Pdlim3 PDZ and LIM domain 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pdlim3provided by RGD
Official Full Name: PDZ and LIM domain 3provided by RGD
Primary source: RGD:620427
See related: EnsemblRapid:ENSRNOG00000012658 AllianceGenome:RGD:620427
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: Alp; Actn2lp
Summary: Enables actinin binding activity. Predicted to be involved in actin cytoskeleton organization; heart development; and muscle structure development. Predicted to act upstream of or within actin filament organization. Located in Z disc. Orthologous to human PDLIM3 (PDZ and LIM domain 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Muscle (RPKM 2943.2), Heart (RPKM 471.9) and 2 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 16q11

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	16	NC_086034.1 (53085020..53116495, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	16	NC_051351.1 (46352460..46383680, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	16	NC_005115.4 (49543140..49574362, complement)

Chromosome 16 - NC_086034.1 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?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH143054 (e-PCR)
- UniSTS:232301

BF390733 (e-PCR)
- UniSTS:249545

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables actin binding	IBA Inferred from Biological aspect of Ancestor more info
enables actinin binding	IDA Inferred from Direct Assay more info	PubMed
enables cytoskeletal protein binding	ISO Inferred from Sequence Orthology more info
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 structural constituent of muscle	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
acts_upstream_of_or_within actin filament organization	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within heart development	ISO Inferred from Sequence Orthology more info
involved_in muscle structure development	IBA Inferred from Biological aspect of Ancestor more info
NOT acts_upstream_of_or_within skeletal muscle tissue development	ISO Inferred from Sequence Orthology more info

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	IEA Inferred from Electronic Annotation more info
located_in actin cytoskeleton	ISO Inferred from Sequence Orthology more info
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	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

General protein information

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Preferred Names: PDZ and LIM domain protein 3

Names: SK-2; actinin alpha 2 associated LIM protein; actinin-associated LIM protein; alpha-actinin-2-associated LIM protein

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_053650.2 → NP_446102.2 PDZ and LIM domain protein 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000016

UniProtKB/Swiss-Prot

O70208, Q66HS7

UniProtKB/TrEMBL

A6JPQ7, D3ZFR7

Related

ENSRNOP00000017054.2, ENSRNOT00000017054.8

Conserved Domains (3) summary

cd09450
Location:294 → 346

LIM_ALP; This family represents the LIM domain of ALP, actinin-associated LIM protein

cd00992
Location:2 → 80

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:184 → 263

DUF4749; Domain of unknown function (DUF4749)

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_086034.1 Reference GRCr8

Range

53085020..53116495 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006253119.5 → XP_006253181.1 PDZ and LIM domain protein 3 isoform X1

See identical proteins and their annotated locations for XP_006253181.1

UniProtKB/TrEMBL

A0A0G2JSM3, A6JPQ8

Related

ENSRNOP00000017568.4, ENSRNOT00000017568.9

Conserved Domains (3) summary

cd09450
Location:246 → 298

LIM_ALP; This family represents the LIM domain of ALP, actinin-associated LIM protein

cd00992
Location:2 → 80

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:137 → 217

DUF4749; Domain of unknown function (DUF4749)
XM_006253120.5 → XP_006253182.1 PDZ and LIM domain protein 3 isoform X2

UniProtKB/TrEMBL

A0A0G2K9W2

Related

ENSRNOP00000075153.2, ENSRNOT00000085535.3

Conserved Domains (3) summary

cd09450
Location:206 → 258

LIM_ALP; This family represents the LIM domain of ALP, actinin-associated LIM protein

cd00992
Location:2 → 80

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:139 → 177

DUF4749; Domain of unknown function (DUF4749)