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    PDLIM5 PDZ and LIM domain 5 [ Homo sapiens (human) ]

    Gene ID: 10611, updated on 6-Sep-2022

    Summary

    Official Symbol
    PDLIM5provided by HGNC
    Official Full Name
    PDZ and LIM domain 5provided by HGNC
    Primary source
    HGNC:HGNC:17468
    See related
    Ensembl:ENSG00000163110 MIM:605904; AllianceGenome:HGNC:17468
    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
    L9; ENH; LIM; ENH1
    Summary
    This gene encodes a member of a family of proteins that possess a 100-amino acid PDZ domain at the N terminus and one to three LIM domains at the C-terminus. This family member functions as a scaffold protein that tethers protein kinases to the Z-disk in striated muscles. It is thought to function in cardiomyocyte expansion and in restraining postsynaptic growth of excitatory synapses. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]
    Expression
    Broad expression in heart (RPKM 70.2), prostate (RPKM 31.5) and 23 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See PDLIM5 in Genome Data Viewer
    Location:
    4q22.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    110 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (94451942..94668223)
    110 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (97767448..97983384)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (95373093..95589374)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L35a pseudogene 11 Neighboring gene Sharpr-MPRA regulatory region 14184 Neighboring gene VISTA enhancer hs1438 Neighboring gene BMPR1B divergent transcript

    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

    EBI GWAS Catalog

    Description
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Identification of seven new prostate cancer susceptibility loci through a genome-wide association study.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables actin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables actin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables actinin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables cadherin binding involved in cell-cell adhesion HDA 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
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase C binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in actin cytoskeleton organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in cell growth involved in cardiac muscle cell development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell-cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in heart development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in muscle structure development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in regulation of dendritic spine morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    is_active_in Z disc IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
     
    located_in adherens junction HDA PubMed 
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of filamentous actin IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in postsynaptic density ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in stress fiber IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    PDZ and LIM domain protein 5
    Names
    enigma homolog
    enigma-like LIM domain protein
    enigma-like PDZ and LIM domains 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.

    mRNA and Protein(s)

    1. NM_001011513.4NP_001011513.4  PDZ and LIM domain protein 5 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      AC093778, AC108067, AC109925
      Consensus CDS
      CCDS47102.1
      Related
      ENSP00000442187.2, ENST00000542407.5
      Conserved Domains (6) summary
      cd09453
      Location:311362
      LIM1_ENH; The first LIM domain of the Enigma Homolog (ENH) family
      cd09459
      Location:429483
      LIM3_ENH; The third LIM domain of the Enigma Homolog (ENH) family
      cd00992
      Location:1082
      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) ...
      pfam05109
      Location:143294
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl02475
      Location:370421
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
      pfam15936
      Location:105195
      DUF4749; Domain of unknown function (DUF4749)
    2. NM_001011515.3NP_001011515.1  PDZ and LIM domain protein 5 isoform d

      See identical proteins and their annotated locations for NP_001011515.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has multiple differences in the coding region, lacks several 3' exons but contains an alternate 3' exon, and it thus has an alternate 3' coding region and 3' UTR, compared to isoform a. The encoded isoform (d) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AA253314, AC093778, AL833151, DA895978
      Consensus CDS
      CCDS47103.1
      UniProtKB/Swiss-Prot
      Q96HC4
      Related
      ENSP00000369527.3, ENST00000380180.7
      Conserved Domains (2) summary
      cd00992
      Location:1082
      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) ...
      cl25776
      Location:105191
      DUF4749; Domain of unknown function (DUF4749)
    3. NM_001011516.3NP_001011516.1  PDZ and LIM domain protein 5 isoform e

      See identical proteins and their annotated locations for NP_001011516.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) has multiple differences in the coding region, lacks several 3' exons but contains an alternate 3' exon, and it thus has an alternate 3' coding region and 3' UTR, compared to isoform a. The encoded isoform (e, also known as ENH4) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AA253314, AC093778, AK291898, BC017902
      Consensus CDS
      CCDS47104.1
      UniProtKB/Swiss-Prot
      Q96HC4
      Related
      ENSP00000322021.5, ENST00000318007.9
      Conserved Domains (2) summary
      cd00992
      Location:1082
      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) ...
      cl25776
      Location:100171
      DUF4749; Domain of unknown function (DUF4749)
    4. NM_001256425.2NP_001243354.2  PDZ and LIM domain protein 5 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the 5' coding region and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AC093778, AC108067, AC109925
      Consensus CDS
      CCDS75166.1
      UniProtKB/TrEMBL
      A0A0A0MSP3
      Related
      ENSP00000398469.2, ENST00000437932.5
      Conserved Domains (2) summary
      cd09453
      Location:95146
      LIM1_ENH; The first LIM domain of the Enigma Homolog (ENH) family
      cl02475
      Location:213267
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
    5. NM_001256426.2NP_001243355.2  PDZ and LIM domain protein 5 isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate in-frame splice site in the 5' coding region, and contains four additional in-frame exons in the central coding region, compared to variant 1, resulting in an isoform (f) that is longer than isoform a.
      Source sequence(s)
      AC093778, AC108067, AC109925
      Consensus CDS
      CCDS58916.1
      Related
      ENSP00000480359.1, ENST00000615540.4
      Conserved Domains (5) summary
      cd09453
      Location:449500
      LIM1_ENH; The first LIM domain of the Enigma Homolog (ENH) family
      cd09459
      Location:567621
      LIM3_ENH; The third LIM domain of the Enigma Homolog (ENH) family
      cd00992
      Location:1082
      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:105201
      DUF4749; Domain of unknown function (DUF4749)
      cl02475
      Location:508559
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
    6. NM_001256427.2NP_001243356.2  PDZ and LIM domain protein 5 isoform g

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) uses an alternate in-frame splice site in the 5' coding region, contains an additional in-frame exon in the central coding region, and uses alternate 3' exon structure and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (g) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AC093778, AC108067, AC109925
      Consensus CDS
      CCDS58917.1
      Related
      ENSP00000424297.1, ENST00000503974.5
      Conserved Domains (5) summary
      cd09453
      Location:317368
      LIM1_ENH; The first LIM domain of the Enigma Homolog (ENH) family
      cd00992
      Location:1082
      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) ...
      pfam05109
      Location:149300
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl02475
      Location:376427
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
      pfam15936
      Location:105201
      DUF4749; Domain of unknown function (DUF4749)
    7. NM_001256428.2NP_001243357.2  PDZ and LIM domain protein 5 isoform h

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) lacks an alternate exon in the 5' coding region and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (h) is shorter at the N-terminus, compared to isoform a.
      Source sequence(s)
      AC093778, AC108067, AC109925
      Conserved Domains (4) summary
      cd09453
      Location:298349
      LIM1_ENH; The first LIM domain of the Enigma Homolog (ENH) family
      pfam05109
      Location:7277
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      cl02475
      Location:416470
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
      pfam15936
      Location:92182
      DUF4749; Domain of unknown function (DUF4749)
    8. NM_001256429.2NP_001243358.1  PDZ and LIM domain protein 5 isoform i

      See identical proteins and their annotated locations for NP_001243358.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) lacks several central and 3' exons but contains an alternate 3' exon, and it thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (i) has the same N-terminus but has a distinct and significantly shorter C-terminus, compared to isoform a.
      Source sequence(s)
      AA922628, AY345240
      Consensus CDS
      CCDS58915.1
      UniProtKB/Swiss-Prot
      Q96HC4
      Related
      ENSP00000352210.4, ENST00000359265.8
    9. NM_006457.5NP_006448.5  PDZ and LIM domain protein 5 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform a (also known as ENH1).
      Source sequence(s)
      AC093778, AC108067, AC109925
      Consensus CDS
      CCDS3641.1
      UniProtKB/Swiss-Prot
      Q8WVK0
      Related
      ENSP00000321746.4, ENST00000317968.9
      Conserved Domains (6) summary
      cd09453
      Location:420471
      LIM1_ENH; The first LIM domain of the Enigma Homolog (ENH) family
      cd09459
      Location:538592
      LIM3_ENH; The third LIM domain of the Enigma Homolog (ENH) family
      cd00992
      Location:1082
      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) ...
      pfam05109
      Location:84399
      Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
      pfam15936
      Location:214294
      DUF4749; Domain of unknown function (DUF4749)
      cl02475
      Location:479530
      LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

    RNA

    1. NR_046186.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) lacks several exons in the central and 3' regions, but contains an alternate 3' exon, compared to variant 1. This variant is represented as non-coding because it lacks the majority of the coding region, as found in variant 1, and it does not have any significant coding potential.
      Source sequence(s)
      AA922628, AC109925, DA381128

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      94451942..94668223
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      97767448..97983384
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)