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    PDLIM4 PDZ and LIM domain 4 [ Homo sapiens (human) ]

    Gene ID: 8572, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PDLIM4provided by HGNC
    Official Full Name
    PDZ and LIM domain 4provided by HGNC
    Primary source
    HGNC:HGNC:16501
    See related
    Ensembl:ENSG00000131435 MIM:603422; AllianceGenome:HGNC:16501
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RIL
    Summary
    Enables alpha-actinin binding activity; protein homodimerization activity; and protein phosphatase binding activity. Involved in actin cytoskeleton organization. Located in several cellular components, including lamellipodium; perinuclear region of cytoplasm; and stress fiber. Part of filamentous actin. Implicated in osteoporosis. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in endometrium (RPKM 8.6), prostate (RPKM 6.1) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PDLIM4 in Genome Data Viewer
    Location:
    5q31.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (132257696..132273454)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (132777576..132793334)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (131593389..131609147)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr5:131520231-131520732 Neighboring gene Sharpr-MPRA regulatory region 7421 Neighboring gene P4HA2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131543137-131543638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131543639-131544138 Neighboring gene prolyl 4-hydroxylase subunit alpha 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16313 Neighboring gene microRNA 6830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131586685-131587186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131587187-131587686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131593943-131594732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23063 Neighboring gene VISTA enhancer hs1449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131603965-131604508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23065 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131605973-131606861 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131607809-131608310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131608311-131608810 Neighboring gene Sharpr-MPRA regulatory region 4855 Neighboring gene uncharacterized LOC124901063 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131613864-131614676 Neighboring gene CAGE-defined mid-level expression enhancer upstream of SLC22A4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16316 Neighboring gene solute carrier family 22 member 4 Neighboring gene MIR3936 host gene Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:131656893-131657393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131657550-131658068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131658069-131658587

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. The human RIL gene: mapping to human chromosome 5q31.1, genomic organization and alternative transcripts. Bashirova AA, et al. Gene, 1998 Apr 14. PMID 9573374
    2. RIL, a LIM gene on 5q31, is silenced by methylation in cancer and sensitizes cancer cells to apoptosis. Boumber YA, et al. Cancer Res, 2007 Mar 1. PMID 17332327
    3. Associations between polymorphisms of the PDLIM4 gene and susceptibility to osteoporotic fracture in an elderly population of Han Chinese. Chen J, et al. Biosci Rep, 2019 Jan 31. PMID 30578378, Free PMC Article
    4. Association of genetic variation of the RIL gene, encoding a PDZ-LIM domain protein and localized in 5q31.1, with low bone mineral density in adult Japanese women. Omasu F, et al. J Hum Genet, 2003. PMID 12908099
    5. How do elderly patients decide where to go for major surgery? Telephone interview survey. Schwartz LM, et al. BMJ, 2005 Oct 8. PMID 16192286, Free PMC Article

    See all (45) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Low expression of PDLIM4 is associated with growth and invasion of ovarian cancer.
      Title: PDZ and LIM domain protein 4 suppresses the growth and invasion of ovarian cancer cells via inactivation of STAT3 signaling.
    2. Our study provides supportive evidence for the contribution of PDLIM4 gene polymorphisms to the susceptibility to osteoporotic fracture and suggests that rs270611 and rs3900945 are genetic risk factors, while rs366512 might be a genetic protective factor against osteoporotic fracture in elderly Han individuals.
      Title: Associations between polymorphisms of the PDLIM4 gene and susceptibility to osteoporotic fracture in an elderly population of Han Chinese.
    3. The levels of the EDNRB, HJURP and p60/CAF-1 proteins were strongly associated with overall survival in high-grade gliomas patients (p<0.001, p<0.001 and p=0.002, respectively), whereas the one of PDLI4 was not (P=0.11).
      Title: Prognostic significance of EDN/RB, HJURP, p60/CAF-1 and PDLI4, four new markers in high-grade gliomas.
    4. Methylation of HIN-1, RASSF1A, RIL and CDH13 in breast cancers was associated with clinical characteristics, but only RASSF1A methylation was associated with time to first recurrence and overall survival.
      Title: Methylation of HIN-1, RASSF1A, RIL and CDH13 in breast cancer is associated with clinical characteristics, but only RASSF1A methylation is associated with outcome.
    5. Actin cytoskeleton remodeling by the alternatively spliced isoform of PDLIM4/RIL protein.
      Title: Actin cytoskeleton remodeling by the alternatively spliced isoform of PDLIM4/RIL protein.
    6. Reversion-induced LIM interaction with Src reveals a novel Src inactivation cycle.
      Title: Reversion-induced LIM interaction with Src reveals a novel Src inactivation cycle.
    7. 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.
    8. several genes that are known to be regulated by DNA methylation were up-regulated dramatically by integrin alpha6beta4 expression, including S100A4, FST, PDLIM4, CAPG, and Nkx2.2.
      Title: Integrin alpha6beta4 controls the expression of genes associated with cell motility, invasion, and metastasis, including S100A4/metastasin.
    9. Results showed that the hypermethylation of PDLIM4 gene could be used as a sensitive molecular tool in detection of prostate.
      Title: PDLIM4 repression by hypermethylation as a potential biomarker for prostate cancer.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.
    Submit: New GeneRIF Correction See all GeneRIFs (13)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Osteoporosis
    MedGen: C0029456 OMIM: 166710 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables alpha-actinin binding IPI
    Inferred from Physical Interaction
    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 protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein phosphatase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 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
    		  
    Component Evidence Code Pubs
    is_active_in Z disc IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in dendritic spine ISS
    Inferred from Sequence or Structural Similarity
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lamellipodium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in postsynaptic membrane ISS
    Inferred from Sequence or Structural Similarity
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    PDZ and LIM domain protein 4
    Names
    LIM domain protein
    LIM protein RIL
    enigma homolog
    reversion-induced LIM protein

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_015836.2 RefSeqGene

      Range
      5039..20797
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001131027.2 → NP_001124499.1  PDZ and LIM domain protein 4 isoform 2

      See identical proteins and their annotated locations for NP_001124499.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a coding exon in the 3' region, as compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      AF153882, AW590987, BC003096, BC016765, BF689609, BF690514, DN997097
      Consensus CDS
      CCDS47261.1
      UniProtKB/TrEMBL
      A0A0S2Z4N4
      Related
      ENSP00000368303.3, ENST00000379018.7
      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:148 → 230
      DUF4749; Domain of unknown function (DUF4749)

    2. NM_003687.4 → NP_003678.2  PDZ and LIM domain protein 4 isoform 1

      See identical proteins and their annotated locations for NP_003678.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AF153882, AW590987, BC016765, BF689609, BF690514, DN997097
      Consensus CDS
      CCDS4152.1
      UniProtKB/Swiss-Prot
      B2R8U1, P50479, Q53Y39, Q96AT8, Q9BTW8, Q9Y292
      UniProtKB/TrEMBL
      A0A0S2Z4P0
      Related
      ENSP00000253754.3, ENST00000253754.8
      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:148 → 220
      DUF4749; Domain of unknown function (DUF4749)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      132257696..132273454
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417848.1 → XP_047273804.1  PDZ and LIM domain protein 4 isoform X1

    2. XM_047417850.1 → XP_047273806.1  PDZ and LIM domain protein 4 isoform X2

    3. XM_017010002.2 → XP_016865491.1  PDZ and LIM domain protein 4 isoform X3

    4. XM_047417851.1 → XP_047273807.1  PDZ and LIM domain protein 4 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      132777576..132793334
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353734.1 → XP_054209709.1  PDZ and LIM domain protein 4 isoform X1

    2. XM_054353735.1 → XP_054209710.1  PDZ and LIM domain protein 4 isoform X2

    3. XM_054353736.1 → XP_054209711.1  PDZ and LIM domain protein 4 isoform X3

    4. XM_054353737.1 → XP_054209712.1  PDZ and LIM domain protein 4 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P50479.2 GenPept UniProtKB/Swiss-Prot:P50479

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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