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    Lims1 LIM and senescent cell antigen-like domains 1 [ Mus musculus (house mouse) ]

    Gene ID: 110829, updated on 5-Feb-2019

    Summary

    Official Symbol
    Lims1provided by MGI
    Official Full Name
    LIM and senescent cell antigen-like domains 1provided by MGI
    Primary source
    MGI:MGI:1195263
    See related
    Ensembl:ENSMUSG00000019920
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    PINCH; Lims1l; PINCH1; AI507642; AU021743; AW551584; 2310016J22Rik; 4921524A02Rik; C430041B13Rik
    Expression
    Ubiquitous expression in bladder adult (RPKM 9.3), liver E14 (RPKM 7.2) and 26 other tissues See more
    Orthologs

    Genomic context

    See Lims1 in Genome Data Viewer
    Location:
    10 B4; 10 29.31 cM
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 10 NC_000076.6 (58323434..58424691)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 10 NC_000076.5 (57786295..57887437)

    Chromosome 10 - NC_000076.6Genomic Context describing neighboring genes Neighboring gene GRIP and coiled-coil domain containing 2 Neighboring gene predicted gene, 40668 Neighboring gene RAN binding protein 2 Neighboring gene coiled-coil domain containing 138 Neighboring gene predicted gene, 18042

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
     
    zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    cell-cell adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell-cell junction organization IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    cell-matrix adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    chordate embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    establishment of protein localization ISO
    Inferred from Sequence Orthology
    more info
     
    establishment or maintenance of cell polarity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of apoptotic process IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of epithelial cell proliferation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of hepatocyte proliferation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of neural precursor cell proliferation IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    negative regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of GTPase activity ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of integrin-mediated signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of substrate adhesion-dependent cell spreading ISO
    Inferred from Sequence Orthology
    more info
     
    protein heterooligomerization ISO
    Inferred from Sequence Orthology
    more info
     
    tumor necrosis factor-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    cell junction IEA
    Inferred from Electronic Annotation
    more info
     
    cell-cell junction ISO
    Inferred from Sequence Orthology
    more info
     
    focal adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    focal adhesion ISO
    Inferred from Sequence Orthology
    more info
     
    colocalizes_with focal adhesion ISO
    Inferred from Sequence Orthology
    more info
     
    membrane 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 ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    LIM and senescent cell antigen-like-containing domain protein 1
    Names
    particularly interesting new Cys-His protein 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_001193303.1NP_001180232.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform 3

      See identical proteins and their annotated locations for NP_001180232.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has multiple differences, compared to variant 1. It encodes isoform 3, which is longer and has distinct N- and C-termini, compared to isoform 1.
      Source sequence(s)
      AC155323, AK009390
      Consensus CDS
      CCDS56703.1
      UniProtKB/TrEMBL
      Q9D7B2
      Related
      ENSMUSP00000020077.3, ENSMUST00000020077.10
      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
    2. NM_001346676.1NP_001333605.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC155323, BQ554039, CN525761
      Consensus CDS
      CCDS83697.1
      UniProtKB/TrEMBL
      E9QP62
      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
    3. NM_001359115.1NP_001346044.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AA989985, AC155323, AW493431, BY714471, CN461732
      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
    4. NM_001359116.1NP_001346045.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC155323, AK152679, BY210263
      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
    5. NM_026148.4NP_080424.2  LIM and senescent cell antigen-like-containing domain protein 1 isoform 1

      See identical proteins and their annotated locations for NP_080424.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AC155323, AK152679, BY714471
      Consensus CDS
      CCDS23860.1
      UniProtKB/Swiss-Prot
      Q99JW4
      UniProtKB/TrEMBL
      A0A0R4J005
      Related
      ENSMUSP00000020078.6, ENSMUST00000020078.13
      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
    6. NM_201242.1NP_957694.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate exon in the 5' UTR and 5' coding region, compared to variant 1. It encodes isoform 2, which is longer and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AC155323
      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: Mus musculus Annotation Release 106

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000076.6 Reference GRCm38.p4 C57BL/6J

      Range
      58323434..58424691
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006513071.2XP_006513134.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X4

      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_006513072.2XP_006513135.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X5

      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_006513073.2XP_006513136.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

      UniProtKB/Swiss-Prot
      Q99JW4
      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_006513070.3XP_006513133.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X3

      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
    5. XM_006513074.3XP_006513137.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X7

      Conserved Domains (1) summary
      cd09331
      Location:72114
      LIM1_PINCH; The first LIM domain of protein PINCH
    6. XM_006513068.3XP_006513131.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X1

      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
    7. XM_006513069.3XP_006513132.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X2

      Related
      ENSMUSP00000101108.1, ENSMUST00000105468.1
      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
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