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    pdlim1 PDZ and LIM domain 1 (elfin) [ Danio rerio (zebrafish) ]

    Gene ID: 550568, updated on 9-Dec-2024

    Summary

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    Official Symbol
    pdlim1provided by ZNC
    Official Full Name
    PDZ and LIM domain 1 (elfin)provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-5227
    See related
    Ensembl:ENSDARG00000019845 AllianceGenome:ZFIN:ZDB-GENE-030131-5227
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    clim1; wu:fa19a03; wu:fy34f10; zgc:110681
    Summary
    Predicted to enable actin binding activity and muscle alpha-actinin binding activity. Predicted to be involved in actin cytoskeleton organization; heart development; and muscle structure development. Predicted to be part of filamentous actin. Predicted to be active in Z disc; adherens junction; and stress fiber. Is expressed in several structures, including anterior axial hypoblast; digestive system; epidermis; nervous system; and yolk syncytial layer. Orthologous to human PDLIM1 (PDZ and LIM domain 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See pdlim1 in Genome Data Viewer
    Location:
    chromosome: 13
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (25762909..25773963, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (25632459..25643513, complement)

    Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene sphingosine-1-phosphate lyase 1 Neighboring gene neurogenin 3 Neighboring gene uncharacterized LOC137487400 Neighboring gene v-rel avian reticuloendotheliosis viral oncogene homolog

    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. Gene expression patterns of the ALP family during zebrafish development. te Velthuis AJ, et al. Gene Expr Patterns, 2007 Jan. PMID 17045553
    2. Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Mishima Y, et al. Genes Dev, 2009 Mar 1. PMID 19240126, Free PMC Article
    3. A comparative map of the zebrafish genome. Woods IG, et al. Genome Res, 2000 Dec. PMID 11116086, Free PMC Article
    4. Targeted Gene Expression in Zebrafish Exposed to Chlorpyrifos-Oxon Confirms Phenotype-Specific Mechanisms Leading to Adverse Outcomes. Garcia-Reyero N, et al. Bull Environ Contam Toxicol, 2016 Jun. PMID 27086301, Free PMC Article
    5. Expression of Protein-Coding Gene Orthologs in Zebrafish and Mouse Inner Ear Non-sensory Supporting Cells. Giffen KP, et al. Front Neurosci, 2019. PMID 31680844, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables actin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables muscle alpha-actinin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in heart development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in muscle structure development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Z disc IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of filamentous actin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in stress fiber IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    PDZ and LIM domain protein 1
    Names
    elfin

    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_001017870.1 → NP_001017870.1  PDZ and LIM domain protein 1

      See identical proteins and their annotated locations for NP_001017870.1

      Status: PROVISIONAL

      Source sequence(s)
      BC092978
      UniProtKB/TrEMBL
      Q567X7
      Related
      ENSDARP00000046980.4, ENSDART00000046981.6
      Conserved Domains (3) summary
      cd09448
      Location:253 → 304
      LIM_CLP36; This family represents the LIM domain of CLP36
      cd00992
      Location:2 → 80
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      pfam15936
      Location:133 → 223
      DUF4749; Domain of unknown function (DUF4749)

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007124.7 Reference GRCz11 Primary Assembly

      Range
      25762909..25773963 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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