Lhx2 LIM homeobox protein 2 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Lhx2provided by MGI
Official Full Name: LIM homeobox protein 2provided by MGI
Primary source: MGI:MGI:96785
See related: Ensembl:ENSMUSG00000000247 AllianceGenome:MGI:96785
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: ap; LH2A; Lh-2; Lim2; apterous
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in negative regulation of neurogenesis; positive regulation of neural precursor cell proliferation; and regulation of gene expression. Acts upstream of or within several processes, including hair follicle development; maintenance of epithelial cell apical/basal polarity; and nervous system development. Located in nucleus. Is expressed in several structures, including branchial arch; limb; nervous system; sensory organ; and septum transversum. Orthologous to human LHX2 (LIM homeobox 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in CNS E14 (RPKM 42.9), whole brain E14.5 (RPKM 35.2) and 6 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 B; 2 24.31 cM

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (38229282..38259747)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (38339271..38369737)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Regulation of chromatin accessibility and gene expression in the developing hippocampal primordium by LIM-HD transcription factor LHX2.
Title: Regulation of chromatin accessibility and gene expression in the developing hippocampal primordium by LIM-HD transcription factor LHX2.
LHX2 in germ cells control tubular organization in the developing mouse testis.
Title: LHX2 in germ cells control tubular organization in the developing mouse testis.
Lhx2 is a progenitor-intrinsic modulator of Sonic Hedgehog signaling during early retinal neurogenesis.
Title: Lhx2 is a progenitor-intrinsic modulator of Sonic Hedgehog signaling during early retinal neurogenesis.
Lhx2 in germ cells suppresses endothelial cell migration in the developing ovary.
Title: Lhx2 in germ cells suppresses endothelial cell migration in the developing ovary.
Decrease of lysyl hydroxylase 2 activity causes abnormal collagen molecular phenotypes, defective mineralization and compromised mechanical properties of bone.
Title: Decrease of lysyl hydroxylase 2 activity causes abnormal collagen molecular phenotypes, defective mineralization and compromised mechanical properties of bone.
REGgamma regulates hair cycle by activating Lgr5 positive hair follicle stem cells.
Title: REGγ regulates hair cycle by activating Lgr5 positive hair follicle stem cells.
An evolutionarily conserved Lhx2-Ldb1 interaction regulates the acquisition of hippocampal cell fate and regional identity.
Title: An evolutionarily conserved Lhx2-Ldb1 interaction regulates the acquisition of hippocampal cell fate and regional identity.
Lhx2 regulates Cux2 expression in cortical layer II-IV during brain development.
Title: Cux2 expression regulated by Lhx2 in the upper layer neurons of the developing cortex.
LHX2 coordinates variations in chromatin accessibility, by competition for nucleosome occupancy and secondary regulation of candidate pioneer factors.
Title: Epigenomic profiling of retinal progenitors reveals LHX2 is required for developmental regulation of open chromatin.
Greek-island-bound transcription factor LHX2 and adaptor protein LDB1 regulate the assembly and maintenance of olfactory receptor compartments, Greek island hubs and olfactory receptor transcription, providing mechanistic insights into and functional support for the role of trans interactions in gene expression
Title: LHX2- and LDB1-mediated trans interactions regulate olfactory receptor choice.

Submit: New GeneRIF Correction See all GeneRIFs (67)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (8) 1 citation
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Lhx2 (e-PCR), detects polymorphism
- UniSTS:507020

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within anatomical structure formation involved in morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within axon extension	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within brain development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cerebral cortex development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cerebral cortex development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dorsal/ventral pattern formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hair follicle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within maintenance of epithelial cell apical/basal polarity	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mesoderm development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression, epigenetic	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transcription regulatory region DNA binding	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural tube closure	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neurogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within olfactory bulb development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of neural precursor cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retina development in camera-type eye	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within telencephalon development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within telencephalon regionalization	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within telencephalon regionalization	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in intracellular anatomical structure	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: LIM/homeobox protein Lhx2

Names: LIM homeo box protein 2; homeobox protein LH-2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001290646.2 → NP_001277575.1 LIM/homeobox protein Lhx2 isoform b

See identical proteins and their annotated locations for NP_001277575.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains an alternate 5' terminal exon and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Variants 2, 5, and 6 all encode the same isoform (b).

Source sequence(s)

AL929186, BX813320

Consensus CDS

CCDS71048.1

UniProtKB/TrEMBL

F6Z9H5

Related

ENSMUSP00000114797.3, ENSMUST00000143783.9

Conserved Domains (4) summary

cd09377
Location:70 → 128

LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family

cd09469
Location:2 → 65

LIM1_Lhx2; The first LIM domain of Lhx2

COG5576
Location:206 → 337

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:229 → 282

Homeobox; Homeobox domain
NM_001420354.1 → NP_001407283.1 LIM/homeobox protein Lhx2 isoform c

Status: VALIDATED

Source sequence(s)

AL929186, BX813320
NM_001420355.1 → NP_001407284.1 LIM/homeobox protein Lhx2 isoform d

Status: VALIDATED

Source sequence(s)

AL929186, BX813320
NM_001420356.1 → NP_001407285.1 LIM/homeobox protein Lhx2 isoform b

Status: VALIDATED

Source sequence(s)

AL929186, BX813320

UniProtKB/TrEMBL

F6Z9H5
NM_001420357.1 → NP_001407286.1 LIM/homeobox protein Lhx2 isoform b

Status: VALIDATED

Source sequence(s)

AL929186, BX813320

UniProtKB/TrEMBL

F6Z9H5
NM_001420359.1 → NP_001407288.1 LIM/homeobox protein Lhx2 isoform e

Status: VALIDATED

Source sequence(s)

AL929186, BX813320
NM_010710.5 → NP_034840.1 LIM/homeobox protein Lhx2 isoform a

See identical proteins and their annotated locations for NP_034840.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes isoform a.

Source sequence(s)

AL929186, BX813320

Consensus CDS

CCDS16008.1

UniProtKB/Swiss-Prot

Q9Z0S2

UniProtKB/TrEMBL

Q543C6

Related

ENSMUSP00000000253.6, ENSMUST00000000253.6

Conserved Domains (4) summary

cd09377
Location:111 → 169

LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family

cd09469
Location:43 → 106

LIM1_Lhx2; The first LIM domain of Lhx2

COG5576
Location:247 → 378

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:270 → 323

Homeobox; Homeobox domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

38229282..38259747

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006497735.3 → XP_006497798.1 LIM/homeobox protein Lhx2 isoform X2

See identical proteins and their annotated locations for XP_006497798.1

Conserved Domains (4) summary

cd09377
Location:78 → 136

LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family

cd09469
Location:2 → 65

LIM1_Lhx2; The first LIM domain of Lhx2

COG5576
Location:214 → 345

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:237 → 290

Homeobox; Homeobox domain
XM_006497736.4 → XP_006497799.1 LIM/homeobox protein Lhx2 isoform X2

See identical proteins and their annotated locations for XP_006497799.1

Conserved Domains (4) summary

cd09377
Location:78 → 136

LIM2_Lhx2_Lhx9; The second LIM domain of Lhx2 and Lhx9 family

cd09469
Location:2 → 65

LIM1_Lhx2; The first LIM domain of Lhx2

COG5576
Location:214 → 345

COG5576; Homeodomain-containing transcription factor [Transcription]

pfam00046
Location:237 → 290

Homeobox; Homeobox domain