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    Lmx1a LIM homeobox transcription factor 1 alpha [ Rattus norvegicus (Norway rat) ]

    Gene ID: 289201, updated on 30-Mar-2024

    Summary

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    Official Symbol
    Lmx1aprovided by RGD
    Official Full Name
    LIM homeobox transcription factor 1 alphaprovided by RGD
    Primary source
    RGD:1304784
    See related
    Ensembl:ENSRNOG00000004642 AllianceGenome:RGD:1304784
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in brain development. Predicted to be active in nucleus. 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 Brain (RPKM 3.9), Muscle (RPKM 3.6) and 5 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    13q24
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (82367493..82511157)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (79834614..79978253)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (85916753..86061534)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102553924 Neighboring gene retinoid X receptor gamma Neighboring gene uncharacterized LOC134481529 Neighboring gene probable serine/threonine-protein kinase dyrk1 Neighboring gene platelet-activating factor acetylhydrolase 1b, catalytic subunit 3, pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Mutation at the Lmx1a locus provokes aberrant brain development in the rat. Kuwamura M, et al. Brain Res Dev Brain Res, 2005 Mar 31. PMID 15804398
    2. Cytoarchitectonic abnormalities in hippocampal formation and cerebellum of dreher mutant mouse. Sekiguchi M, et al. Brain Res Dev Brain Res, 1992 May 22. PMID 1638738
    3. Control of roof plate formation by Lmx1a in the developing spinal cord. Chizhikov VV, et al. Development, 2004 Jun. PMID 15148302
    4. Roof plate and dorsal spinal cord dl1 interneuron development in the dreher mutant mouse. Millen KJ, et al. Dev Biol, 2004 Jun 15. PMID 15183721
    5. Wnt1-lmx1a forms a novel autoregulatory loop and controls midbrain dopaminergic differentiation synergistically with the SHH-FoxA2 pathway. Chung S, et al. Cell Stem Cell, 2009 Dec 4. PMID 19951692, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within central nervous system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of central nervous system neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within central nervous system neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cerebellum development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within dentate gyrus development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within dopaminergic neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within hippocampus development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in locomotory behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in memory ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within midbrain development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in midbrain dopaminergic neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in olfactory behavior ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of cell growth ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synapse organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    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

    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_001105967.2 → NP_001099437.2  LIM homeobox transcription factor 1-alpha

      See identical proteins and their annotated locations for NP_001099437.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000013
      UniProtKB/TrEMBL
      F1LRJ8
      Related
      ENSRNOP00000006163.4, ENSRNOT00000006163.6
      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_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086031.1 Reference GRCr8

      Range
      82367493..82511157
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017598709.3 → XP_017454198.1  LIM homeobox transcription factor 1-alpha isoform X1

      UniProtKB/TrEMBL
      F1LRJ8
      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

    Gene LinkOut

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

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