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

    Gene ID: 8572, updated on 27-Nov-2024

    Summary

    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, Nov 2024]
    Expression
    Ubiquitous expression in endometrium (RPKM 8.6), prostate (RPKM 6.1) and 21 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    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_001131027.2NP_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:280
      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:148230
      DUF4749; Domain of unknown function (DUF4749)
    2. NM_003687.4NP_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:255307
      LIM_RIL; The LIM domain of RIL
      cd00992
      Location:280
      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:148220
      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_047417848.1XP_047273804.1  PDZ and LIM domain protein 4 isoform X1

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

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

    4. XM_047417851.1XP_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_054353734.1XP_054209709.1  PDZ and LIM domain protein 4 isoform X1

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

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

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