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

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 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, Nov 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

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_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Requirement for PINCH in skeletal myoblast differentiation.
Title: Requirement for PINCH in skeletal myoblast differentiation.
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.
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.
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.
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.
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.
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.
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.
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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

UniSTS:470540 (e-PCR)
- UniSTS:470540

Lims1 (e-PCR), detects polymorphism
- UniSTS:470540

NoName (e-PCR)
- UniSTS:224541

NoName (e-PCR)
- UniSTS:236355

AI507642 (e-PCR)
- UniSTS:180041

AW551584 (e-PCR)
- UniSTS:180043

AU021743 (e-PCR)
- UniSTS:208518

Lims1l (e-PCR), detects polymorphism
- UniSTS:143780

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
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
is_active_in focal adhesion	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)

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
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
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
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
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
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

NC_000076.7 Reference GRCm39 C57BL/6J

Range

58159164..58260513

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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