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    lims1 LIM and senescent cell antigen-like domains 1 [ Danio rerio (zebrafish) ]

    Gene ID: 554019, updated on 2-Nov-2024

    Summary

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    Official Symbol
    lims1provided by ZNC
    Official Full Name
    LIM and senescent cell antigen-like domains 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-050522-236
    See related
    Ensembl:ENSDARG00000026985 AllianceGenome:ZFIN:ZDB-GENE-050522-236
    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
    wu:fc32c03; zgc:112533
    Summary
    Predicted to enable metal ion binding activity. Acts upstream of or within heart contraction and regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction. Located in Z disc and intercalated disc. Is expressed in EVL; hatching gland; heart; periderm; and polster. Orthologous to human LIMS1 (LIM zinc finger domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    all
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    Genomic context

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    See lims1 in Genome Data Viewer
    Location:
    chromosome: 11
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 11 NC_007122.7 (33600340..33618578, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 11 NC_007122.6 (33337538..33355778, complement)

    Chromosome 11 - NC_007122.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC103911847 Neighboring gene contactin associated protein family member 5 like Neighboring gene thrombospondin, type I, domain containing 7Bb Neighboring gene uncharacterized LOC137496717 Neighboring gene speckle type BTB/POZ protein like b

    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 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. PINCH proteins regulate cardiac contractility by modulating integrin-linked kinase-protein kinase B signaling. Meder B, et al. Mol Cell Biol, 2011 Aug. PMID 21670146, Free PMC Article
    2. The evolutionary legacy of size-selective harvesting extends from genes to populations. Uusi-Heikkilä S, et al. Evol Appl, 2015 Jul. PMID 26136825, Free PMC Article
    3. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    See all (6) 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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell-cell junction organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within heart contraction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of integrin-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of substrate adhesion-dependent cell spreading IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Z disc IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cell-cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in focal adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in focal adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intercalated disc IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    LIM and senescent cell antigen-like-containing domain protein 1
    Names
    pinch1

    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_001024389.1 → NP_001019560.1  LIM and senescent cell antigen-like-containing domain protein 1

      See identical proteins and their annotated locations for NP_001019560.1

      Status: PROVISIONAL

      Source sequence(s)
      BC095840
      UniProtKB/TrEMBL
      Q501W5
      Related
      ENSDARP00000035109.5, ENSDART00000033980.7
      Conserved Domains (5) summary
      cd09331
      Location:21 → 79
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:82 → 133
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:146 → 196
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:202 → 255
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:263 → 316
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    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_007122.7 Reference GRCz11 Primary Assembly

      Range
      33600340..33618578 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021479621.2 → XP_021335296.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A8M9QHP1
      Conserved Domains (5) summary
      cd09331
      Location:21 → 79
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:82 → 133
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:146 → 196
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:202 → 255
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:263 → 316
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    2. XM_021479620.2 → XP_021335295.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8M9QLM6
      Conserved Domains (5) summary
      cd09331
      Location:21 → 79
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:82 → 133
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:146 → 196
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:202 → 255
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:263 → 316
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    Nucleotide Protein
    Heading Accession and Version

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