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    PDLIM2 PDZ and LIM domain 2 [ Homo sapiens (human) ]

    Gene ID: 64236, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PDLIM2provided by HGNC
    Official Full Name
    PDZ and LIM domain 2provided by HGNC
    Primary source
    HGNC:HGNC:13992
    See related
    Ensembl:ENSG00000120913 MIM:609722; AllianceGenome:HGNC:13992
    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
    SLIM; MYSTIQUE
    Summary
    This gene encodes a member of the ALP subfamily of PDZ-LIM domain proteins. The encoded protein suppresses anchorage-dependent growth and promotes cell migration and adhesion through interactions with the actin cytoskeleton via the PDZ domain. The encoded protein is also a putative tumor suppressor protein, and decreased expression of this gene is associated with several malignancies including breast cancer and adult T-cell leukemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2011]
    Expression
    Broad expression in spleen (RPKM 22.4), lung (RPKM 9.5) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PDLIM2 in Genome Data Viewer
    Location:
    8p21.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (22578741..22598026)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (22852592..22871886)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (22436254..22455539)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene protein phosphatase 3 catalytic subunit gamma Neighboring gene uncharacterized LOC124901905 Neighboring gene BTF3 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22406579-22407079 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22408405-22409369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22409593-22410470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22410471-22411346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27081 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22413914-22414436 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18990 Neighboring gene Sharpr-MPRA regulatory region 12029 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22421349-22422242 Neighboring gene sorbin and SH3 domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18991 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22429393-22430084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22430085-22430775 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22431841-22432559 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22435755-22436448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18994 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18995 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18997 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22439222-22439914 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22442189-22442858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22447071-22448071 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22454615-22455362 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22455363-22456110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22458799-22459676 Neighboring gene uncharacterized LOC107986876 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27082 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:22462104-22462604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19003 Neighboring gene chromosome 8 open reading frame 58 Neighboring gene cell cycle and apoptosis regulator 2 Neighboring gene bridging integrator 3

    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
    • 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. Central Nervous System-Infecting Pathogens Escherichia coli and Cryptococcus neoformans Exploit the Host Pdlim2 for Intracellular Traversal and Exocytosis in the Blood-Brain Barrier. Li Z, et al. Infect Immun, 2021 Sep 16. PMID 34228504, Free PMC Article
    2. PDLIM2 expression is driven by vitamin D and is involved in the pro-adhesion, and anti-migration and -invasion activity of vitamin D. Vanoirbeek E, et al. Oncogene, 2014 Apr 10. PMID 23584482
    3. Pull-down Assay on Streptavidin Beads and Surface Plasmon Resonance Chips for SWATH-MS-based Interactomics. Maryáš J, et al. Cancer Genomics Proteomics, 2018 Sep-Oct. PMID 30194080, Free PMC Article
    4. PDLIM2 Is a Marker of Adhesion and β-Catenin Activity in Triple-Negative Breast Cancer. Cox OT, et al. Cancer Res, 2019 May 15. PMID 30885980
    5. Systematic profiling identifies PDLIM2 as a novel prognostic predictor for oesophageal squamous cell carcinoma (ESCC). Song G, et al. J Cell Mol Med, 2019 Aug. PMID 31222932, Free PMC Article

    See all (51) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Tumor promoting effect of PDLIM2 downregulation involves mitochondrial ROS, oncometabolite accumulations and HIF-1alpha activation.
      Title: Tumor promoting effect of PDLIM2 downregulation involves mitochondrial ROS, oncometabolite accumulations and HIF-1α activation.
    2. PDLIM2 can inactivate the TGF-beta/Smad pathway to inhibit the malignant behavior of ovarian cancer cells.
      Title: PDLIM2 can inactivate the TGF-β/Smad pathway to inhibit the malignant behavior of ovarian cancer cells.
    3. High Expression of PDLIM2 Predicts a Poor Prognosis in Prostate Cancer and Is Correlated with Epithelial-Mesenchymal Transition and Immune Cell Infiltration.
      Title: High Expression of PDLIM2 Predicts a Poor Prognosis in Prostate Cancer and Is Correlated with Epithelial-Mesenchymal Transition and Immune Cell Infiltration.
    4. Kruppel like factor 10 up-regulates PDZ and LIM domain containing protein 2 via nuclear factor kappa-B pathway to inhibit proliferation and inflammatory of fibroblastoid synovial cell in rheumatoid arthritis.
      Title: Kruppel like factor 10 up-regulates PDZ and LIM domain containing protein 2 via nuclear factor kappa-B pathway to inhibit proliferation and inflammatory of fibroblastoid synovial cell in rheumatoid arthritis.
    5. Systematic evaluation of the prognostic and immunological role of PDLIM2 across 33 cancer types.
      Title: Systematic evaluation of the prognostic and immunological role of PDLIM2 across 33 cancer types.
    6. Central Nervous System-Infecting Pathogens Escherichia coli and Cryptococcus neoformans Exploit the Host Pdlim2 for Intracellular Traversal and Exocytosis in the Blood-Brain Barrier.
      Title: Central Nervous System-Infecting Pathogens Escherichia coli and Cryptococcus neoformans Exploit the Host Pdlim2 for Intracellular Traversal and Exocytosis in the Blood-Brain Barrier.
    7. PDLIM2 acts as a cancer suppressor gene in non-small cell lung cancer via the down regulation of NF-kappaB signaling.
      Title: PDLIM2 acts as a cancer suppressor gene in non-small cell lung cancer via the down regulation of NF-κB signaling.
    8. Systematic profiling identifies PDLIM2 as a novel prognostic predictor for oesophageal squamous cell carcinoma (ESCC).
      Title: Systematic profiling identifies PDLIM2 as a novel prognostic predictor for oesophageal squamous cell carcinoma (ESCC).
    9. Compared to normal lung tissues, the expression of PDLIM2 was significantly decreased in human lung cancers.
      Title: Causative role of PDLIM2 epigenetic repression in lung cancer and therapeutic resistance.
    10. study shows that PDLIM2 expression defines a subset of triple-negative breast cancer that may benefit from targeting the beta-catenin and adhesion signaling pathways
      Title: PDLIM2 Is a Marker of Adhesion and β-Catenin Activity in Triple-Negative Breast Cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (27)

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34715

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables filamin binding IEA
    Inferred from Electronic Annotation
    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 myosin heavy chain binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin protein ligase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    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 protein catabolic process IEA
    Inferred from Electronic Annotation
    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 cortical actin cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of filamentous actin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    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 2

    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.

    Genomic

    1. NG_030435.2 RefSeqGene

      Range
      6735..20558
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001368120.1 → NP_001355049.1  PDZ and LIM domain protein 2 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC037459
      Consensus CDS
      CCDS94264.1
      UniProtKB/Swiss-Prot
      D3DSR5, J3KNH4, Q7Z584, Q86WM8, Q8WZ29, Q96JY6, Q9H4L9, Q9H7I2
      Related
      ENSP00000387084.1, ENST00000409417.6

    2. NM_021630.6 → NP_067643.3  PDZ and LIM domain protein 2 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC037459
      Consensus CDS
      CCDS6032.2
      UniProtKB/Swiss-Prot
      Q96JY6
      Related
      ENSP00000312634.7, ENST00000308354.11
      Conserved Domains (3) summary
      cd09449
      Location:536 → 588
      LIM_Mystique; The LIM domain of Mystique, a subfamily of ALP LIM domain proteins
      cd00992
      Location:259 → 330
      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:462 → 505
      DUF4749; Domain of unknown function (DUF4749)

    3. NM_176871.5 → NP_789847.1  PDZ and LIM domain protein 2 isoform 1

      See identical proteins and their annotated locations for NP_789847.1

      Status: REVIEWED

      Source sequence(s)
      AC037459
      Consensus CDS
      CCDS34860.1
      UniProtKB/Swiss-Prot
      Q96JY6
      Related
      ENSP00000265810.4, ENST00000265810.8
      Conserved Domains (3) summary
      cd09449
      Location:286 → 342
      LIM_Mystique; The LIM domain of Mystique, a subfamily of ALP LIM domain proteins
      cd00992
      Location:9 → 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:212 → 255
      DUF4749; Domain of unknown function (DUF4749)

    4. NM_198042.4 → NP_932159.1  PDZ and LIM domain protein 2 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC037459
      Consensus CDS
      CCDS34861.1
      UniProtKB/TrEMBL
      C9JS55
      Related
      ENSP00000386868.1, ENST00000409141.5
      Conserved Domains (2) summary
      cd00992
      Location:9 → 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:212 → 257
      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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      22578741..22598026
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      22852592..22871886
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96JY6.1 GenPept UniProtKB/Swiss-Prot:Q96JY6

    Gene LinkOut

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

    Chemical Information
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    Research Materials
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