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PDLIM7 PDZ and LIM domain 7 [ Homo sapiens (human) ]

Gene ID: 9260, updated on 15-Apr-2019

Summary

Official Symbol
PDLIM7provided by HGNC
Official Full Name
PDZ and LIM domain 7provided by HGNC
Primary source
HGNC:HGNC:22958
See related
Ensembl:ENSG00000196923 MIM:605903
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
LMP1; LMP3
Summary
The protein encoded by this gene is representative of a family of proteins composed of conserved PDZ and LIM domains. LIM domains are proposed to function in protein-protein recognition in a variety of contexts including gene transcription and development and in cytoskeletal interaction. The LIM domains of this protein bind to protein kinases, whereas the PDZ domain binds to actin filaments. The gene product is involved in the assembly of an actin filament-associated complex essential for transmission of ret/ptc2 mitogenic signaling. The biological function is likely to be that of an adapter, with the PDZ domain localizing the LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]
Expression
Broad expression in endometrium (RPKM 61.1), prostate (RPKM 52.9) and 22 other tissues See more
Orthologs

Genomic context

See PDLIM7 in Genome Data Viewer
Location:
5q35.3
Exon count:
15
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (177483394..177497605, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176910395..176924606, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene G protein-coupled receptor kinase 6 Neighboring gene PRR7 antisense RNA 1 Neighboring gene proline rich 7, synaptic Neighboring gene drebrin 1 Neighboring gene docking protein 3 Neighboring gene DEAD-box helicase 41

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?

Pathways from BioSystems

  • Axon guidance, organism-specific biosystem (from REACTOME)
    Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • EBV LMP1 signaling, organism-specific biosystem (from WikiPathways)
    EBV LMP1 signaling, organism-specific biosystem
    EBV LMP1 signaling
  • RET signaling, organism-specific biosystem (from REACTOME)
    RET signaling, organism-specific biosystemThe RET proto-oncogene encodes a receptor tyrosine kinase expressed primarily in urogenital precursor cells, spermatogonocytes, dopaminergic neurons, motor neurons and neural crest progenitors and de...
  • Signaling events regulated by Ret tyrosine kinase, organism-specific biosystem (from Pathway Interaction Database)
    Signaling events regulated by Ret tyrosine kinase, organism-specific biosystem
    Signaling events regulated by Ret tyrosine kinase

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
actin cytoskeleton organization IEA
Inferred from Electronic Annotation
more info
 
axon guidance TAS
Traceable Author Statement
more info
 
ossification IEA
Inferred from Electronic Annotation
more info
 
positive regulation of osteoblast differentiation IEA
Inferred from Electronic Annotation
more info
 
receptor-mediated endocytosis TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
actin cytoskeleton IDA
Inferred from Direct Assay
more info
 
cell-cell adherens junction IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
focal adhesion IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
ruffle IEA
Inferred from Electronic Annotation
more info
 
stress fiber IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
PDZ and LIM domain protein 7
Names
1110003B01Rik
LIM domain protein
LMP
Lim mineralization protein 3
PDZ and LIM domain 7 (enigma)
protein enigma

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_005451.5NP_005442.2  PDZ and LIM domain protein 7 isoform 1

    See identical proteins and their annotated locations for NP_005442.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    BC001093, HY026171
    Consensus CDS
    CCDS4422.1
    UniProtKB/Swiss-Prot
    Q9NR12
    Related
    ENSP00000348099.2, ENST00000355841.7
    Conserved Domains (5) summary
    cd09452
    Location:282333
    LIM1_Enigma; The first LIM domain of Enigma
    cd09456
    Location:341392
    LIM2_Enigma; The second LIM domain of Enigma
    cd09458
    Location:400454
    LIM3_Enigma; The third LIM domain of Enigma
    cd00992
    Location:579
    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) ...
    cl26464
    Location:81254
    Atrophin-1; Atrophin-1 family
  2. NM_203352.2NP_976227.1  PDZ and LIM domain protein 7 isoform 2

    See identical proteins and their annotated locations for NP_976227.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. This variant encodes isoform 2 which is shorter than isoform 1.
    Source sequence(s)
    AF345905, BC001093, HY026171
    Consensus CDS
    CCDS4423.1
    UniProtKB/Swiss-Prot
    Q9NR12
    Related
    ENSP00000352964.2, ENST00000359895.6
    Conserved Domains (5) summary
    cd09452
    Location:248299
    LIM1_Enigma; The first LIM domain of Enigma
    cd09456
    Location:307358
    LIM2_Enigma; The second LIM domain of Enigma
    cd09458
    Location:366420
    LIM3_Enigma; The third LIM domain of Enigma
    cd00992
    Location:579
    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:93147
    DUF4749; Domain of unknown function (DUF4749)
  3. NM_213636.2NP_998801.1  PDZ and LIM domain protein 7 isoform 4

    See identical proteins and their annotated locations for NP_998801.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks several exons and has an alternate 3' terminal exon, compared to variant 1. The resulting isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC014521, HY026171
    Consensus CDS
    CCDS4424.1
    UniProtKB/Swiss-Prot
    Q9NR12
    Related
    ENSP00000347776.2, ENST00000355572.6
    Conserved Domains (1) summary
    cd00992
    Location:579
    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) ...

RNA

  1. NR_103804.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) has an alternate splice site in the central region, 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)
    BC001093, BC067806, BU956109, HY026171
    Related
    ENST00000486828.6

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_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    177483394..177497605 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534698.2XP_011533000.1  PDZ and LIM domain protein 7 isoform X1

    Conserved Domains (4) summary
    cd09452
    Location:189240
    LIM1_Enigma; The first LIM domain of Enigma
    cd09456
    Location:248299
    LIM2_Enigma; The second LIM domain of Enigma
    cd09458
    Location:307361
    LIM3_Enigma; The third LIM domain of Enigma
    pfam15936
    Location:4488
    DUF4749; Domain of unknown function (DUF4749)
  2. XM_011534699.2XP_011533001.1  PDZ and LIM domain protein 7 isoform X2

    Conserved Domains (3) summary
    cd09456
    Location:193244
    LIM2_Enigma; The second LIM domain of Enigma
    cd09458
    Location:252306
    LIM3_Enigma; The third LIM domain of Enigma
    cl02475
    Location:134185
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_203353.1: Suppressed sequence

    Description
    NM_203353.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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