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PDLIM3 PDZ and LIM domain 3 [ Homo sapiens (human) ]

Gene ID: 27295, updated on 9-Dec-2018

Summary

Official Symbol
PDLIM3provided by HGNC
Official Full Name
PDZ and LIM domain 3provided by HGNC
Primary source
HGNC:HGNC:20767
See related
Ensembl:ENSG00000154553 MIM:605889
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
ALP
Summary
The protein encoded by this gene contains a PDZ domain and a LIM domain, indicating that it may be involved in cytoskeletal assembly. In support of this, the encoded protein has been shown to bind the spectrin-like repeats of alpha-actinin-2 and to colocalize with alpha-actinin-2 at the Z lines of skeletal muscle. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Aberrant alternative splicing of this gene may play a role in myotonic dystrophy. [provided by RefSeq, Apr 2012]
Expression
Broad expression in esophagus (RPKM 61.1), heart (RPKM 58.0) and 19 other tissues See more
Orthologs

Genomic context

See PDLIM3 in Genome Data Viewer
Location:
4q35.1
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (185500660..185535558, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (186421814..186456712, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene chromosome 4 open reading frame 47 Neighboring gene UFM1 specific peptidase 2 Neighboring gene uncharacterized LOC105377590 Neighboring gene coiled-coil domain containing 110 Neighboring gene sorbin and SH3 domain containing 2 Neighboring gene uncharacterized LOC101928929 Neighboring gene RNA, U4 small nuclear 64, pseudogene

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 FunctionsWhat's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ26096, DKFZp686L0362

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cytoskeletal protein binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
structural constituent of muscle IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
actin filament organization IEA
Inferred from Electronic Annotation
more info
 
heart development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Z disc IEA
Inferred from Electronic Annotation
more info
 
actin cytoskeleton IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
PDZ and LIM domain protein 3
Names
alpha-actinin-2-associated LIM protein
enigma homolog

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.

Genomic

  1. NG_032576.2 RefSeqGene

    Range
    5001..39899
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001114107.4NP_001107579.1  PDZ and LIM domain protein 3 isoform b

    See identical proteins and their annotated locations for NP_001107579.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two consecutive exons in the coding region and contains an alternate coding exon, but maintains the reading frame, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
    Source sequence(s)
    AC106897, BC027870, BI913867
    Consensus CDS
    CCDS47172.1
    UniProtKB/Swiss-Prot
    Q53GG5
    Related
    ENSP00000284771.6, ENST00000284771.6
    Conserved Domains (3) summary
    cd09450
    Location:246298
    LIM_ALP; This family represents the LIM domain of ALP, actinin-associated LIM protein
    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:137218
    DUF4749; Domain of unknown function (DUF4749)
  2. NM_001257962.1NP_001244891.1  PDZ and LIM domain protein 3 isoform c

    See identical proteins and their annotated locations for NP_001244891.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
    Source sequence(s)
    AC106897, BI913867, C03422, CD625728
    Consensus CDS
    CCDS75219.1
    UniProtKB/TrEMBL
    A0A0A0MQY0
    Related
    ENSP00000481771.2, ENST00000620787.5
    Conserved Domains (3) summary
    cd09450
    Location:206258
    LIM_ALP; This family represents the LIM domain of ALP, actinin-associated LIM protein
    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:132177
    DUF4749; Domain of unknown function (DUF4749)
  3. NM_001257963.1NP_001244892.1  PDZ and LIM domain protein 3 isoform d

    See identical proteins and their annotated locations for NP_001244892.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks three exons in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (d) is shorter than isoform a.
    Source sequence(s)
    AC106897, BI913867, DA898089
    Consensus CDS
    CCDS75218.1
    UniProtKB/TrEMBL
    A0A087WYF8
    Related
    ENSP00000284770.5, ENST00000284770.10
    Conserved Domains (2) summary
    cd09450
    Location:127179
    LIM_ALP; This family represents the LIM domain of ALP, actinin-associated LIM protein
    pfam15936
    Location:5398
    DUF4749; Domain of unknown function (DUF4749)
  4. NM_014476.5NP_055291.2  PDZ and LIM domain protein 3 isoform a

    See identical proteins and their annotated locations for NP_055291.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC106897, AK313253, BI913867
    Consensus CDS
    CCDS3844.1
    UniProtKB/Swiss-Prot
    Q53GG5
    Related
    ENSP00000284767.7, ENST00000284767.10
    Conserved Domains (3) summary
    cd09450
    Location:294346
    LIM_ALP; This family represents the LIM domain of ALP, actinin-associated LIM protein
    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:184265
    DUF4749; Domain of unknown function (DUF4749)

RNA

  1. NR_047562.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks two consecutive internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC106897, AK129863, BI913867

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    185500660..185535558 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_938723.3 RNA Sequence

  2. XR_001741206.2 RNA Sequence

  3. XR_938724.3 RNA Sequence

    Related
    ENST00000643009.1
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