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

Gene ID: 554019, updated on 11-Apr-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 protein kinase B signaling. 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, Apr 2022]
Orthologs
all
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Genomic context

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Location:
chromosome: 11
Exon count:
11
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 11 NC_007122.7 (33598614..33618583, 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 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
  • 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: Danio rerio Annotation Release 106 details...Open this link in a new tab

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
    33598614..33618583 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021479621.1 → 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_021479620.1 → 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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