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    LIMS1 LIM zinc finger domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 3987, updated on 22-Apr-2024

    Summary

    Official Symbol
    LIMS1provided by HGNC
    Official Full Name
    LIM zinc finger domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:6616
    See related
    Ensembl:ENSG00000169756 MIM:602567; AllianceGenome:HGNC:6616
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PINCH; PINCH1; PINCH-1
    Summary
    The protein encoded by this gene is an adaptor protein which contains five LIM domains, or double zinc fingers. The protein is likely involved in integrin signaling through its LIM domain-mediated interaction with integrin-linked kinase, found in focal adhesion plaques. It is also thought to act as a bridge linking integrin-linked kinase to NCK adaptor protein 2, which is involved in growth factor receptor kinase signaling pathways. Its localization to the periphery of spreading cells also suggests that this protein may play a role in integrin-mediated cell adhesion or spreading. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
    Expression
    Ubiquitous expression in endometrium (RPKM 18.5), adrenal (RPKM 16.0) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LIMS1 in Genome Data Viewer
    Location:
    2q12.3
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (108533671..108687246)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (108994291..109147842)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (109150127..109303702)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene small integral membrane protein 12 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr2:109064602-109065584 and GRCh37_chr2:109065585-109066566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:109066652-109067152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:109067153-109067653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16343 Neighboring gene GRIP and coiled-coil domain containing 2 Neighboring gene 2q12.3 distal recombination region Neighboring gene GCC2 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 7983 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16344 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:109191556-109192512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16345 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:109210352-109211551 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16348 Neighboring gene NANOG hESC enhancer GRCh37_chr2:109225689-109226190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16349 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:109252737-109253311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:109271409-109272023 Neighboring gene Sharpr-MPRA regulatory region 6630 Neighboring gene LIMS1 antisense RNA 1 Neighboring gene cytochrome c oxidase subunit 7B, mitochondrial-like Neighboring gene ribosomal protein L10 pseudogene 5

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    involved_in cellular response to transforming growth factor beta stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    NOT involved_in epithelial to mesenchymal transition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in establishment of protein localization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of GTPase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of canonical NF-kappaB signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell-substrate adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of focal adhesion assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of gene expression 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
     
    involved_in positive regulation of substrate adhesion-dependent cell spreading IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT involved_in regulation of epithelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in tumor necrosis factor-mediated signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in cell-cell junction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cell-cell junction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in focal adhesion HDA PubMed 
    is_active_in focal adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    colocalizes_with focal adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in focal adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     

    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
    particularly interesting new Cys-His protein 1
    renal carcinoma antigen NY-REN-48
    senescent cell antigen

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001193482.2NP_001180411.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform c

      Status: REVIEWED

      Source sequence(s)
      AC010095, AC012487, AF527762, AL110164
      Consensus CDS
      CCDS54383.1
      UniProtKB/Swiss-Prot
      P48059
      Related
      ENSP00000386926.1, ENST00000410093.5
      Conserved Domains (5) summary
      cd09331
      Location:1472
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:75126
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:139189
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:195248
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:256309
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    2. NM_001193483.3NP_001180412.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform d

      See identical proteins and their annotated locations for NP_001180412.1

      Status: REVIEWED

      Source sequence(s)
      AC010095, AC012487
      Consensus CDS
      CCDS54382.1
      UniProtKB/Swiss-Prot
      P48059
      Related
      ENSP00000437912.1, ENST00000544547.6
      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
    3. NM_001193484.2NP_001180413.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform e

      See identical proteins and their annotated locations for NP_001180413.1

      Status: REVIEWED

      Source sequence(s)
      AC010095, AF527761, AK304260, AL110164
      Consensus CDS
      CCDS54384.1
      UniProtKB/Swiss-Prot
      P48059
      Related
      ENSP00000387264.1, ENST00000409441.5
      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
    4. NM_001193485.3NP_001180414.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform a

      See identical proteins and their annotated locations for NP_001180414.1

      Status: REVIEWED

      Source sequence(s)
      AC010095, AF527759, AL110164
      Consensus CDS
      CCDS54385.1
      UniProtKB/Swiss-Prot
      P48059
      Related
      ENSP00000337598.4, ENST00000338045.7
      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
    5. NM_001193488.2NP_001180417.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform b

      See identical proteins and their annotated locations for NP_001180417.1

      Status: REVIEWED

      Source sequence(s)
      AC010095, AC012487, AF527763, AL110164, BC005341
      Consensus CDS
      CCDS2078.1
      UniProtKB/Swiss-Prot
      B2RAJ4, B7Z483, B7Z7R3, B7Z907, P48059, Q53TE0, Q9BS44
      Related
      ENSP00000376987.1, ENST00000393310.5
      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
    6. NM_001371494.1NP_001358423.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform f

      Status: REVIEWED

      Source sequence(s)
      AC010095
      Consensus CDS
      CCDS92833.1
      UniProtKB/TrEMBL
      A0A8Q3WKK6
      Related
      ENSP00000511985.1, ENST00000695522.1
      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
    7. NM_001371495.1NP_001358424.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform g

      Status: REVIEWED

      Source sequence(s)
      AC010095, AC012487
      Consensus CDS
      CCDS92830.1
      UniProtKB/TrEMBL
      A0A8Q3WKP0
      Related
      ENSP00000511980.1, ENST00000695517.1
      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
    8. NM_001371496.1NP_001358425.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform h

      Status: REVIEWED

      Source sequence(s)
      AC010095, AC012487
      Consensus CDS
      CCDS92829.1
      UniProtKB/TrEMBL
      A0A8Q3WKI3
      Related
      ENSP00000511979.1, ENST00000695516.1
      Conserved Domains (5) summary
      cd09331
      Location:3189
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:92143
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:156206
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:212265
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:273326
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    9. NM_001371497.1NP_001358426.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform i

      Status: REVIEWED

      Source sequence(s)
      AC010095, AC012487
      Consensus CDS
      CCDS92831.1
      UniProtKB/TrEMBL
      A0A8Q3WKJ2
      Related
      ENSP00000511982.1, ENST00000695519.1
      Conserved Domains (5) summary
      cd09331
      Location:1775
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:78129
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:142192
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:198251
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:259312
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    10. NM_001371498.1NP_001358427.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform b

      Status: REVIEWED

      Source sequence(s)
      AC010095, AC012487
      Consensus CDS
      CCDS2078.1
      UniProtKB/Swiss-Prot
      B2RAJ4, B7Z483, B7Z7R3, B7Z907, P48059, Q53TE0, Q9BS44
      Related
      ENSP00000511981.1, ENST00000695518.1
      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
    11. NM_001371499.1NP_001358428.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform j

      Status: REVIEWED

      Source sequence(s)
      AC010095
      Consensus CDS
      CCDS92832.1
      UniProtKB/TrEMBL
      B2R5G4, F8WC86
      Related
      ENSP00000399267.2, ENST00000414829.2
      Conserved Domains (1) summary
      cd09331
      Location:72114
      LIM1_PINCH; The first LIM domain of protein PINCH
    12. NM_001371500.1NP_001358429.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform k

      Status: REVIEWED

      Source sequence(s)
      AC010095
      UniProtKB/TrEMBL
      F8WE10
      Conserved Domains (1) summary
      cd09331
      Location:4789
      LIM1_PINCH; The first LIM domain of protein PINCH
    13. NM_001394896.1NP_001381825.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform l

      Status: REVIEWED

      Source sequence(s)
      AC010095, AC012487
      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
    14. NM_001394897.1NP_001381826.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform m

      Status: REVIEWED

      Source sequence(s)
      AC010095, AC012487
      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
    15. NM_001394898.1NP_001381827.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform n

      Status: REVIEWED

      Source sequence(s)
      AC010095, AC012487
      Conserved Domains (1) summary
      cd09331
      Location:3173
      LIM1_PINCH; The first LIM domain of protein PINCH
    16. NM_004987.6NP_004978.2  LIM and senescent cell antigen-like-containing domain protein 1 isoform b

      See identical proteins and their annotated locations for NP_004978.2

      Status: REVIEWED

      Source sequence(s)
      AC010095, AL110164, BG942518, U09284
      Consensus CDS
      CCDS2078.1
      UniProtKB/Swiss-Prot
      B2RAJ4, B7Z483, B7Z7R3, B7Z907, P48059, Q53TE0, Q9BS44
      Related
      ENSP00000331775.6, ENST00000332345.10
      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

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      108533671..108687246
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      108994291..109147842
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)