Pdlim4 PDZ and LIM domain 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pdlim4provided by RGD
Official Full Name: PDZ and LIM domain 4provided by RGD
Primary source: RGD:3575
See related: EnsemblRapid:ENSRNOG00000050794 AllianceGenome:RGD:3575
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: Ril; H-Rev18
Summary: Enables alpha-actinin binding activity. Involved in several processes, including excitatory chemical synaptic transmission; positive regulation of stress fiber assembly; and regulation of postsynaptic membrane neurotransmitter receptor levels. Located in several cellular components, including endosome lumen; postsynaptic membrane; and stress fiber. Is active in glutamatergic synapse and postsynaptic density. Human ortholog(s) of this gene implicated in osteoporosis. Orthologous to human PDLIM4 (PDZ and LIM domain 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Adrenal (RPKM 107.7), Heart (RPKM 60.1) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q22

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (38699444..38713696, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (38198686..38212935, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (39390578..39405322, complement)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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?

Reversion induced LIM domain protein (RIL) is a Daam1-interacting protein and regulator of the actin cytoskeleton during non-canonical Wnt signaling.
Title: Reversion induced LIM domain protein (RIL) is a Daam1-interacting protein and regulator of the actin cytoskeleton during non-canonical Wnt signaling.
The RIL 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.
Ril modulates actin stress fiber turnover and enhances the association with actinin and actins.
Title: The PDZ-LIM protein RIL modulates actin stress fiber turnover and enhances the association of alpha-actinin with F-actin.
RIL directs the transport of GluR-A-containing AMPA receptors to and/or within dendritic spines, in an alpha-actinin/actin-dependent manner.
Title: Actin/alpha-actinin-dependent transport of AMPA receptors in dendritic spines: role of the PDZ-LIM protein RIL.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables actin binding	IBA Inferred from Biological aspect of Ancestor more info
enables actinin binding	IPI Inferred from Physical Interaction more info	PubMed
enables alpha-actinin binding	IEA Inferred from Electronic Annotation more info
enables alpha-actinin binding	IPI Inferred from Physical Interaction more info	PubMed
enables alpha-actinin 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 protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein phosphatase binding	IEA Inferred from Electronic Annotation more info
enables protein phosphatase binding	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	IDA Inferred from Direct Assay more info	PubMed
involved_in actin cytoskeleton organization	IEA Inferred from Electronic Annotation more info
involved_in actin cytoskeleton organization	ISO Inferred from Sequence Orthology more info
involved_in excitatory chemical synaptic transmission	IDA Inferred from Direct Assay more info	PubMed
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
involved_in muscle structure development	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of stress fiber assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of stress fiber assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of postsynaptic membrane neurotransmitter receptor levels	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 actin cytoskeleton	IPI Inferred from Physical Interaction more info	PubMed
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in dendritic spine	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome lumen	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome membrane	IEA Inferred from Electronic Annotation more info
part_of filamentous actin	IBA Inferred from Biological aspect of Ancestor more info
part_of filamentous actin	IEA Inferred from Electronic Annotation more info
part_of filamentous actin	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IMP Inferred from Mutant Phenotype more info	PubMed
located_in lamellipodium	IEA Inferred from Electronic Annotation more info
located_in lamellipodium	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic density	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
located_in recycling endosome lumen	IDA Inferred from Direct Assay more info	PubMed
located_in recycling endosome membrane	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
located_in stress fiber	ISO Inferred from Sequence Orthology more info
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: PDZ and LIM domain protein 4

Names: LIM protein RIL; RIT-18; reversion induced LIM; reversion-induced 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_001393871.1 → NP_001380800.1 PDZ and LIM domain protein 4 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

P36202

Related

ENSRNOP00000064261.2, ENSRNOT00000074616.3

Conserved Domains (3) summary

cd09451
Location:260 → 312

LIM_RIL; The LIM domain of RIL

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 → 235

DUF4749; Domain of unknown function (DUF4749)
NM_001393872.1 → NP_001380801.1 PDZ and LIM domain protein 4 isoform 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

Conserved Domains (1) summary

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) ...
NM_001393873.1 → NP_001380802.1 PDZ and LIM domain protein 4 isoform 4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A0A8I6GEQ8

Related

ENSRNOP00000086241.1, ENSRNOT00000101447.2

Conserved Domains (2) summary

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:134 → 229

DUF4749; Domain of unknown function (DUF4749)
NM_001430034.1 → NP_001416963.1 PDZ and LIM domain protein 4 isoform 5

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010
NM_001430035.1 → NP_001416964.1 PDZ and LIM domain protein 4 isoform 6

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010
NM_001430036.1 → NP_001416965.1 PDZ and LIM domain protein 4 isoform 7

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010
NM_017062.3 → NP_058758.2 PDZ and LIM domain protein 4 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

P36202

UniProtKB/TrEMBL

A6HEG3, M0R4H5

Conserved Domains (3) summary

cd09451
Location:255 → 307

LIM_RIL; The LIM domain of RIL

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:134 → 230

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_086028.1 Reference GRCr8

Range

38699444..38713696 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039085241.2 → XP_038941169.1 PDZ and LIM domain protein 4 isoform X1

Conserved Domains (2) summary

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 → 234

DUF4749; Domain of unknown function (DUF4749)