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

Gene ID: 110648, updated on 11-Apr-2024

Summary

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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 memory; midbrain dopaminergic neuron differentiation; and olfactory behavior. 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; genitourinary system; and notochord. 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, Apr 2022]
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

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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_000067.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 34207 Neighboring gene STARR-seq mESC enhancer starr_02951 Neighboring gene leucine rich repeat containing 52 Neighboring gene STARR-seq mESC enhancer starr_02952 Neighboring gene retinoid X receptor gamma Neighboring gene STARR-seq mESC enhancer starr_02953 Neighboring gene STARR-seq mESC enhancer starr_02954 Neighboring gene STARR-seq mESC enhancer starr_02955 Neighboring gene STARR-seq mESC enhancer starr_02957 Neighboring gene STARR-seq mESC enhancer starr_02958 Neighboring gene pre B cell leukemia homeobox 1 Neighboring gene STARR-seq mESC enhancer starr_02965 Neighboring gene predicted gene, 51671 Neighboring gene predicted gene, 39696

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Identification of a novel mutant allele of LIM homeobox transcription factor 1 alpha (dreher) in mice. Suto JI. Congenit Anom (Kyoto), 2022 Jan. PMID 34816488
  2. Purkinje cell compartmentalization in the cerebellum of the spontaneous mutant mouse dreher. Sillitoe RV, et al. Brain Struct Funct, 2014 Jan. PMID 23160833, Free PMC Article
  3. Lmx1a allows context-specific isolation of progenitors of GABAergic or dopaminergic neurons during neural differentiation of embryonic stem cells. Nefzger CM, et al. Stem Cells, 2012 Jul. PMID 22495882
  4. Generation of knockout mice expressing a GFP-reporter under the control of the Lmx1a locus. Griesel G, et al. Gene Expr Patterns, 2011 Jun-Jul. PMID 21440093
  5. Expression of the LIM-homeodomain gene Lmx1a in the postnatal mouse central nervous system. Zou HL, et al. Brain Res Bull, 2009 Mar 30. PMID 19111912

See all (227) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Lmx1a is a master regulator of the cortical hem.
    Title: Lmx1a is a master regulator of the cortical hem.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC129356, MGC129357

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 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 multicellular organism development IEA
Inferred from Electronic Annotation
more info
  
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 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
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
  

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)

  1. 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

  2. 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

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    167515864..167676310
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9JKU8.1 GenPept UniProtKB/Swiss-Prot:Q9JKU8

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