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    lmx1al LIM homeobox transcription factor 1, alpha-like [ Danio rerio (zebrafish) ]

    Gene ID: 100149437, updated on 27-Mar-2024

    Summary

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    Official Symbol
    lmx1alprovided by ZNC
    Official Full Name
    LIM homeobox transcription factor 1, alpha-likeprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-131213-1
    See related
    Ensembl:ENSDARG00000077915 AllianceGenome:ZFIN:ZDB-GENE-131213-1
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    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 neuron differentiation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of transcription, DNA-templated. Predicted to be active in nucleus. Is expressed in diencephalon; epiphysis; hindbrain; midline column; and superior raphe nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    all
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    Genomic context

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    See lmx1al in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (52805941..52885752)
    105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (52551535..52629624)

    Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene collagen beta(1-O)galactosyltransferase 1a Neighboring gene GEM interacting protein Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 5 Neighboring gene ATPase 13A1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Integration of genomic and functional approaches reveals enhancers at LMX1A and LMX1B. Burzynski GM, et al. Mol Genet Genomics, 2013 Nov. PMID 23942840, Free PMC Article
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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

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    Preferred Names
    LIM homeobox transcription factor 1-alpha

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007114.7 Reference GRCz11 Primary Assembly

      Range
      52805941..52885752
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009299784.3 → XP_009298059.1  LIM homeobox transcription factor 1-alpha

      UniProtKB/TrEMBL
      A0A8M3AYC8, F1QFN7
      Related
      ENSDARP00000089596.4, ENSDART00000098826.6
      Conserved Domains (3) summary
      cd09371
      Location:52 → 104
      LIM1_Lmx1b; The first LIM domain of Lmx1b
      pfam00046
      Location:212 → 265
      Homeobox; Homeobox domain
      cl02475
      Location:111 → 165
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
    Nucleotide Protein Strain
    Heading Accession and Version

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