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

Gene ID: 10611, updated on 5-Jul-2020

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
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

Genomic context

See PDLIM5 in Genome Data Viewer
Location:
4q22.3
Exon count:
21
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (94451857..94668227)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (95373008..95589378)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene hematopoietic prostaglandin D synthase Neighboring gene ribosomal protein L35a pseudogene 11 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

NHGRI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
NHGRI GWA Catalog
Identification of seven new prostate cancer susceptibility loci through a genome-wide association study.
NHGRI GWA 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
actin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
actin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
actinin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
cadherin binding involved in cell-cell adhesion HDA PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
muscle alpha-actinin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein N-terminus binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase C binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell growth involved in cardiac muscle cell development ISS
Inferred from Sequence or Structural Similarity
more info
 
cell-cell adhesion IEA
Inferred from Electronic Annotation
more info
 
heart development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
muscle structure development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of dendritic spine morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
Z disc IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
actin cytoskeleton IDA
Inferred from Direct Assay
more info
 
adherens junction HDA PubMed 
adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell projection IEA
Inferred from Electronic Annotation
more info
 
cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
filamentous actin IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
postsynaptic density ISS
Inferred from Sequence or Structural Similarity
more info
 
presynapse IEA
Inferred from Electronic Annotation
more info
 
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)

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
  2. NM_001011515.2NP_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_001011516.2NP_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, DA895978
    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_001256425.1NP_001243354.1  PDZ and LIM domain protein 5 isoform c

    See identical proteins and their annotated locations for NP_001243354.1

    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)
    AA614664, AC108067, BC026029, DA895978
    Consensus CDS
    CCDS75166.1
    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_001256426.1NP_001243355.1  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)
    AA614664, AC093778, AC108067, AL832686, DA895978
    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:105191
    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
  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
  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
    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 Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    94451857..94668227
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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