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

Gene ID: 110829, updated on 8-Dec-2022

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 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 cell-matrix adhesion; negative regulation of cell population proliferation; 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, Apr 2022]
Expression
Ubiquitous expression in bladder adult (RPKM 9.3), liver E14 (RPKM 7.2) and 26 other tissues See more
Orthologs
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Genomic context

See Lims1 in Genome Data Viewer
Location:
10 B4; 10 29.31 cM
Exon count:
14
Annotation release Status Assembly Chr Location
109 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 predicted gene 9919 Neighboring gene GRIP and coiled-coil domain containing 2 Neighboring gene predicted gene, 23058 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 Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
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
PubMed 
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
PubMed 
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 NIK/NF-kappaB signaling 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
PubMed 
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
PubMed 
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
located_in cell junction IEA
Inferred from Electronic Annotation
more info
 
is_active_in cell-cell junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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 membrane IEA
Inferred from Electronic Annotation
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

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

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_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
    A0A8C6GTP8, Q9D7B2
    Related
    ENSMUSP00000020077.4, ENSMUST00000020077.11
    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
    A0A6P5QGP9, E9QP62
    Related
    ENSMUSP00000101108.2, ENSMUST00000105468.2
    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
    UniProtKB/TrEMBL
    A0A6P5Q9Z3
    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
    UniProtKB/Swiss-Prot
    Q9D5T4
    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, A0A6P5QMW4
    Related
    ENSMUSP00000020078.7, ENSMUST00000020078.14
    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
    Consensus CDS
    CCDS88008.1
    UniProtKB/TrEMBL
    A0A5F8MPJ3
    Related
    ENSMUSP00000158997.2, ENSMUST00000238939.2
    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 109 details...Open this link in a new tab

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_030244824.1XP_030100684.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X3

    UniProtKB/TrEMBL
    A0A8C6MTG4
    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_036155505.1XP_036011398.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

    Conserved Domains (4) summary
    cd09332
    Location:758
    LIM2_PINCH; The second LIM domain of protein PINCH
    cd09333
    Location:71121
    LIM3_PINCH; The third LIM domain of protein PINCH
    cd09334
    Location:127180
    LIM4_PINCH; The fourth LIM domain of protein PINCH
    cd09335
    Location:188241
    LIM5_PINCH; The fifth LIM domain of protein PINCH
  3. XM_036155504.1XP_036011397.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X5

    UniProtKB/Swiss-Prot
    Q9D5T4
    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_006513072.2XP_006513135.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X4

    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_006513070.5XP_006513133.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X2

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

    UniProtKB/TrEMBL
    A0A6P7RC77
    Conserved Domains (1) summary
    cd09331
    Location:72114
    LIM1_PINCH; The first LIM domain of protein PINCH
  7. XM_006513068.4XP_006513131.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X1

    UniProtKB/TrEMBL
    A0A6P7RRQ6
    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