Lims1 LIM zinc finger domain containing 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Lims1provided by RGD
Official Full Name: LIM zinc finger domain containing 1provided by RGD
Primary source: RGD:1560732
See related: Ensembl:ENSRNOG00000037765 AllianceGenome:RGD:1560732
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Pinch1; RGD1560732
Summary: Predicted to enable protein kinase binding activity and zinc ion binding activity. Predicted to be involved in several processes, including positive regulation of cell-substrate adhesion; positive regulation of signal transduction; and regulation of gene expression. Predicted to act upstream of or within several processes, including cell-matrix adhesion; negative regulation of apoptotic process; and negative regulation of cell population proliferation. Part of protein-containing complex. Orthologous to human LIMS1 (LIM zinc finger domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Lung (RPKM 216.0), Heart (RPKM 197.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20q11

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (26851364..26961607)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (26309833..26418511)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (27895981..28004767)

Chromosome 20 - NC_086038.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PINCH/GSK3beta/ERK pathway induced in kidney in unilateral ureteral obstruction
Title: Early Activation of PINCH/ Glycogen-Synthase Kinase 3β/ERK Pathway in Obstructive Nephropathy Rat Model.
TGF-beta1-induced alteration of the PIP complex formation may be importantly implicated in the development and progression of glomerular failure shown in several kidney diseases.
Title: TGF-beta1-induced PINCH-1-ILK-alpha-parvin complex formation regulates mesangial cell proliferation and hypertrophy.

Submit: New GeneRIF Correction

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

AW551584 (e-PCR)
- UniSTS:180043

AU028036 (e-PCR)
- UniSTS:112722

D20Rat34 (e-PCR), detects polymorphism
- UniSTS:118641

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables protein domain specific binding	IC Inferred by Curator more info	PubMed
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed
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	ISO Inferred from Sequence Orthology more info
involved_in cell-cell junction organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell-cell junction organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell-matrix adhesion	ISO Inferred from Sequence Orthology more info
involved_in cellular response to transforming growth factor beta stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of cholangiocyte proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chordate embryonic development	ISO Inferred from Sequence Orthology more info
NOT involved_in epithelial to mesenchymal transition	ISO Inferred from Sequence Orthology more info
involved_in establishment of protein localization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment or maintenance of cell polarity	ISO Inferred from Sequence Orthology more info
acts_upstream_of hepatocyte apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of integrin-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of hepatocyte apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of hepatocyte proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neural precursor cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of neural precursor cell proliferation	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	ISO Inferred from Sequence Orthology more info
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
NOT involved_in regulation of epithelial cell proliferation	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	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	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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

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_001145456.2 → NP_001138928.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform 1

See identical proteins and their annotated locations for NP_001138928.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000020

UniProtKB/TrEMBL

A0A8I6GA69, C0KUC5

Related

ENSRNOP00000062647.1, ENSRNOT00000064288.4

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
NM_001415155.1 → NP_001402084.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000020

UniProtKB/TrEMBL

A0A8I5ZPU7, A0A8I6GA69, A6K3T1

Related

ENSRNOP00000078972.1, ENSRNOT00000094679.1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086038.1 Reference GRCr8

Range

26851364..26961607

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006256389.5 → XP_006256451.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

UniProtKB/TrEMBL

A6K3T3

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_006256390.5 → XP_006256452.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform X8

UniProtKB/TrEMBL

A6K3T3

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_063279474.1 → XP_063135544.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform X10

UniProtKB/TrEMBL

A0A8I6GA69
XM_017601761.3 → XP_017457250.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform X1

UniProtKB/TrEMBL

A6K3T3
XM_063279472.1 → XP_063135542.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform X7
XM_006256388.5 → XP_006256450.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform X5

UniProtKB/TrEMBL

A0A8I6GA69

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_017601763.3 → XP_017457252.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform X3

UniProtKB/TrEMBL

A0A8I5ZKY9, A0A8I6GA69

Related

ENSRNOP00000078506.1
XM_006256387.5 → XP_006256449.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform X4

See identical proteins and their annotated locations for XP_006256449.1

UniProtKB/TrEMBL

A6K3T3, C0KUC6

Related

ENSRNOP00000073371.1

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
XM_006256385.5 → XP_006256447.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform X2

See identical proteins and their annotated locations for XP_006256447.1

UniProtKB/TrEMBL

A0A8I6A6W3, A6K3T3

Related

ENSRNOP00000087973.1

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
XM_063279473.1 → XP_063135543.1 LIM and senescent cell antigen-like-containing domain protein 1 isoform X9

UniProtKB/TrEMBL

A6K3T3