abnormal liver, telencephalon, olfactory bulb, basal ganglion, and eye morphology.

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All GO Annotations

55
GO References

27

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

1645
Tissues

486
cDNA Data

48
Literature Summary

371

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

GEISHA LHX2

Xenbase lhx2

ZFIN lhx2a, lhx2b

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All Sequences

70
RefSeq

18
UniProt

6
CCDS

CCDS16008.1, CCDS71048.1

Ensembl

ENSMUSG00000000247 (Evidence)
NCBI Gene

16870

			Length	Strain/Species	Flank
genomic	ENSMUSG00000000247	Ensembl Gene Model \| MGI Sequence Detail	30453	C57BL/6J	± kb
transcript	ENSMUST00000000253	Ensembl \| MGI Sequence Detail	2840	Not Applicable
polypeptide	ENSMUSP00000000253	Ensembl \| MGI Sequence Detail	406	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000009792 LIM/homeobox protein Lhx2

(term hierarchy)
InterPro Domains

IPR017970 Homeobox, conserved site

IPR001356 Homeodomain

IPR009057 Homeodomain-like superfamily

IPR050453 LIM/homeobox transcription factors

IPR001781 Zinc finger, LIM-type

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All nucleic 95

cDNA 54

Primer pair 8

Other 33

Antibodies 22

Microarray probesets 3

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MGD-MRK-11805

Summaries

All 453

Developmental Gene Expression 371

Gene Ontology 27

Phenotypes 84
Earliest

J:3610 Xu Y, et al., LH-2: a LIM/homeodomain gene expressed in developing lymphocytes and neural cells. Proc Natl Acad Sci U S A. 1993 Jan 1;90(1):227-31
Latest

J:388885 Lin CY, et al., A 3D amphioxus brain atlas illuminates the blueprint of the ancestral chordate brain and highlights unique vertebrate innovations. Sci Adv. 2026 Jul 3;12(27):eaee5076

Lhx2 expression regulated by:

Feature	Feature Type	Location	Reference
Rr555999, regulatory region 555999	enhancer	Chr2:37835556-37836267	J:362224
Rr556004, regulatory region 556004	enhancer	Chr2:37862281-37863027	J:362224

TSS for Lhx2:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr17535	Chr2:38229270-38229290 (+)	-13 bp
Tssr17536	Chr2:38231080-38231092 (+)	1,793 bp
Tssr17537	Chr2:38241072-38241092 (+)	11,789 bp
Tssr17538	Chr2:38241217-38241226 (+)	11,929 bp
Tssr17539	Chr2:38241236-38241258 (+)	11,954 bp
Tssr484	Chr2:38241508-38241527 (+)	12,225 bp
Tssr17540	Chr2:38241692-38241702 (+)	12,404 bp
Tssr17541	Chr2:38244761-38244776 (+)	15,476 bp
Tssr17542	Chr2:38244806-38244816 (+)	15,518 bp
Tssr17543	Chr2:38259108-38259119 (+)	29,821 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