PDLIM4 (PDZ and LIM domain 4)

Gene

• Entrez ID: 8572
• Gene name: PDZ and LIM domain 4
• Gene symbol: PDLIM4
• Synonyms (NCBI Gene): RIL
• Chromosome: 5
• Chromosome location: 5q31.1
• Summary: This gene encodes a protein which may be involved in bone development. Mutations in this gene are associated with susceptibility to osteoporosis. [provided by RefSeq, Nov 2009]

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT018921	hsa-miR-335-5p	Microarray	18185580
MIRT1222217	hsa-miR-125a-5p	CLIP-seq
MIRT1222218	hsa-miR-125b	CLIP-seq
MIRT1222219	hsa-miR-3653	CLIP-seq
MIRT1222220	hsa-miR-3658	CLIP-seq
MIRT1222221	hsa-miR-4300	CLIP-seq
MIRT1222222	hsa-miR-4319	CLIP-seq
MIRT1222223	hsa-miR-4432	CLIP-seq
MIRT1222224	hsa-miR-4446-5p	CLIP-seq
MIRT1222225	hsa-miR-4690-5p	CLIP-seq
MIRT1222226	hsa-miR-4732-3p	CLIP-seq
MIRT1222227	hsa-miR-4755-5p	CLIP-seq
MIRT1222228	hsa-miR-499-5p	CLIP-seq
MIRT1222229	hsa-miR-670	CLIP-seq
MIRT1222230	hsa-miR-920	CLIP-seq
MIRT2064360	hsa-miR-1973	CLIP-seq
MIRT2064361	hsa-miR-3679-3p	CLIP-seq
MIRT2064362	hsa-miR-507	CLIP-seq
MIRT2064363	hsa-miR-557	CLIP-seq
MIRT2064360	hsa-miR-1973	CLIP-seq
MIRT2064361	hsa-miR-3679-3p	CLIP-seq
MIRT2064362	hsa-miR-507	CLIP-seq
MIRT2064363	hsa-miR-557	CLIP-seq
MIRT2590723	hsa-miR-3168	CLIP-seq
MIRT1222223	hsa-miR-4432	CLIP-seq
MIRT1222224	hsa-miR-4446-5p	CLIP-seq
MIRT1222227	hsa-miR-4755-5p	CLIP-seq
MIRT1222228	hsa-miR-499-5p	CLIP-seq
MIRT1222229	hsa-miR-670	CLIP-seq
MIRT2590723	hsa-miR-3168	CLIP-seq
MIRT1222223	hsa-miR-4432	CLIP-seq
MIRT1222224	hsa-miR-4446-5p	CLIP-seq
MIRT1222227	hsa-miR-4755-5p	CLIP-seq
MIRT1222228	hsa-miR-499-5p	CLIP-seq
MIRT1222229	hsa-miR-670	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001725	Component	Stress fiber	IBA	21873635
GO:0001725	Component	Stress fiber	IDA	21636573
GO:0003779	Function	Actin binding	IBA	21873635
GO:0005515	Function	Protein binding	IPI	10826496, 19307596, 21636573, 32296183
GO:0005634	Component	Nucleus	IDA	10826496, 21636573
GO:0005737	Component	Cytoplasm	IDA	21636573
GO:0005856	Component	Cytoskeleton	IDA	21636573
GO:0005912	Component	Adherens junction	IBA	21873635
GO:0007507	Process	Heart development	IBA	21873635
GO:0019903	Function	Protein phosphatase binding	IPI	19307596
GO:0030018	Component	Z disc	IBA	21873635
GO:0030027	Component	Lamellipodium	IDA	10826496
GO:0030036	Process	Actin cytoskeleton organization	IBA	21873635
GO:0031532	Process	Actin cytoskeleton reorganization	IDA	21636573
GO:0031901	Component	Early endosome membrane	IEA
GO:0031905	Component	Early endosome lumen	ISS
GO:0031941	Component	Filamentous actin	IBA	21873635
GO:0031941	Component	Filamentous actin	IDA	10826496
GO:0034777	Component	Recycling endosome lumen	ISS
GO:0042803	Function	Protein homodimerization activity	IDA	25158098
GO:0043197	Component	Dendritic spine	ISS
GO:0045211	Component	Postsynaptic membrane	ISS
GO:0046872	Function	Metal ion binding	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	IDA	19307596
GO:0051371	Function	Muscle alpha-actinin binding	IBA	21873635
GO:0051393	Function	Alpha-actinin binding	IPI	20120020
GO:0055038	Component	Recycling endosome membrane	IEA
GO:0061061	Process	Muscle structure development	IBA	21873635
GO:0098976	Process	Excitatory chemical synaptic transmission	ISS

Other IDs

• MIM: 603422
• HGNC: 16501
• e!Ensembl: ENSG00000131435

Protein

• UniProt ID: P50479
• Protein name: PDZ and LIM domain protein 4 (LIM protein RIL) (Reversion-induced LIM protein)
• Protein function: [Isoform 1]: Suppresses SRC activation by recognizing and binding to active SRC and facilitating PTPN13-mediated dephosphorylation of SRC 'Tyr-419' leading to its inactivation. Inactivated SRC dissociates from this protein allowing the initiatio
• PDB: 2EEG, 2V1W, 4Q2O
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00595	PDZ	4 → 81	PDZ domain	Domain
  PF15936	DUF4749	147 → 228	Domain of unknown function (DUF4749)	Family
  PF00412	LIM	255 → 309	LIM domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: [Isoform 2]: Found in brain. {ECO:0000269|PubMed:9573374}.
• Sequence:

  MPHSVTLRGPSPWGFRLVGGRDFSAPLTISRVHAGSKAALAALCPGDLIQAINGESTELM
  THLEAQNRIKGCHDHLTLSVSRPEGRSWPSAPDDSKAQAHRIHIDPEIQDGSPTTSRRPS
  GTGTGPEDGRPSLGSPYGQPPRFPVPHNGSSEATLPAQMSTLHVSPPPSADPARGLPRSR
  DCRVDLGSEVYRMLREPAEPVAAEPKQSGSFRYLQGMLEAGEGGDWPGPGGPRNLKPTAS
  KLGAPLSGLQGLPECTRCGHGIVGTIVKARDKLYHPECFMCSDCGLNLKQRGYFFLDERL
  YCESHAKARVKPPEGYDVVAVYPNAKVELV

• Sequence length: 330

Pathways

KEGG:

Cytoskeleton in muscle cells

Associated diseases

Causal
Disease term	Disease name	dbSNP ID	References
Lung cancer	Malignant neoplasm of lung	rs121913530, rs121913529, rs878855122, rs1057519784, rs770315135	27935865
Osteoporosis	Osteoporosis, Age-Related, Osteoporosis, Osteoporosis, Senile, Post-Traumatic Osteoporosis	rs72658152, rs72667023, rs587776916, rs72656370, rs768615287

Unknown
Disease term	Disease name	Evidence	References	Source
Inflammatory Bowel Disease	Inflammatory Bowel Disease			GWAS

Associations from Text Mining
Disease Name	Relationship Type	References
Bipolar Disorder	Associate	23031404
Bone Marrow Diseases	Associate	30578378
Breast Neoplasms	Associate	17764565, 22695491, 36936167, 38235137
Carcinoma Renal Cell	Associate	20154727
Colorectal Neoplasms	Associate	19307596
Epstein Barr Virus Infections	Associate	40116629
Fractures Bone	Associate	30578378
Glioblastoma	Associate	35456975
Leukemia Myelogenous Chronic BCR ABL Positive	Associate	21760961
Lymphatic Metastasis	Associate	20642860
Neoplasms	Associate	17764565, 19307596, 20154727, 20642860, 22695491, 31006665, 31082426
Neoplasms	Inhibit	22600741
Osteoporotic Fractures	Associate	30578378
Prostatic Neoplasms	Associate	19229700, 21694441
Stomach Neoplasms	Associate	35982735
Thyroid Neoplasms	Associate	31006665
Triple Negative Breast Neoplasms	Associate	17764565