Pdlim4 PDZ and LIM domain 4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Pdlim4provided by MGI
Official Full Name: PDZ and LIM domain 4provided by MGI
Primary source: MGI:MGI:1353470
See related: Ensembl:ENSMUSG00000020388 AllianceGenome:MGI:1353470
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Ril
Summary: Enables protein phosphatase binding activity. Predicted to be involved in several processes, including actin cytoskeleton organization; excitatory chemical synaptic transmission; and positive regulation of stress fiber assembly. Predicted to be located in several cellular components, including endosome lumen; lamellipodium; and postsynaptic membrane. Predicted to be part of filamentous actin. Predicted to be active in Z disc; adherens junction; and stress fiber. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; genitourinary system; and sensory organ. 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: Broad expression in ovary adult (RPKM 165.2), stomach adult (RPKM 74.2) and 17 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 B1.3; 11 32.13 cM

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (53945754..53959814, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (54054928..54069032, complement)

Chromosome 11 - NC_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

findings have identified Pdlim4 as a JMJD3 target gene that affects T-cell trafficking by cooperating with S1P1, and provided insights into the molecular mechanisms by which JMJD3 regulates genes involved in T cell trafficking.
Title: JMJD3 regulates CD4 T cell trafficking by targeting actin cytoskeleton regulatory gene Pdlim4.
Pdlim4 is required for dendritic cell migration via CCR7-JNK, dendrite formation, and subsequent development of functional T-cell responses.
Title: Pdlim4 is essential for CCR7-JNK-mediated dendritic cell migration and F-actin-related dendrite formation.
PDLIM4 may function as a tumor suppressor, involved in the control of cell proliferation by associating with actin in prostate cancer cells.
Title: PDLIM4, an actin binding protein, suppresses prostate cancer cell growth.
RIL C-terminus proper, but not the RIL LIM domain, can interact with protein tyrosine phosphatase BL
Title: The interaction of PTP-BL PDZ domains with RIL: an enigmatic role for the RIL LIM domain.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables actin binding	IBA Inferred from Biological aspect of Ancestor more info
enables actinin binding	ISO Inferred from Sequence Orthology more info
enables alpha-actinin binding	IEA Inferred from Electronic Annotation more info
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	IPI Inferred from Physical Interaction more info	PubMed
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	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	ISO Inferred from Sequence Orthology more info
involved_in excitatory chemical synaptic transmission	ISS Inferred from Sequence or Structural Similarity more info
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	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 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	ISO Inferred from Sequence Orthology more info
located_in cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in dendritic spine	ISO Inferred from Sequence Orthology more info
located_in dendritic spine	ISS Inferred from Sequence or Structural Similarity more info
located_in early endosome lumen	ISO Inferred from Sequence Orthology more info
located_in early endosome lumen	ISS Inferred from Sequence or Structural Similarity more info
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
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
located_in postsynaptic membrane	ISO Inferred from Sequence Orthology more info
located_in postsynaptic membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in recycling endosome lumen	ISO Inferred from Sequence Orthology more info
located_in recycling endosome lumen	ISS Inferred from Sequence or Structural Similarity more info
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	IEA Inferred from Electronic Annotation more info
located_in stress fiber	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: PDZ and LIM domain protein 4

Names: LIM protein RIL; 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_001425512.1 → NP_001412441.1 PDZ and LIM domain protein 4 isoform 2

Status: VALIDATED

Source sequence(s)

AL596444
NM_001425513.1 → NP_001412442.1 PDZ and LIM domain protein 4 isoform 3

Status: VALIDATED

Source sequence(s)

AL596444
NM_001425514.1 → NP_001412443.1 PDZ and LIM domain protein 4 isoform 4

Status: VALIDATED

Source sequence(s)

AL596444

UniProtKB/TrEMBL

Q5SWV3

Related

ENSMUSP00000090797.5, ENSMUST00000093109.11
NM_001425515.1 → NP_001412444.1 PDZ and LIM domain protein 4 isoform 5

Status: VALIDATED

Source sequence(s)

AL596444
NM_019417.4 → NP_062290.2 PDZ and LIM domain protein 4 isoform 1

See identical proteins and their annotated locations for NP_062290.2

Status: VALIDATED

Source sequence(s)

AL596444

Consensus CDS

CCDS24690.1

UniProtKB/Swiss-Prot

P70271, Q5SWV2, Q8K0W4

Related

ENSMUSP00000018755.4, ENSMUST00000018755.10

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:150 → 226

DUF4749; Domain of unknown function (DUF4749)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000077.7 Reference GRCm39 C57BL/6J

Range

53945754..53959814 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030246067.1 → XP_030101927.1 PDZ and LIM domain protein 4 isoform X1

Conserved Domains (2) summary

cl02475
Location:196 → 248

LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

pfam15936
Location:91 → 171

DUF4749; Domain of unknown function (DUF4749)