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    pdlim5b PDZ and LIM domain 5b [ Danio rerio (zebrafish) ]

    Gene ID: 393165, updated on 4-Jan-2025

    Summary

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    Official Symbol
    pdlim5bprovided by ZNC
    Official Full Name
    PDZ and LIM domain 5bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-908
    See related
    Ensembl:ENSDARG00000027600 AllianceGenome:ZFIN:ZDB-GENE-040426-908
    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
    zgc:56116; zgc:86712
    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 digestive system; epidermis; musculature system; and periderm. Orthologous to human PDLIM5 (PDZ and LIM domain 5). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    all
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    Genomic context

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    See pdlim5b in Genome Data Viewer
    Location:
    chromosome: 10
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 10 NC_007121.7 (1187444..1275732, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 10 NC_007121.6 (1192754..1281143, complement)

    Chromosome 10 - NC_007121.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137496532 Neighboring gene unc-5 netrin receptor Cb Neighboring gene bone morphogenetic protein receptor, type IBb Neighboring gene opsin 4xa Neighboring gene glial cell derived neurotrophic factor a

    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. Mutation in the type IB bone morphogenetic protein receptor Alk6b impairs germ-cell differentiation and causes germ-cell tumors in zebrafish. Neumann JC, et al. Proc Natl Acad Sci U S A, 2011 Aug 9. PMID 21775673, Free PMC Article
    2. Unexpected diversity and photoperiod dependence of the zebrafish melanopsin system. Matos-Cruz V, et al. PLoS One, 2011. PMID 21966429, Free PMC Article
    3. A high-resolution mRNA expression time course of embryonic development in zebrafish. White RJ, et al. Elife, 2017 Nov 16. PMID 29144233, Free PMC Article
    4. Intrinsic myocardial defects underlie an Rbfox-deficient zebrafish model of hypoplastic left heart syndrome. Huang M, et al. Nat Commun, 2022 Oct 5. PMID 36198703, Free PMC Article
    5. Comparative phosphoproteomics of zebrafish Fyn/Yes morpholino knockdown embryos. Lemeer S, et al. Mol Cell Proteomics, 2008 Nov. PMID 18550893

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC56116

    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 5b

    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_001009895.1 → NP_001009895.1  PDZ and LIM domain protein 5b isoform 1

      See identical proteins and their annotated locations for NP_001009895.1

      Status: PROVISIONAL

      Source sequence(s)
      BC071389
      UniProtKB/TrEMBL
      Q6IQL6
      Related
      ENSDARP00000139485.2, ENSDART00000168127.2
      Conserved Domains (2) summary
      cd00992
      Location:11 → 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:141 → 160
      DUF4749; Domain of unknown function (DUF4749)

    2. NM_200196.1 → NP_956490.1  PDZ and LIM domain protein 5b isoform 2

      See identical proteins and their annotated locations for NP_956490.1

      Status: PROVISIONAL

      Source sequence(s)
      BC045922
      UniProtKB/TrEMBL
      Q7ZVC1
      Related
      ENSDARP00000137887.2, ENSDART00000169779.2
      Conserved Domains (5) summary
      cd09361
      Location:452 → 503
      LIM1_Enigma_like; The first LIM domain of Enigma-like family
      cd09362
      Location:511 → 562
      LIM2_Enigma_like; The second LIM domain of Enigma-like family
      cd00992
      Location:11 → 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:243 → 335
      DUF4749; Domain of unknown function (DUF4749)
      cl02475
      Location:570 → 624
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

    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_007121.7 Reference GRCz11 Primary Assembly

      Range
      1187444..1275732 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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