Pdlim1 PDZ and LIM domain 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pdlim1provided by RGD
Official Full Name: PDZ and LIM domain 1provided by RGD
Primary source: RGD:68324
See related: EnsemblRapid:ENSRNOG00000016166 AllianceGenome:RGD:68324
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: CLP36
Summary: Enables actin binding activity. Involved in several processes, including actin cytoskeleton organization; fibroblast migration; and maintenance of cell polarity. Located in Z disc and stress fiber. Orthologous to human PDLIM1 (PDZ and LIM domain 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Heart (RPKM 397.1), Muscle (RPKM 228.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q54

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (248991818..249040409, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (239042372..239091074, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (259308326..259357006, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Decreased PDLIM1 expression in endothelial cells contributes to the development of intracranial aneurysm.
Title: Decreased PDLIM1 expression in endothelial cells contributes to the development of intracranial aneurysm.
The CLP36 has a redundant role in the formation of stress fibers, but have different effects on stress fiber dynamics in F2408 cells.
Title: CLP36 and RIL recruit α-actinin-1 to stress fibers and differentially regulate stress fiber dynamics in F2408 fibroblasts.
expression linked to the differentiation of Rcho-1 cells
Title: Expression of stress fiber-associated protein CLP36 during differentiation of Rcho-1 trophoblast giant cells.
CLP36 may interact with palladin to influence neurite outgrowth during sciatic nerve regeneration.
Title: CLP36 interacts with palladin in dorsal root ganglion neurons.
This study suggested that CLP36 serves as a scaffold to form a multiprotein complex that regulates actin cytoskeleton dynamics and plays a role in controlling neurite outgrowth.
Title: Characterization of CLP36/Elfin/PDLIM1 in the nervous system.
These findings indicate that CLP36 plays a critical role in stress fiber formation and the assembly of focal adhesions in BeWo cells.
Title: The PDZ-LIM protein CLP36 is required for actin stress fiber formation and focal adhesion assembly in BeWo cells.

Submit: New GeneRIF Correction

General gene information

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Markers

AI029470 (e-PCR)
- UniSTS:246023

AU047677 (e-PCR)
- UniSTS:110273

BE108553 (e-PCR)
- UniSTS:247797

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables actin binding	IBA Inferred from Biological aspect of Ancestor more info
enables actin binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables muscle alpha-actinin binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in actin cytoskeleton organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in establishment or maintenance of actin cytoskeleton polarity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in fibroblast migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
involved_in maintenance of cell polarity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in muscle structure development	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in response to hypoxia	IEP Inferred from Expression Pattern more info	PubMed
involved_in stress fiber assembly	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in Z disc	IBA Inferred from Biological aspect of Ancestor more info
located_in Z disc	IDA Inferred from Direct Assay more info	PubMed
located_in Z disc	ISO Inferred from Sequence Orthology more info
located_in actin cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoskeleton	ISO Inferred from Sequence Orthology more info
part_of filamentous actin	IBA Inferred from Biological aspect of Ancestor more info
is_active_in stress fiber	IBA Inferred from Biological aspect of Ancestor more info
located_in stress fiber	IDA Inferred from Direct Assay more info	PubMed
located_in stress fiber	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: PDZ and LIM domain protein 1

Names: C-terminal LIM domain protein 1; LIM domain protein CLP-36; LIM protein; elfin

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_017365.2 → NP_059061.1 PDZ and LIM domain protein 1

See identical proteins and their annotated locations for NP_059061.1

Status: PROVISIONAL

Source sequence(s)

U23769

UniProtKB/Swiss-Prot

P52944, Q6IN45

UniProtKB/TrEMBL

A6JH56

Related

ENSRNOP00000022000.2, ENSRNOT00000022000.6

Conserved Domains (3) summary

cd09448
Location:258 → 309

LIM_CLP36; This family represents the LIM domain of CLP36

cd00992
Location:5 → 81

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam15936
Location:136 → 228

DUF4749; Domain of unknown function (DUF4749)