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

Gene ID: 3987, updated on 29-Nov-2020

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
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

Genomic context

See LIMS1 in Genome Data Viewer
Location:
2q12.3
Exon count:
19
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (108533671..108687246)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (109150811..109303702)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes 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 6630 Neighboring gene LIMS1 antisense RNA 1 Neighboring gene cytochrome c oxidase subunit 7B, mitochondrial pseudogene 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

Homology

Gene Ontology Provided by GOA

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

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, ENST00000544547.5
    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
    P48059
    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
    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
    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
    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
    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
    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
    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
    Conserved Domains (1) summary
    cd09331
    Location:4789
    LIM1_PINCH; The first LIM domain of protein PINCH
  13. 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
    P48059
    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: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

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