Lhx6 LIM homeobox protein 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Lhx6provided by MGI
Official Full Name: LIM homeobox protein 6provided by MGI
Primary source: MGI:MGI:1306803
See related: Ensembl:ENSMUSG00000026890 AllianceGenome:MGI:1306803
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: Lhx6.1
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Acts upstream of or within forebrain development and neuron maturation. Located in nucleus. Is expressed in several structures, including alimentary system; branchial arch; forebrain; genitourinary system; and sensory organ. Orthologous to human LHX6 (LIM homeobox 6). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in CNS E18 (RPKM 4.6), whole brain E14.5 (RPKM 3.8) and 18 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 B; 2 24.17 cM

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (35971962..35996004, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (36081950..36105992, 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 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?

Lhx6 deficiency causes human embryonic palatal mesenchymal cell mitophagy dysfunction in cleft palate.
Title: Lhx6 deficiency causes human embryonic palatal mesenchymal cell mitophagy dysfunction in cleft palate.
MTG8 interacts with LHX6 to specify cortical interneuron subtype identity.
Title: MTG8 interacts with LHX6 to specify cortical interneuron subtype identity.
Interneuron function and cognitive behavior are preserved upon postnatal removal of Lhx6.
Title: Interneuron function and cognitive behavior are preserved upon postnatal removal of Lhx6.
Gene regulatory networks controlling differentiation, survival, and diversification of hypothalamic Lhx6-expressing GABAergic neurons.
Title: Gene regulatory networks controlling differentiation, survival, and diversification of hypothalamic Lhx6-expressing GABAergic neurons.
Lhx6 regulates canonical Wnt signaling to control the fate of mesenchymal progenitor cells during mouse molar root patterning.
Title: Lhx6 regulates canonical Wnt signaling to control the fate of mesenchymal progenitor cells during mouse molar root patterning.
Study in Nf1 knockout mice discovered that loss of Nf1 results in a dose-dependent decrease in Lhx6 expression, the transcription factor necessary to establish somatostatin- and parvalbumin-positive cortical GABAergic interneurons (CINs), which was rescued by the MEK inhibitor SL327, revealing a mechanism whereby a neurofibromin/Ras/MEK pathway regulates a critical CIN developmental milestone.
Title: Nf1 deletion results in depletion of the Lhx6 transcription factor and a specific loss of parvalbumin(+) cortical interneurons.
Lhx6 was expressed in retinal ganglion cells and amacrine cells in both the adult and developing mouse retina
Title: Expression of Lhx6 in the adult and developing mouse retina.
studies identify Lhx6-positive GABAergic neurons in the ventral zona incerta that promote sleep
Title: Lhx6-positive GABA-releasing neurons of the zona incerta promote sleep.
LHX6 inhibits breast cancer cell proliferation and invasion via repression of the Wnt/beta-catenin signaling pathway.
Title: LHX6 inhibits breast cancer cell proliferation and invasion via repression of the Wnt/β-catenin signaling pathway.
Lhx6 and Lhx8 promote palate development through negative regulation of a cell cycle inhibitor gene, p57Kip2
Title: Lhx6 and Lhx8 promote palate development through negative regulation of a cell cycle inhibitor gene, p57Kip2.

Submit: New GeneRIF Correction See all GeneRIFs (23)

Variation

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Alleles

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

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Lhx6 (e-PCR), detects polymorphism
- UniSTS:507024

AJ000337 (e-PCR)
- UniSTS:163279

D2Mit372 (e-PCR), detects polymorphism
- UniSTS:129269

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	NAS Non-traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
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 double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cerebral cortex GABAergic interneuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cerebral cortex neuron differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cerebral cortex radially oriented cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cerebral cortex tangential migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in forebrain neuron development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within forebrain neuron development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within forebrain neuron fate commitment	IGI Inferred from Genetic Interaction more info	PubMed
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuron maturation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron migration	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
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
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	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: LIM/homeobox protein Lhx6

Names: LIM-homeodomain protein 6.1; LIM/homeobox protein Lhx6.1

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_001083125.1 → NP_001076594.1 LIM/homeobox protein Lhx6 isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region resulting in a frameshift and a shorter 3' UTR compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AK140987, CO042780

Consensus CDS

CCDS38110.1

UniProtKB/TrEMBL

E9QN32

Related

ENSMUSP00000108591.5, ENSMUST00000112967.12

Conserved Domains (3) summary

cd09380
Location:99 → 152

LIM1_Lhx6; The first LIM domain of Lhx6

cd09382
Location:160 → 214

LIM2_Lhx6; The second LIM domain of Lhx6

pfam00046
Location:252 → 304

Homeobox; Homeobox domain
NM_001083126.1 → NP_001076595.1 LIM/homeobox protein Lhx6 isoform 3

See identical proteins and their annotated locations for NP_001076595.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) represents the use of an alternate promoter, differs in the 5' UTR and uses a downstream start codon compared to variant 1. The encoded isoform (3, also known as Lhx6.1a) has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AB031040, BC065077

Consensus CDS

CCDS38113.1

UniProtKB/Swiss-Prot

O88706, Q6P1H2, Q9R1R0, Q9R1R1

Related

ENSMUSP00000108585.4, ENSMUST00000112961.10

Conserved Domains (3) summary

cd09380
Location:70 → 123

LIM1_Lhx6; The first LIM domain of Lhx6

cd09382
Location:131 → 185

LIM2_Lhx6; The second LIM domain of Lhx6

pfam00046
Location:223 → 276

Homeobox; Homeobox domain
NM_001083127.1 → NP_001076596.1 LIM/homeobox protein Lhx6 isoform 4

See identical proteins and their annotated locations for NP_001076596.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) represents the use of an alternate promoter and has multiple differences compared to variant 1. These differences result in distinct 5' and 3' UTRs, the use of a downstream start codon and a translational frameshift in the 3' coding region compared to variant 1. The encoded isoform (4, also known as Lhx6.1b) has a shorter N-terminus and a distinct C-terminus compared to isoform 1. Variants 4 and 5 both encode the same isoform (4).

Source sequence(s)

AB031039, BC065077

Consensus CDS

CCDS38111.1

UniProtKB/Swiss-Prot

Q9R1R0

Related

ENSMUSP00000108590.4, ENSMUST00000112966.10

Conserved Domains (3) summary

cd09380
Location:70 → 123

LIM1_Lhx6; The first LIM domain of Lhx6

cd09382
Location:131 → 185

LIM2_Lhx6; The second LIM domain of Lhx6

pfam00046
Location:223 → 275

Homeobox; Homeobox domain
NM_001355125.1 → NP_001342054.1 LIM/homeobox protein Lhx6 isoform 4

Status: VALIDATED

Description

Transcript Variant: This variant (5) has multiple differences compared to variant 1. These differences result in distinct 5' and 3' UTRs, the use of a downstream start codon and a translational frameshift in the 3' coding region compared to variant 1. The encoded isoform (4, also known as Lhx6.1b) has a shorter N-terminus and a distinct C-terminus compared to isoform 1. Variants 4 and 5 both encode the same isoform (4).

Source sequence(s)

AL773525

Consensus CDS

CCDS38111.1

Conserved Domains (3) summary

cd09380
Location:70 → 123

LIM1_Lhx6; The first LIM domain of Lhx6

cd09382
Location:131 → 185

LIM2_Lhx6; The second LIM domain of Lhx6

pfam00046
Location:223 → 275

Homeobox; Homeobox domain
NM_008500.2 → NP_032526.2 LIM/homeobox protein Lhx6 isoform 1

Status: VALIDATED

Description

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

Source sequence(s)

AK140987, BC065077

Consensus CDS

CCDS38112.1

UniProtKB/TrEMBL

H9H9T0

Related

ENSMUSP00000108584.2, ENSMUST00000112960.8

Conserved Domains (3) summary

cd09380
Location:99 → 152

LIM1_Lhx6; The first LIM domain of Lhx6

cd09382
Location:160 → 214

LIM2_Lhx6; The second LIM domain of Lhx6

pfam00046
Location:252 → 304

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

35971962..35996004 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006497744.5 → XP_006497807.1 LIM/homeobox protein Lhx6 isoform X1

See identical proteins and their annotated locations for XP_006497807.1

UniProtKB/Swiss-Prot

O88706, Q6P1H2, Q9R1R0, Q9R1R1

Conserved Domains (3) summary

cd09380
Location:70 → 123

LIM1_Lhx6; The first LIM domain of Lhx6

cd09382
Location:131 → 185

LIM2_Lhx6; The second LIM domain of Lhx6

pfam00046
Location:223 → 276

Homeobox; Homeobox domain