LIMS1 LIM and senescent cell antigen-like domains 1 [Homo sapiens] - Gene

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Summary

Official Symbol: LIMS1provided by HGNC
Official Full Name: LIM and senescent cell antigen-like domains 1provided by HGNC
Primary source: HGNC:6616
See related: Ensembl:ENSG00000169756; HPRD:03978; 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]

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Genomic context

Location :: 2q12.3

Sequence :: Chromosome: 2; NC_000002.11 (109150811..109303702)

See LIMS1 in Epigenomics, MapViewer

Chromosome 2 - NC_000002.11 Genomic Context describing neighboring genes

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Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

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Bibliography

GeneRIFs: Gene References Into Functions What's a GeneRIF?

PINCH mRNA overexpression in colorectal carcinomas is correlated with VEGF and FAS mRNA expression
Title: PINCH mRNA overexpression in colorectal carcinomas correlated with VEGF and FAS mRNA expression.
PINCH may function as a neuron-specific host-mediated response to challenge by HIV-related factors in the CNS.
Title: Neuronal PINCH is regulated by TNF-α and is required for neurite extension.
PINCH1 can shuttle into the nucleus from cytoplasm in podocytes, wherein it interacts with WT1 and suppresses podocyte-specific gene expression.
Title: PINCH1 is transcriptional regulator in podocytes that interacts with WT1 and represses podocalyxin expression.
Review provides an overview of the current knowledge of the molecular interactions of PINCH with other components of focal adhesions and discusses its potential implication for human heart disease.
Title: Particularly interesting cysteine- and histidine-rich protein in cardiac development and remodeling.
data reveal how specific domains of PINCH-1 direct two independent pathways: one utilizing ILK to allow cell attachment, and the other recruiting Rsu-1 to activate Rac1 in order to promote cell spreading
Title: The roles of two distinct regions of PINCH-1 in the regulation of cell attachment and spreading.
PINCH staining at the tumour invasive margin was related to survival in poorly differentiated tumours but not in better differentiated tumours, indicating that the impact of PINCH on prognosis was dependent on differentiation status.
Title: Impact of PINCH expression on survival in colorectal cancer patients.
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.
Findings of increased PINCH protein in more advanced stages of human pancreatic ductal adenocarcinoma, as well as in metastatic tumours in the animal model, support the hypothesis that PINCH is an important controller of cell survival and migration.
Title: Prognostic significance of PINCH signalling in human pancreatic ductal adenocarcinoma.
PINCH expression markedly increased in tumor-associated stroma in endometrioid carcinoma compared to normal endometrium and atypical endometrial hyperplasia; results suggest PINCH seems to play a role in tumorigenesis and development of endometrial cancer
Title: PINCH protein expression in normal endometrium, atypical endometrial hyperplasia and endometrioid endometrial carcinoma.
zincs are coordinated by PINCH1 LIM1, and suggests that conformational flexibility and twisting between the 2 zinc fingers within the LIM1 domain may be important for ILK binding.
Title: The structural basis of integrin-linked kinase-PINCH interactions.

Submit: New GeneRIF Correction See all (19)

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Phenotypes

Review eQTL and phenotype association data in this region using PheGenI

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Products	Interactant	Other Gene	Source	Pubs	Description
NP_004978.2	NP_004508.1	ILK	BIND	PubMed	PINCH interacts with ILK.
NP_004978.2	NP_003572.2	NCK2	BIND	PubMed	Nck-2 interacts with PINCH
NP_004978.2	NP_066932.1	TMSB4X	BIND	PubMed	PINCH interacts with Thymosin Beta-4.
P48059	Q96KQ7	EHMT2	HPRD	PubMed
P48059	Q13418	ILK	HPRD	PubMed
P48059	O60711	LPXN	HPRD	PubMed
P48059	O43639	NCK2	HPRD	PubMed
P48059	Q9NVD7	PARVA	HPRD	PubMed
P48059	Q99708	RBBP8	HPRD	PubMed
P48059	Q15404	RSU1	HPRD	PubMed
P48059	Q9HCE7	SMURF1	HPRD	PubMed
P48059	P36897	TGFBR1	HPRD	PubMed
P48059	P62328	TMSB4X	HPRD	PubMed
BioGRID:110175	BioGRID:119378	ACP6	BioGRID	PubMed	Affinity Capture-MS
BioGRID:110175	BioGRID:116123	EHMT2	BioGRID	PubMed	Two-hybrid
BioGRID:110175	BioGRID:109824	ILK	BioGRID	PubMed	Affinity Capture-Western; Reconstituted Complex; Two-hybrid
BioGRID:110175	BioGRID:114801	LPXN	BioGRID	PubMed	Two-hybrid
BioGRID:110175	BioGRID:114020	NCK2	BioGRID	PubMed	Reconstituted Complex; Two-hybrid
BioGRID:110175	BioGRID:111867	RBBP8	BioGRID	PubMed	Two-hybrid
BioGRID:110175	BioGRID:112670	STK11	BioGRID	PubMed	Affinity Capture-MS
BioGRID:110175	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS

Function	Evidence Code	Pubs
metal ion binding	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info
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
cellular response to transforming growth factor beta stimulus	IEP Inferred from Expression Pattern more info
negative regulation of transcription, DNA-dependent	IDA Inferred from Direct Assay more info

Component	Evidence Code	Pubs
cell junction	IEA Inferred from Electronic Annotation more info
cytosol	TAS Traceable Author Statement more info
focal adhesion	IDA Inferred from Direct Assay more info
colocalizes_with focal adhesion	IDA Inferred from Direct Assay more info	PubMed
perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info
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-containing domain protein 1; renal carcinoma antigen NY-REN-48; particularly interesting new Cys-His protein 1

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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)

NM_001193482.1 → NP_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

Related

ENSP00000386926, OTTHUMP00000203429, ENST00000410093, OTTHUMT00000330221

Conserved Domains (5) summary

cd09331
Location:14 – 72
Blast Score: 213

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:75 – 126
Blast Score: 255

LIM2_PINCH; The second LIM domain of protein PINCH.

cd09333
Location:139 – 189
Blast Score: 224

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:195 – 248
Blast Score: 261

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:256 – 308
Blast Score: 237

LIM5_PINCH; The fifth LIM domain of protein PINCH
NM_001193483.2 → NP_001180412.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform d

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, ENST00000544547

Conserved Domains (5) summary

cd09331
Location:22 – 80
Blast Score: 216

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:83 – 134
Blast Score: 258

LIM2_PINCH; The second LIM domain of protein PINCH.

cd09333
Location:147 – 197
Blast Score: 226

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:203 – 256
Blast Score: 263

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:264 – 316
Blast Score: 242

LIM5_PINCH; The fifth LIM domain of protein PINCH
NM_001193484.1 → NP_001180413.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform e

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

Related

ENSP00000387264, OTTHUMP00000203426, ENST00000409441, OTTHUMT00000330218

Conserved Domains (5) summary

cd09331
Location:47 – 105
Blast Score: 219

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:108 – 159
Blast Score: 263

LIM2_PINCH; The second LIM domain of protein PINCH.

cd09333
Location:172 – 222
Blast Score: 229

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:228 – 281
Blast Score: 268

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:289 – 341
Blast Score: 246

LIM5_PINCH; The fifth LIM domain of protein PINCH
NM_001193485.2 → NP_001180414.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform a

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

Related

ENSP00000446121, ENST00000542845

Conserved Domains (5) summary

cd09331
Location:72 – 130
Blast Score: 217

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:133 – 184
Blast Score: 263

LIM2_PINCH; The second LIM domain of protein PINCH.

cd09333
Location:197 – 247
Blast Score: 229

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:253 – 306
Blast Score: 267

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:314 – 366
Blast Score: 246

LIM5_PINCH; The fifth LIM domain of protein PINCH
NM_001193488.1 → NP_001180417.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform b

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, OTTHUMP00000161608, ENST00000393310, OTTHUMT00000253596

Conserved Domains (5) summary

cd09331
Location:10 – 68
Blast Score: 213

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:71 – 122
Blast Score: 256

LIM2_PINCH; The second LIM domain of protein PINCH.

cd09333
Location:135 – 185
Blast Score: 224

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:191 – 244
Blast Score: 261

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:252 – 304
Blast Score: 238

LIM5_PINCH; The fifth LIM domain of protein PINCH
NM_004987.5 → NP_004978.2 LIM and senescent cell antigen-like-containing domain protein 1 isoform b

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, OTTHUMP00000203425, ENST00000332345, OTTHUMT00000330217

Conserved Domains (5) summary

cd09331
Location:10 – 68
Blast Score: 213

LIM1_PINCH; The first LIM domain of protein PINCH

cd09332
Location:71 – 122
Blast Score: 256

LIM2_PINCH; The second LIM domain of protein PINCH.

cd09333
Location:135 – 185
Blast Score: 224

LIM3_PINCH; The third LIM domain of protein PINCH

cd09334
Location:191 – 244
Blast Score: 261

LIM4_PINCH; The fourth LIM domain of protein PINCH

cd09335
Location:252 – 304
Blast Score: 238

LIM5_PINCH; The fifth LIM domain of protein PINCH

RefSeqs of Annotated Genomes: Build 37.3

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

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000002.11 Reference GRCh37.p5 Primary Assembly

Range

109150811..109303702

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000134.1 Alternate HuRef

Range

102803913..102903724

Download

GenBank, FASTA, Sequence Viewer (Graphics)

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Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AC010095.6	AAY14983.1
genomic	AC012487.12 (127679..156601)	None
genomic	CH471182.2	EAW53877.1
		EAW53878.1
		EAW53879.1
		EAW53880.1
genomic	HI179074.1	CBX53845.1
mRNA	AF527759.1	None
mRNA	AF527760.1	None
mRNA	AF527761.1	None
mRNA	AF527762.1	None
mRNA	AF527763.1	None
mRNA	AK025661.1	None
mRNA	AK098109.1	None
mRNA	AK296992.1	BAH12469.1
mRNA	AK302411.1	BAH13699.1
mRNA	AK304260.1	BAH14143.1
mRNA	AK310547.1	None
mRNA	AK314217.1	BAG36891.1
mRNA	AL110164.1	None
mRNA	BC005341.1	AAH05341.1
mRNA	BC015843.1	None
mRNA	BC022365.1	None
mRNA	BG942518.1	None
mRNA	DC401794.1	None
mRNA	U09284.2	AAA20086.2
other-genetic	EU446859.1	ABZ92388.1