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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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