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

Gene ID: 550568, updated on 4-Jan-2025

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, Jan 2025]
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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