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

    Gene ID: 110648, updated on 21-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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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