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

    Gene ID: 110648, updated on 27-Nov-2024

    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
    NEW
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    Genomic context

    See Lmx1a in Genome Data Viewer
    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC129356, MGC129357

    Gene Ontology Provided by MGI

    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

    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)

    NEW Try the new Transcript table

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

      Status: VALIDATED

      Source sequence(s)
      AC093452, AC160530
      UniProtKB/Swiss-Prot
      Q9JKU8
      UniProtKB/TrEMBL
      Q543W2
    2. NM_033652.6NP_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:3586
      LIM1_Lmx1a; The first LIM domain of Lmx1a
      cd09378
      Location:94148
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:198252
      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_017321684.2XP_017177173.1  LIM homeobox transcription factor 1-alpha isoform X1

      UniProtKB/Swiss-Prot
      Q9JKU8
      UniProtKB/TrEMBL
      Q543W2
      Conserved Domains (3) summary
      cd09370
      Location:3586
      LIM1_Lmx1a; The first LIM domain of Lmx1a
      cd09378
      Location:94148
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:198252
      Homeobox; Homeobox domain
    2. XM_030242132.2XP_030097992.1  LIM homeobox transcription factor 1-alpha isoform X1

      UniProtKB/Swiss-Prot
      Q9JKU8
      UniProtKB/TrEMBL
      Q543W2
      Conserved Domains (3) summary
      cd09370
      Location:3586
      LIM1_Lmx1a; The first LIM domain of Lmx1a
      cd09378
      Location:94148
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:198252
      Homeobox; Homeobox domain