Lhx3 LIM homeobox protein 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Lhx3provided by MGI
Official Full Name: LIM homeobox protein 3provided by MGI
Primary source: MGI:MGI:102673
See related: Ensembl:ENSMUSG00000026934 AllianceGenome:MGI:102673
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: Lim3; P-LIM; mLIM3; mLim-3
Summary: Enables transcription cis-regulatory region binding activity and transcription coactivator binding activity. Involved in positive regulation of DNA-templated transcription. Acts upstream of or within several processes, including nervous system development; placenta development; and positive regulation of transcription by RNA polymerase II. Located in chromatin. Part of transcription regulator complex. Is expressed in several structures, including alimentary system; cardiovascular system; central nervous system; genitourinary system; and sensory organ. Used to study hypopituitarism. Human ortholog(s) of this gene implicated in panhypopituitarism. Orthologous to human LHX3 (LIM homeobox 3). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Low expression observed in reference dataset See more
Orthologs: human all
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Genomic context

Location:: 2 A3; 2 18.44 cM

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (26090224..26098261, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (26200212..26208249, complement)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Lhx4 surpasses its paralog Lhx3 in promoting the differentiation of spinal V2a interneurons.
Title: Lhx4 surpasses its paralog Lhx3 in promoting the differentiation of spinal V2a interneurons.
A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice.
Title: A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice.
Results show that specific genomic loci associated with Islet-1 (Isl1) , LIM-homeobox 3 (Lhx3), and LMO4 genes recruit the Isl1-Lhx3 complex to activate the transcription of Isl1, Lhx3, and Lmo4.
Title: The Isl1-Lhx3 Complex Promotes Motor Neuron Specification by Activating Transcriptional Pathways that Enhance Its Own Expression and Formation.
Together, the authors show the antagonistic regulation of the alpha-enhancer activity by Pax6 and the LIM protein complex is necessary for the establishment of an inner retinal circuitry, which controls visual adaptation.
Title: The LIM protein complex establishes a retinal circuitry of visual adaptation by regulating Pax6 α-enhancer activity.
conditional deletion of Shh in the anterior hypothalamus results in a fully penetrant phenotype characterised by a complete arrest of (Rathke's pouch) RP development, with lack of Lhx3/Lhx4 expression in RP epithelium.
Title: Hypothalamic sonic hedgehog is required for cell specification and proliferation of LHX3/LHX4 pituitary embryonic precursors.
Expression of motor neuron effector genes is maintained by transient enhancers bound by Isl1/Lhx3 in nascent motor neurons and Isl1/Onecut1 in maturing hypaxial motor neurons.
Title: Expression of Terminal Effector Genes in Mammalian Neurons Is Maintained by a Dynamic Relay of Transient Enhancers.
All E1 sequences from lamprey to mouse responded equally well to Phox2a and the Isl1-Lhx3 complex. Conversely, E2, the enhancer for limb-innervating motor neurons, was only found in tetrapod animals
Title: Functional Diversification of Motor Neuron-specific Isl1 Enhancers during Evolution.
We discovered that expression of Cdkn1a is expanded dorsally in the pituitary primordium of both Lhx3 and Lhx4 mutants.
Title: Lhx4 deficiency: increased cyclin-dependent kinase inhibitor expression and pituitary hypoplasia.
Lhx3-LIM domains play critical roles in transactivation of the Isl1-Lhx3 complex by not only directing the assembly of the Isl1-Lhx3 complex but also recruiting coactivators to the complex.
Title: Critical Roles of the LIM Domains of Lhx3 in Recruiting Coactivators to the Motor Neuron-Specifying Isl1-Lhx3 Complex.
This treatment leads to activation of Lhx3 gene expression.
Title: The role of DNA methylation in regulation of the murine Lhx3 gene.

Submit: New GeneRIF Correction See all GeneRIFs (26)

Variation

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Alleles

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

Targeted (7) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:225298

NoName (e-PCR)
- UniSTS:495492

Lhx3 (e-PCR), detects polymorphism
- UniSTS:507021

NoName (e-PCR)
- UniSTS:489147

L38248 (e-PCR)
- UniSTS:158930

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription coactivator binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coregulator binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of apoptotic process	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
involved_in inner ear development	IEA Inferred from Electronic Annotation more info
involved_in lung development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within medial motor column neuron differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within motor neuron axon guidance	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within negative regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within pituitary gland development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within placenta development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within 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	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 positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within prolactin secreting cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within somatotropin secreting cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within spinal cord association neuron differentiation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within spinal cord motor neuron cell fate specification	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within thyroid-stimulating hormone-secreting cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ventral spinal cord interneuron specification	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
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	ISO Inferred from Sequence Orthology more info	PubMed
part_of transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: LIM/homeobox protein Lhx3

Names: LIM homeo box protein 3; homeobox protein LIM-3; homeobox protein P-LIM

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_001039653.2 → NP_001034742.1 LIM/homeobox protein Lhx3 isoform a

See identical proteins and their annotated locations for NP_001034742.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AL773595, CD741809, L38248

Consensus CDS

CCDS38081.1

UniProtKB/TrEMBL

A2ALD8

Related

ENSMUSP00000028302.7, ENSMUST00000028302.8

Conserved Domains (3) summary

cd09376
Location:95 → 150

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

cd09467
Location:33 → 87

LIM1_Lhx3b; The first LIM domain of Lhx3b

pfam00046
Location:165 → 218

Homeobox; Homeobox domain
NM_010711.2 → NP_034841.2 LIM/homeobox protein Lhx3 isoform b

See identical proteins and their annotated locations for NP_034841.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform a.

Source sequence(s)

AL773595, CD741809, L38248

Consensus CDS

CCDS71004.1

UniProtKB/Swiss-Prot

A2ALD9, P50481, Q61800, Q61801

Related

ENSMUSP00000056822.10, ENSMUST00000054099.16

Conserved Domains (3) summary

cd09376
Location:93 → 148

LIM2_Lhx3_Lhx4; The second LIM domain of Lhx3-Lhx4 family

cd09467
Location:31 → 85

LIM1_Lhx3b; The first LIM domain of Lhx3b

pfam00046
Location:163 → 216

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

26090224..26098261 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011239031.2 → XP_011237333.1 LIM/homeobox protein Lhx3 isoform X1

Conserved Domains (1) summary

pfam00046
Location:27 → 81

Homeobox; Homeobox domain