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    Lims1 LIM zinc finger domain containing 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 499443, updated on 19-Mar-2019

    Summary

    Official Symbol
    Lims1provided by RGD
    Official Full Name
    LIM zinc finger domain containing 1provided by RGD
    Primary source
    RGD:1560732
    See related
    Ensembl:ENSRNOG00000037765
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Pinch1; RGD1560732
    Expression
    Biased expression in Lung (RPKM 216.0), Heart (RPKM 197.1) and 9 other tissues See more
    Orthologs

    Genomic context

    See Lims1 in Genome Data Viewer
    Location:
    20q11
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (27895981..28004767)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 20 NC_005119.3 (29715580..29824252)

    Chromosome 20 - NC_005119.4Genomic Context describing neighboring genes Neighboring gene similar to eukaryotic translation elongation factor 1 alpha 2 Neighboring gene GRIP and coiled-coil domain containing 2 Neighboring gene RAN binding protein 2 Neighboring gene coiled-coil domain containing 138

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein domain specific binding IC
    Inferred by Curator
    more info
    PubMed 
    protein kinase binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
     
    zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    cell-cell adhesion ISO
    Inferred from Sequence Orthology
    more info
     
    cell-cell junction organization ISO
    Inferred from Sequence Orthology
    more info
     
    cell-matrix adhesion ISO
    Inferred from Sequence Orthology
    more info
     
    cellular response to transforming growth factor beta stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to transforming growth factor beta stimulus ISO
    Inferred from Sequence Orthology
    more info
     
    chordate embryonic development ISO
    Inferred from Sequence Orthology
    more info
     
    NOT epithelial to mesenchymal transition ISO
    Inferred from Sequence Orthology
    more info
     
    establishment of protein localization IEA
    Inferred from Electronic Annotation
    more info
     
    establishment of protein localization ISO
    Inferred from Sequence Orthology
    more info
     
    establishment or maintenance of cell polarity ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of epithelial cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of hepatocyte proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of neural precursor cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    negative regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of GTPase activity IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of GTPase activity ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of NIK/NF-kappaB signaling IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of NIK/NF-kappaB signaling ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of cell-substrate adhesion ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of focal adhesion assembly IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of focal adhesion assembly ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of integrin-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of substrate adhesion-dependent cell spreading IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of substrate adhesion-dependent cell spreading ISO
    Inferred from Sequence Orthology
    more info
     
    protein heterooligomerization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein heterooligomerization IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    NOT regulation of epithelial cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    tumor necrosis factor-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    tumor necrosis factor-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    cell-cell junction IEA
    Inferred from Electronic Annotation
    more info
     
    cell-cell junction ISO
    Inferred from Sequence Orthology
    more info
     
    focal adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    focal adhesion ISO
    Inferred from Sequence Orthology
    more info
     
    colocalizes_with focal adhesion ISO
    Inferred from Sequence Orthology
    more info
     
    perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    LIM and senescent cell antigen-like-containing domain protein 1
    Names
    LIM and senescent cell antigen-like domains 1
    LIM-type zinc finger domains 1

    NCBI Reference Sequences (RefSeq)

    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_001145456.1NP_001138928.1  LIM and senescent cell antigen-like-containing domain protein 1

      See identical proteins and their annotated locations for NP_001138928.1

      Status: PROVISIONAL

      Source sequence(s)
      FJ640984
      UniProtKB/TrEMBL
      C0KUC5
      Related
      ENSRNOP00000062647.1, ENSRNOT00000064288.3
      Conserved Domains (5) summary
      cd09331
      Location:47105
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:108159
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:172222
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:228281
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:289342
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    RefSeqs of Annotated Genomes: Rattus norvegicus 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 Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005119.4 Reference Rnor_6.0 Primary Assembly

      Range
      27895981..28004767
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006256389.3XP_006256451.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

      Conserved Domains (5) summary
      cd09331
      Location:2280
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:83134
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:147197
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:203256
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:264317
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    2. XM_006256390.3XP_006256452.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X7

      Conserved Domains (5) summary
      cd09331
      Location:1068
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:71122
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:135185
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:191244
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:252305
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    3. XM_006256391.3XP_006256453.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X8

      Conserved Domains (5) summary
      cd09331
      Location:1068
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:71122
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:135185
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:191244
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:252305
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    4. XM_017601761.1XP_017457250.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X1

    5. XM_017601762.1XP_017457251.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X1

    6. XM_006256388.3XP_006256450.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X5

      Conserved Domains (5) summary
      cd09331
      Location:47105
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:108159
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:172222
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:228281
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:289342
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    7. XM_017601763.1XP_017457252.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X3

    8. XM_006256385.3XP_006256447.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X2

      See identical proteins and their annotated locations for XP_006256447.1

      Conserved Domains (5) summary
      cd09331
      Location:72130
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:133184
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:197247
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:253306
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:314367
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    9. XM_006256387.3XP_006256449.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X4

      See identical proteins and their annotated locations for XP_006256449.1

      UniProtKB/TrEMBL
      C0KUC6
      Related
      ENSRNOP00000073371.1, ENSRNOT00000092075.1
      Conserved Domains (5) summary
      cd09331
      Location:72130
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:133184
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:197247
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:253306
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:314367
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    Alternate Rn_Celera

    Genomic

    1. AC_000088.1 Alternate Rn_Celera

      Range
      27819971..27867155
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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