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Pdlim7 PDZ and LIM domain 7 [ Rattus norvegicus (Norway rat) ]

Gene ID: 286908, updated on 11-Apr-2024

Summary

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Official Symbol
Pdlim7provided by RGD
Official Full Name
PDZ and LIM domain 7provided by RGD
Primary source
RGD:628769
See related
Ensembl:ENSRNOG00000013653 AllianceGenome:RGD:628769
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
Enigma
Summary
Predicted to enable actin binding activity and muscle alpha-actinin binding activity. Involved in positive regulation of osteoblast differentiation. Predicted to be located in several cellular components, including focal adhesion; nucleoplasm; and ruffle. Predicted to be part of filamentous actin. Predicted to be active in Z disc; adherens junction; and stress fiber. Orthologous to human PDLIM7 (PDZ and LIM domain 7). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Muscle (RPKM 461.2), Heart (RPKM 130.7) and 7 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Pdlim7 in Genome Data Viewer
Location:
17p14
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (9129603..9144956)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (9124565..9139814)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (9653510..9668715)

Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene DEAD-box helicase 41 Neighboring gene microRNA 3542 Neighboring gene docking protein 3 Neighboring gene uncharacterized LOC134482675 Neighboring gene drebrin 1 Neighboring gene proline rich 7 (synaptic)

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. The PDZ-LIM protein CLP36 is required for actin stress fiber formation and focal adhesion assembly in BeWo cells. Tamura N, et al. Biochem Biophys Res Commun, 2007 Dec 21. PMID 17964547
  2. LMP-1, a LIM-domain protein, mediates BMP-6 effects on bone formation. Boden SD, et al. Endocrinology, 1998 Dec. PMID 9832452
  3. Postsynaptic PDLIM5/Enigma Homolog binds SPAR and causes dendritic spine shrinkage. Herrick S, et al. Mol Cell Neurosci, 2010 Feb. PMID 19900557, Free PMC Article
  4. LIM Mineralization Protein-1 Enhances Bone Morphogenetic Protein-2-Mediated Osteogenesis Through Activation of ERK1/2 MAPK Pathway and Upregulation of Runx2 Transactivity. Pan H, et al. J Bone Miner Res, 2015 Aug. PMID 25677945
  5. Caveolin-1, Id3a and two LIM protein genes are upregulated by estrogen in vascular smooth muscle cells. Watanabe T, et al. Life Sci, 2004 Jul 23. PMID 15219810

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. findings describe a positive regulatory effect of LMP-1 on BMP-2 expression and BMP-2-mediated osteogenesis. This effect occurs through activation of ERK1/2 pathway and subsequent upregulation of Runx2 transactivity.
    Title: LIM Mineralization Protein-1 Enhances Bone Morphogenetic Protein-2-Mediated Osteogenesis Through Activation of ERK1/2 MAPK Pathway and Upregulation of Runx2 Transactivity.
  2. These findings indicate that CLP36 plays a critical role in stress fiber formation and the assembly of focal adhesions in BeWo cells.
    Title: The PDZ-LIM protein CLP36 is required for actin stress fiber formation and focal adhesion assembly in BeWo cells.
  3. In rats, estrogen was found to up-regulate enigma(LIM domain protein) genes in smooth muscle vascular cells.
    Title: Caveolin-1, Id3a and two LIM protein genes are upregulated by estrogen in vascular smooth muscle cells.
Submit: New GeneRIF Correction

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by RGD

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 actin cytoskeleton organization IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within actin cytoskeleton organization ISO
Inferred from Sequence Orthology
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 positive regulation of osteoblast differentiation IDA
Inferred from Direct Assay
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 ISO
Inferred from Sequence Orthology
more info
  
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in adherens junction IEA
Inferred from Electronic Annotation
more info
  
located_in adherens junction ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
part_of filamentous actin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in focal adhesion IEA
Inferred from Electronic Annotation
more info
  
located_in focal adhesion ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in ruffle IEA
Inferred from Electronic Annotation
more info
  
located_in ruffle ISO
Inferred from Sequence Orthology
more info
  
is_active_in stress fiber IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in stress fiber IEA
Inferred from Electronic Annotation
more info
  
located_in stress fiber ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
PDZ and LIM domain protein 7
Names
LIM mineralization protein 2
LMP
enigma (LIM domain protein)
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_173125.2 → NP_775148.1  PDZ and LIM domain protein 7

    See identical proteins and their annotated locations for NP_775148.1

    Status: PROVISIONAL

    Source sequence(s)
    JAXUCZ010000017
    UniProtKB/Swiss-Prot
    Q9Z1Z9
    UniProtKB/TrEMBL
    A0A8I6AKU2, A6KAR4
    Related
    ENSRNOP00000018899.3, ENSRNOT00000018899.4
    Conserved Domains (4) 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) ...

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086035.1 Reference GRCr8

    Range
    9129603..9144956
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039095428.2 → XP_038951356.1  PDZ and LIM domain protein 7 isoform X1

    UniProtKB/TrEMBL
    A0A8I6AKU2
    Conserved Domains (6) summary
    cd09452
    Location:289 → 340
    LIM1_Enigma; The first LIM domain of Enigma
    cd09456
    Location:348 → 399
    LIM2_Enigma; The second LIM domain of Enigma
    cd09458
    Location:407 → 461
    LIM3_Enigma; The third LIM domain of Enigma
    PHA03247
    Location:11 → 261
    PHA03247; large tegument protein UL36; Provisional
    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:163 → 192
    DUF4749; Domain of unknown function (DUF4749)

  2. XM_006253610.5 → XP_006253672.3  PDZ and LIM domain protein 7 isoform X2

    UniProtKB/TrEMBL
    A0A8I6AKU2, A0A8I6GK07
    Related
    ENSRNOP00000092912.1

  3. XM_063276122.1 → XP_063132192.1  PDZ and LIM domain protein 7 isoform X3

  4. XM_039095429.2 → XP_038951357.1  PDZ and LIM domain protein 7 isoform X4

    Conserved Domains (4) summary
    cd09452
    Location:289 → 340
    LIM1_Enigma; The first LIM domain of Enigma
    PHA03247
    Location:82 → 259
    PHA03247; large tegument protein UL36; Provisional
    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:163 → 192
    DUF4749; Domain of unknown function (DUF4749)

  5. XM_039095430.2 → XP_038951358.1  PDZ and LIM domain protein 7 isoform X6

    Conserved Domains (2) 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) ...
    pfam15936
    Location:170 → 192
    DUF4749; Domain of unknown function (DUF4749)

  6. XM_006253611.5 → XP_006253673.3  PDZ and LIM domain protein 7 isoform X7

    UniProtKB/TrEMBL
    A0A8I6AH90, A6KAR6
    Related
    ENSRNOP00000092278.1
    Conserved Domains (2) 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) ...
    pfam15936
    Location:163 → 185
    DUF4749; Domain of unknown function (DUF4749)

  7. XM_006253612.5 → XP_006253674.3  PDZ and LIM domain protein 7 isoform X9

    UniProtKB/TrEMBL
    A6KAR7
    Conserved Domains (2) 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) ...
    pfam15936
    Location:129 → 151
    DUF4749; Domain of unknown function (DUF4749)

  8. XM_063276123.1 → XP_063132193.1  PDZ and LIM domain protein 7 isoform X1

  9. XM_063276124.1 → XP_063132194.1  PDZ and LIM domain protein 7 isoform X5

    UniProtKB/Swiss-Prot
    Q9Z1Z9
    UniProtKB/TrEMBL
    A6KAR4

  10. XM_039095433.2 → XP_038951361.1  PDZ and LIM domain protein 7 isoform X8

    UniProtKB/TrEMBL
    A6KAS0
    Conserved Domains (3) summary
    cd09456
    Location:193 → 244
    LIM2_Enigma; The second LIM domain of Enigma
    pfam15936
    Location:8 → 37
    DUF4749; Domain of unknown function (DUF4749)
    cl02475
    Location:252 → 306
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

  11. XM_039095432.2 → XP_038951360.1  PDZ and LIM domain protein 7 isoform X8

    UniProtKB/TrEMBL
    A6KAS0
    Conserved Domains (3) summary
    cd09456
    Location:193 → 244
    LIM2_Enigma; The second LIM domain of Enigma
    pfam15936
    Location:8 → 37
    DUF4749; Domain of unknown function (DUF4749)
    cl02475
    Location:252 → 306
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

RNA

  1. XR_005495240.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Z1Z9.1 GenPept UniProtKB/Swiss-Prot:Q9Z1Z9

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