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

    Gene ID: 110829, updated on 9-Dec-2024

    Summary

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    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 AllianceGenome:MGI:1195263
    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; 2310016J22Rik; 4921524A02Rik; C430041B13Rik
    Summary
    Predicted to enable protein kinase binding activity and zinc ion binding activity. Acts upstream of or within several processes, including negative regulation of cell population proliferation; negative regulation of hepatocyte apoptotic process; and positive regulation of integrin-mediated signaling pathway. Located in focal adhesion. Is expressed in several structures, including alimentary system; central nervous system; early conceptus; genitourinary system; and liver and biliary system. Orthologous to human LIMS1 (LIM zinc finger domain containing 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in bladder adult (RPKM 9.3), liver E14 (RPKM 7.2) and 26 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Lims1 in Genome Data Viewer
    Location:
    10 B4; 10 29.31 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (58159164..58260513)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (58323342..58424691)

    Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E2935 Neighboring gene double homeobox family member 5 Neighboring gene GRIP and coiled-coil domain containing 2 Neighboring gene STARR-positive B cell enhancer ABC_E575 Neighboring gene STARR-seq mESC enhancer starr_26754 Neighboring gene STARR-positive B cell enhancer ABC_E6854 Neighboring gene predicted gene, 23058 Neighboring gene STARR-positive B cell enhancer ABC_E2936 Neighboring gene RAN binding protein 2 Neighboring gene STARR-positive B cell enhancer ABC_E10608 Neighboring gene coiled-coil domain containing 138 Neighboring gene STARR-positive B cell enhancer ABC_E10609 Neighboring gene STARR-seq mESC enhancer starr_26758 Neighboring gene predicted gene, 18042

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. PINCH-1 promotes Δ(1)-pyrroline-5-carboxylate synthase expression and contributes to proline metabolic reprogramming in lung adenocarcinoma. Cui C, et al. Amino Acids, 2021 Dec. PMID 34283311
    2. Mechanical stretch inhibits oxidized low density lipoprotein-induced apoptosis in vascular smooth muscle cells by up-regulating integrin alphavbeta3 and stablization of PINCH-1. Cheng J, et al. J Biol Chem, 2007 Nov 23. PMID 17878168
    3. A new LIM protein containing an autoepitope homologous to "senescent cell antigen". Rearden A. Biochem Biophys Res Commun, 1994 Jun 30. PMID 7517666
    4. Requirement for PINCH in skeletal myoblast differentiation. Liao H, et al. Cell Tissue Res, 2023 Jan. PMID 36385586, Free PMC Article
    5. PINCH-1 promotes IGF-1 receptor expression and skin cancer progression through inhibition of the GRB10-NEDD4 complex. Wang X, et al. Theranostics, 2022. PMID 35401828, Free PMC Article

    See all (75) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The bone-liver interaction modulates immune and hematopoietic function through Pinch-Cxcl12-Mbl2 pathway.
      Title: The bone-liver interaction modulates immune and hematopoietic function through Pinch-Cxcl12-Mbl2 pathway.
    2. Requirement for PINCH in skeletal myoblast differentiation.
      Title: Requirement for PINCH in skeletal myoblast differentiation.
    3. PINCH-1 promotes Delta(1)-pyrroline-5-carboxylate synthase expression and contributes to proline metabolic reprogramming in lung adenocarcinoma.
      Title: PINCH-1 promotes Δ(1)-pyrroline-5-carboxylate synthase expression and contributes to proline metabolic reprogramming in lung adenocarcinoma.
    4. PINCH-1 interacts with myoferlin to promote breast cancer progression and metastasis.
      Title: PINCH-1 interacts with myoferlin to promote breast cancer progression and metastasis.
    5. PINCH-1 regulates mitochondrial dynamics to promote proline synthesis and tumor growth.
      Title: PINCH-1 regulates mitochondrial dynamics to promote proline synthesis and tumor growth.
    6. findings suggest that PINCH-1 regulates integrin-mediated adhesion of keratinocytes through the interactions with ILK as well as EPLIN.
      Title: The focal adhesion protein PINCH-1 associates with EPLIN at integrin adhesion sites.
    7. Rsu-1 expression is dramatically decreased in PINCH double knockout mouse livers.
      Title: Role of PINCH and its partner tumor suppressor Rsu-1 in regulating liver size and tumorigenesis.
    8. PINCH is increased and binds to hp-Tau. These studies address a new mechanism by which AD and HIV may intersect and identify PINCH as a contributing factor to the accumulation of hyperphosphorylated Tau.
      Title: PINCH in the cellular stress response to tau-hyperphosphorylation.
    9. PINCH-1 inhibits JNK-mediated apoptosis by stabilising the PINCH-1 binding protein RSU-1 and promotes Bcl-2-dependent pro-survival signalling downstream of integrins.
      Title: PINCH-1 promotes Bcl-2-dependent survival signalling and inhibits JNK-mediated apoptosis in the primitive endoderm.
    10. Data suggest that the adapter protein PINCH1 critically participates in the regulation of the cellular radiosensitivity of normal and malignant cells similarly under adhesion and suspension conditions.
      Title: The role of the focal adhesion protein PINCH1 for the radiosensitivity of adhesion and suspension cell cultures.
    Submit: New GeneRIF Correction See all GeneRIFs (21)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (2) 
    • Targeted (5)  1 citation

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables actin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cell-cell adhesion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cell-cell junction organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cell-cell junction organization IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within cell-matrix adhesion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of cholangiocyte proliferation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within chordate embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in establishment of protein localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within establishment or maintenance of cell polarity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of hepatocyte apoptotic process IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of integrin-mediated signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of cholangiocyte proliferation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of hepatocyte apoptotic process IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of hepatocyte proliferation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of neural precursor cell proliferation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of neural precursor cell proliferation IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in positive regulation of GTPase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of canonical NF-kappaB signal transduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of cell-substrate adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of focal adhesion assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of integrin-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of integrin-mediated signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in positive regulation of substrate adhesion-dependent cell spreading IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of substrate adhesion-dependent cell spreading ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in tumor necrosis factor-mediated signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cell-cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cell-cell junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in focal adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    colocalizes_with focal adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in focal adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of protein-containing complex ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    LIM and senescent cell antigen-like-containing domain protein 1
    Names
    particularly interesting new Cys-His protein 1

    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_001193303.1 → NP_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
      Q4ZJB3, Q9D7B2
      Related
      ENSMUSP00000020077.4, ENSMUST00000020077.11
      Conserved Domains (5) summary
      cd09331
      Location:72 → 130
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:133 → 184
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:197 → 247
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:253 → 306
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:314 → 367
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    2. NM_001346676.1 → NP_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, Q4ZJB3
      Related
      ENSMUSP00000101108.2, ENSMUST00000105468.2
      Conserved Domains (5) summary
      cd09331
      Location:72 → 130
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:133 → 184
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:197 → 247
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:253 → 306
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:314 → 367
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    3. NM_001359115.1 → NP_001346044.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AA989985, AC155323, AW493431, BY714471, CN461732
      UniProtKB/TrEMBL
      A8CVP4
      Conserved Domains (5) summary
      cd09331
      Location:22 → 80
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:83 → 134
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:147 → 197
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:203 → 256
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:264 → 317
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    4. NM_001359116.1 → NP_001346045.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC155323, AK152679, BY210263
      UniProtKB/Swiss-Prot
      Q3UAT7, Q8BTR6, Q99JW4, Q9D5T4
      UniProtKB/TrEMBL
      A8CVP4
      Conserved Domains (5) summary
      cd09331
      Location:10 → 68
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:71 → 122
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:135 → 185
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:191 → 244
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:252 → 305
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    5. NM_026148.4 → NP_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/TrEMBL
      A0A0R4J005, A8CVP4
      Related
      ENSMUSP00000020078.7, ENSMUST00000020078.14
      Conserved Domains (5) summary
      cd09331
      Location:22 → 80
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:83 → 134
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:147 → 197
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:203 → 256
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:264 → 317
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    6. NM_201242.1 → NP_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
      Consensus CDS
      CCDS88008.1
      UniProtKB/TrEMBL
      A0A5F8MPJ3, A8CVP1
      Related
      ENSMUSP00000158997.2, ENSMUST00000238939.2
      Conserved Domains (5) summary
      cd09331
      Location:47 → 105
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:108 → 159
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:172 → 222
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:228 → 281
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:289 → 342
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000076.7 Reference GRCm39 C57BL/6J

      Range
      58159164..58260513
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030244824.1 → XP_030100684.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X3

      UniProtKB/TrEMBL
      A8CVP4
      Conserved Domains (5) summary
      cd09331
      Location:22 → 80
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:83 → 134
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:147 → 197
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:203 → 256
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:264 → 317
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    2. XM_036155505.1 → XP_036011398.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

      UniProtKB/TrEMBL
      A8CVP4
      Conserved Domains (4) summary
      cd09332
      Location:7 → 58
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:71 → 121
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:127 → 180
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:188 → 241
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    3. XM_036155504.1 → XP_036011397.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X5

      UniProtKB/Swiss-Prot
      Q3UAT7, Q8BTR6, Q99JW4, Q9D5T4
      UniProtKB/TrEMBL
      A8CVP4
      Conserved Domains (5) summary
      cd09331
      Location:10 → 68
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:71 → 122
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:135 → 185
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:191 → 244
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:252 → 305
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    4. XM_006513072.2 → XP_006513135.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X4

      UniProtKB/TrEMBL
      A8CVP4
      Conserved Domains (5) summary
      cd09331
      Location:10 → 68
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:71 → 122
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:135 → 185
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:191 → 244
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:252 → 305
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    5. XM_006513070.5 → XP_006513133.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X2

      UniProtKB/TrEMBL
      A8CVP1
      Conserved Domains (5) summary
      cd09331
      Location:47 → 105
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:108 → 159
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:172 → 222
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:228 → 281
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:289 → 342
      LIM5_PINCH; The fifth LIM domain of protein PINCH

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

      Conserved Domains (1) summary
      cd09331
      Location:72 → 114
      LIM1_PINCH; The first LIM domain of protein PINCH

    7. XM_006513068.4 → XP_006513131.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X1

      UniProtKB/TrEMBL
      Q4ZJB3
      Conserved Domains (5) summary
      cd09331
      Location:72 → 130
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:133 → 184
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:197 → 247
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:253 → 306
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:314 → 367
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99JW4.3 GenPept UniProtKB/Swiss-Prot:Q99JW4

    Gene LinkOut

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