Lmx1a LIM homeobox transcription factor 1 alpha [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Lmx1aprovided by MGI
Official Full Name: LIM homeobox transcription factor 1 alphaprovided by MGI
Primary source: MGI:MGI:1888519
See related: Ensembl:ENSMUSG00000026686 AllianceGenome:MGI:1888519
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: dr; sst; Lmx1.1; dreher
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including midbrain dopaminergic neuron differentiation; olfactory behavior; and positive regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including negative regulation of neuron differentiation; nervous system development; and regulation of cell growth. Predicted to be active in nucleus. Is expressed in several structures, including brain; ear; embryo ectoderm; notochord; and somite. Used to study Parkinson's disease. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 7. Orthologous to human LMX1A (LIM homeobox transcription factor 1 alpha). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in CNS E11.5 (RPKM 3.7), placenta adult (RPKM 2.2) and 8 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 H2.3; 1 75.08 cM

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (167515864..167676310)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (167688230..167848741)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Lmx1a is a master regulator of the cortical hem.
Title: Lmx1a is a master regulator of the cortical hem.
Lmx1a-Dependent Activation of miR-204/211 Controls the Timing of Nurr1-Mediated Dopaminergic Differentiation.
Title: Lmx1a-Dependent Activation of miR-204/211 Controls the Timing of Nurr1-Mediated Dopaminergic Differentiation.
Identification of a novel mutant allele of LIM homeobox transcription factor 1 alpha (dreher) in mice.
Title: Identification of a novel mutant allele of LIM homeobox transcription factor 1 alpha (dreher) in mice.
Interaction with ectopic cochlear crista sensory epithelium disrupts basal cochlear sensory epithelium development in Lmx1a mutant mice.
Title: Interaction with ectopic cochlear crista sensory epithelium disrupts basal cochlear sensory epithelium development in Lmx1a mutant mice.
homeobox TF Lmx1a can activate the Cux2 enhancer through activation of a conserved intronic enhancer
Title: Lmx1a drives Cux2 expression in the cortical hem through activation of a conserved intronic enhancer.
we provide genetic evidence that a transcription factor, Lmx1a, interacts with its negative regulator, Lmo4, to pattern various vestibular and auditory components of the mammalian inner ear.
Title: Reciprocal Negative Regulation Between Lmx1a and Lmo4 Is Required for Inner Ear Formation.
Homozygous Lmx1a mutant mice (Dreher) are deaf with dysmorphic ears with an abnormal morphogenesis and fused and misshapen sensory organs; however, computed tomography performed on a hearing-impaired family member did not reveal any cochleovestibular malformations.
Title: A variant in LMX1A causes autosomal recessive severe-to-profound hearing impairment.
Data show that sustained expression of Lmx1a and Lmx1b is required for the survival of adult midbrain dopaminergic neurons.
Title: Lmx1a and Lmx1b regulate mitochondrial functions and survival of adult midbrain dopaminergic neurons.
Lmx1a and Lmx1b regulate Plxnc1 expression.Lmx1a is required for the topographical organization of dopaminergic innervation in the striatum.
Title: Transcriptional repression of Plxnc1 by Lmx1a and Lmx1b directs topographic dopaminergic circuit formation.
Lmx1a is expressed in enterochromaffin cells and functions downstream of Nkx2.2.
Title: The novel enterochromaffin marker Lmx1a regulates serotonin biosynthesis in enteroendocrine cell lineages downstream of Nkx2.2.

Submit: New GeneRIF Correction See all GeneRIFs (35)

Variation

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Alleles

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

Endonuclease-mediated (2)
Spontaneous (16) 1 citation
Targeted (5) 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:234262

G49220 (e-PCR)
- UniSTS:108976

G49223 (e-PCR)
- UniSTS:108979

Lmx1a (e-PCR), detects polymorphism
- UniSTS:547256

G49229 (e-PCR)
- UniSTS:108985

G49236 (e-PCR)
- UniSTS:108992

D0M1Mit110 (e-PCR)
- UniSTS:116694

D1Mit110 (e-PCR), detects polymorphism
- UniSTS:116694

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay 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 transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within central nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of central nervous system neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within central nervous system neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cerebellum development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dentate gyrus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dopaminergic neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hippocampus development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in locomotory behavior	IGI Inferred from Genetic Interaction more info	PubMed
involved_in memory	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within midbrain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in midbrain dopaminergic neuron differentiation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of neuron differentiation	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 neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in olfactory behavior	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of canonical Wnt signaling pathway	IC Inferred by Curator 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 regulation of cell growth	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of gene expression	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 synapse organization	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: LIM homeobox transcription factor 1-alpha

Names: LIM/homeobox protein 1.1; LIM/homeobox protein LMX1A; LMX-1.1; shaker short-tail

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_001417483.1 → NP_001404412.1 LIM homeobox transcription factor 1-alpha

Status: VALIDATED

Source sequence(s)

AC093452, AC160530

UniProtKB/Swiss-Prot

Q9JKU8

UniProtKB/TrEMBL

Q543W2
NM_033652.6 → NP_387501.1 LIM homeobox transcription factor 1-alpha

See identical proteins and their annotated locations for NP_387501.1

Status: VALIDATED

Source sequence(s)

AC093452, AC160530

Consensus CDS

CCDS15460.1

UniProtKB/Swiss-Prot

Q9JKU8

UniProtKB/TrEMBL

Q543W2

Related

ENSMUSP00000028003.7, ENSMUST00000028003.9

Conserved Domains (3) summary

cd09370
Location:35 → 86

LIM1_Lmx1a; The first LIM domain of Lmx1a

cd09378
Location:94 → 148

LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b

pfam00046
Location:198 → 252

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_000067.7 Reference GRCm39 C57BL/6J

Range

167515864..167676310

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017321684.2 → XP_017177173.1 LIM homeobox transcription factor 1-alpha isoform X1

UniProtKB/Swiss-Prot

Q9JKU8

UniProtKB/TrEMBL

Q543W2

Conserved Domains (3) summary

cd09370
Location:35 → 86

LIM1_Lmx1a; The first LIM domain of Lmx1a

cd09378
Location:94 → 148

LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b

pfam00046
Location:198 → 252

Homeobox; Homeobox domain
XM_030242132.2 → XP_030097992.1 LIM homeobox transcription factor 1-alpha isoform X1

UniProtKB/Swiss-Prot

Q9JKU8

UniProtKB/TrEMBL

Q543W2

Conserved Domains (3) summary

cd09370
Location:35 → 86

LIM1_Lmx1a; The first LIM domain of Lmx1a

cd09378
Location:94 → 148

LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b

pfam00046
Location:198 → 252

Homeobox; Homeobox domain