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

Gene ID: 9260, updated on 7-Apr-2024

Summary

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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; AllianceGenome:HGNC:22958
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
mouse all
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Genomic context

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See PDLIM7 in Genome Data Viewer
Location:
5q35.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (177483394..177497604, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (178026382..178040598, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176910395..176924605, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene PRR7 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176874472-176875100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176876138-176876638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176876639-176877139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176881361-176882061 Neighboring gene proline rich 7, synaptic Neighboring gene Sharpr-MPRA regulatory region 1974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16691 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176884168-176884868 Neighboring gene drebrin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176894101-176894646 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:176895193-176895738 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:176895739-176896284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176897377-176897922 Neighboring gene hESC enhancers GRCh37_chr5:176899493-176899996 and GRCh37_chr5:176899997-176900498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176904724-176905224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176911017-176911732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176911733-176912448 Neighboring gene Sharpr-MPRA regulatory region 15492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176918835-176919378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176919379-176919920 Neighboring gene Sharpr-MPRA regulatory region 583 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176923257-176923998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176925479-176926218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176929555-176930508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176930509-176931460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23727 Neighboring gene docking protein 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176943204-176944028 Neighboring gene DEAD-box helicase 41

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Epstein-Barr virus in gastric cancer and association with 30 bp del-latent membrane protein 1 polymorphism. Santos ERCD, et al. Rev Assoc Med Bras (1992), 2023. PMID 37222327, Free PMC Article
  2. Enigma of the cholesterol paradox in acute myocardial infarction: lessons from an 8-year follow-up of all-cause mortality in an age-matched and sex-matched case-control study with controls from the patients' recruitment area. Nilsson G, et al. BMJ Open, 2022 Jul 27. PMID 35896296, Free PMC Article
  3. Overexpression of LMP-1 Decreases Apoptosis in Human Nucleus Pulposus Cells via Suppressing the NF-ÎşB Signaling Pathway. Liu Y, et al. Oxid Med Cell Longev, 2020. PMID 33414896, Free PMC Article
  4. Direct conversion of mouse embryonic fibroblast to osteoblast cells using hLMP-3 with Yamanaka factors. Ahmed MF, et al. Int J Biochem Cell Biol, 2019 Jan. PMID 30453092
  5. Specific Soft-Tissue Invasion and LMP1 Expression Are Potential Indicators of Extranodal NK/T Cell Lymphoma, Nasal Type. Jiang M, et al. Med Sci Monit, 2018 Oct 25. PMID 30356034, Free PMC Article

See all (136) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Regulatory and Interacting Partners of PDLIM7 in Thyroid Cancer.
    Title: Regulatory and Interacting Partners of PDLIM7 in Thyroid Cancer.
  2. Epstein-Barr virus in gastric cancer and association with 30 bp del-latent membrane protein 1 polymorphism.
    Title: Epstein-Barr virus in gastric cancer and association with 30 bp del-latent membrane protein 1 polymorphism.
  3. Enigma of the cholesterol paradox in acute myocardial infarction: lessons from an 8-year follow-up of all-cause mortality in an age-matched and sex-matched case-control study with controls from the patients' recruitment area.
    Title: Enigma of the cholesterol paradox in acute myocardial infarction: lessons from an 8-year follow-up of all-cause mortality in an age-matched and sex-matched case-control study with controls from the patients' recruitment area.
  4. Overexpression of LMP-1 Decreases Apoptosis in Human Nucleus Pulposus Cells via Suppressing the NF-kappaB Signaling Pathway.
    Title: Overexpression of LMP-1 Decreases Apoptosis in Human Nucleus Pulposus Cells via Suppressing the NF-ÎşB Signaling Pathway.
  5. Forces acting on integrins recruit Enigma family proteins (PDLIM5 AND PDLIM7) to trigger YAP activation during mechanotransduction.
    Title: Enigma proteins regulate YAP mechanotransduction.
  6. reported for the first time the effect of combining Yamanaka factors with hLMP-3 to induce osteoblast cells from MEF both in vitro and in vivo.
    Title: Direct conversion of mouse embryonic fibroblast to osteoblast cells using hLMP-3 with Yamanaka factors.
  7. A role for PDLIM7 and CDH18, regulating MDM2 protein in CDK4/6 inhibitor-treated cells.
    Title: PDLIM7 and CDH18 regulate the turnover of MDM2 during CDK4/6 inhibitor therapy-induced senescence.
  8. Cox proportional-hazards regression indicated that high LMP1 expression and the nasal floor thickness >2.0 mm or nasal septum thickness >2.5 mm were the independent risk factors for poor OS of ENKTL-NT (HR=3.0655, p=0.028; HR=2.3650, p=0.0452, respectively).
    Title: Specific Soft-Tissue Invasion and LMP1 Expression Are Potential Indicators of Extranodal NK/T Cell Lymphoma, Nasal Type.
  9. In enigma siRNA-transfected cells, cell viability, and the protein levels of AKT and survivin decreased.
    Title: Enigma Plays Roles in Survival of Thyroid Carcinoma Cells through PI3K/AKT Signaling and Survivin.
  10. LMOD1, SYNPO2, PDLIM7, PLN, and SYNM down-regulation reflect the altered phenotype of smooth muscle cells in vascular disease and could be early sensitive markers of SMC dedifferentiation.
    Title: Phenotypic Modulation of Smooth Muscle Cells in Atherosclerosis Is Associated With Downregulation of LMOD1, SYNPO2, PDLIM7, PLN, and SYNM.
Submit: New GeneRIF Correction See all GeneRIFs (36)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables actin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
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 
Process Evidence Code Pubs
involved_in actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell differentiation IEA
Inferred from Electronic Annotation
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
  
involved_in ossification IEA
Inferred from Electronic Annotation
more info
  
involved_in receptor-mediated endocytosis TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in Z disc IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in actin cytoskeleton IDA
Inferred from Direct Assay
more info
  
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in adherens junction IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
part_of filamentous actin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in focal adhesion IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in ruffle IEA
Inferred from Electronic Annotation
more info
  
is_active_in stress fiber IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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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)

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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_005451.5 → NP_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
    Q14250, Q5XG82, Q6NVZ5, Q96C91, Q9BXB8, Q9BXB9, Q9NR12
    Related
    ENSP00000348099.2, ENST00000355841.7
    Conserved Domains (5) summary
    cd09452
    Location:282 → 333
    LIM1_Enigma; The first LIM domain of Enigma
    cd09456
    Location:341 → 392
    LIM2_Enigma; The second LIM domain of Enigma
    cd09458
    Location:400 → 454
    LIM3_Enigma; The third LIM domain of Enigma
    cd00992
    Location:5 → 79
    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:81 → 254
    Atrophin-1; Atrophin-1 family

  2. NM_203352.3 → NP_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:248 → 299
    LIM1_Enigma; The first LIM domain of Enigma
    cd09456
    Location:307 → 358
    LIM2_Enigma; The second LIM domain of Enigma
    cd09458
    Location:366 → 420
    LIM3_Enigma; The third LIM domain of Enigma
    cd00992
    Location:5 → 79
    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:93 → 147
    DUF4749; Domain of unknown function (DUF4749)

  3. NM_213636.3 → NP_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/TrEMBL
    H7BYK4
    Related
    ENSP00000347776.2, ENST00000355572.6
    Conserved Domains (1) summary
    cd00992
    Location:5 → 79
    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_103804.2 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: GCF_000001405.40-RS_2023_10

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
    177483394..177497604 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    178026382..178040598 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NR12.1 GenPept UniProtKB/Swiss-Prot:Q9NR12

Gene LinkOut

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