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    Lmx1b LIM homeobox transcription factor 1 beta [ Rattus norvegicus (Norway rat) ]

    Gene ID: 114501, updated on 9-Dec-2024

    Summary

    Official Symbol
    Lmx1bprovided by RGD
    Official Full Name
    LIM homeobox transcription factor 1 betaprovided by RGD
    Primary source
    RGD:620843
    See related
    EnsemblRapid:ENSRNOG00000017019 AllianceGenome:RGD:620843
    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 factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including memory; olfactory behavior; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including collagen fibril organization; nervous system development; and trabecular meshwork development. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in nail-patella syndrome. Orthologous to human LMX1B (LIM homeobox transcription factor 1 beta). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Restricted expression toward (RPKM 13.6) See more
    Orthologs
    NEW
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    Genomic context

    See Lmx1b in Genome Data Viewer
    Location:
    3p11
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (37257025..37338675, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (16862195..16940899, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (12608748..12686937, complement)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102550017 Neighboring gene small nucleolar RNA SNORA48 Neighboring gene ribosomal protein L39 like 3 Neighboring gene uncharacterized LOC134486075

    Genomic regions, transcripts, and products

    Expression

    • 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

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
     
    acts_upstream_of_or_within camera-type eye development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within cell population proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within central nervous system neuron development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within cerebellum morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within collagen fibril organization ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within dopaminergic neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in dopaminergic neuron differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in dorsal/ventral pattern formation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within limb morphogenesis 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 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
     
    acts_upstream_of_or_within neuron migration ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in olfactory behavior ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within organ growth ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of autophagy 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 intracellular transport 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
     
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synapse organization ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within trabecular meshwork development ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    LIM homeobox transcription factor 1-beta

    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_053709.1NP_446161.1  LIM homeobox transcription factor 1-beta

      See identical proteins and their annotated locations for NP_446161.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      G3V877
      Related
      ENSRNOP00000022953.6, ENSRNOT00000022953.8
      Conserved Domains (3) summary
      cd09371
      Location:56108
      LIM1_Lmx1b; The first LIM domain of Lmx1b
      cd09378
      Location:115169
      LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b
      pfam00046
      Location:222276
      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_086021.1 Reference GRCr8

      Range
      37257025..37338675 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063282994.1XP_063139064.1  LIM homeobox transcription factor 1-beta isoform X1