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

Gene ID: 3987, updated on 8-Jul-2018
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; Vega:OTTHUMG00000130983
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
See LIMS1 in Genome Data Viewer
Location:
2q12.3
Exon count:
18
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (108534355..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 LIMS1 antisense RNA 1 Neighboring gene cytochrome c oxidase subunit 7B, mitochondrial pseudogene Neighboring gene ribosomal protein L10 pseudogene 5

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Products Interactant Other Gene Complex Source Pubs Description

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 
Component Evidence Code Pubs
cell-cell junction IMP
Inferred from Mutant Phenotype
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
focal adhesion HDA 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
 
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

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

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (c) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC010095, AF527762, AL110164
    Consensus CDS
    CCDS54383.1
    UniProtKB/Swiss-Prot
    P48059
    Related
    ENSP00000386926.1, OTTHUMP00000203429, ENST00000410093.5, OTTHUMT00000330221
    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_001193483.2NP_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

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (d) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC010095, AK296992, AL110164, DC401794
    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_001193484.1NP_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

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (e) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC010095, AF527761, AK304260, AL110164
    Consensus CDS
    CCDS54384.1
    UniProtKB/Swiss-Prot
    P48059
    Related
    ENSP00000387264.1, OTTHUMP00000203426, ENST00000409441.5, OTTHUMT00000330218
    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_001193485.2NP_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

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC010095, AF527759, AL110164
    Consensus CDS
    CCDS54385.1
    UniProtKB/Swiss-Prot
    P48059
    Related
    ENSP00000337598.4, OTTHUMP00000203448, ENST00000338045.7, OTTHUMT00000330254
    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_001193488.1NP_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

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
    Source sequence(s)
    AC010095, AF527763, AL110164, BC005341
    Consensus CDS
    CCDS2078.1
    UniProtKB/Swiss-Prot
    P48059
    Related
    ENSP00000376987.1, OTTHUMP00000161608, ENST00000393310.5, OTTHUMT00000253596
    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_004987.5NP_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

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
    Source sequence(s)
    AC010095, AL110164, BG942518, U09284
    Consensus CDS
    CCDS2078.1
    UniProtKB/Swiss-Prot
    P48059
    Related
    ENSP00000331775.6, OTTHUMP00000203425, ENST00000332345.10, OTTHUMT00000330217
    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 Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    108534355..108687246
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004092.1XP_016859581.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

  2. XM_005263949.1XP_005264006.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X3

    See identical proteins and their annotated locations for XP_005264006.1

    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
  3. XM_017004094.1XP_016859583.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

  4. XM_005263951.5XP_005264008.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X4

    See identical proteins and their annotated locations for XP_005264008.1

    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
  5. XM_005263950.2XP_005264007.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X4

    See identical proteins and their annotated locations for XP_005264007.1

    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
  6. XM_024452885.1XP_024308653.1  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
  7. XM_005263948.4XP_005264005.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X2

    See identical proteins and their annotated locations for XP_005264005.1

    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
  8. XM_017004093.1XP_016859582.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

  9. XM_017004091.1XP_016859580.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

  10. XM_005263946.1XP_005264003.1  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
  11. XM_017004095.1XP_016859584.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X7

  12. XM_017004096.1XP_016859585.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X8

    UniProtKB/TrEMBL
    F8WC86
    Related
    ENSP00000399267.2, OTTHUMP00000203428, ENST00000414829.2, OTTHUMT00000330220
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