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PDLIM7 Gene(Protein Coding)

PDZ And LIM Domain 7

GCID:
GC05M177483
GIFtS:
49
Genes Participants
UDN Logo

Aliases for PDLIM7 Gene

Aliases for PDLIM7 Gene

  • PDZ And LIM Domain 7 2 3 5
  • PDZ And LIM Domain 7 (Enigma) 2 3
  • Protein Enigma 3 4
  • LMP 3 4
  • Lim Mineralization Protein 3 3
  • PDZ And LIM Domain Protein 7 3
  • LIM Mineralization Protein 4
  • LIM Domain Protein 3
  • 1110003B01Rik 3
  • ENIGMA 4
  • LMP1 3
  • LMP3 3

External Ids for PDLIM7 Gene

Previous GeneCards Identifiers for PDLIM7 Gene

  • GC00U914366
  • GC05M177024
  • GC05M176843
  • GC05M176912
  • GC05M171830

Summaries for PDLIM7 Gene

Entrez Gene Summary for PDLIM7 Gene

  • 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]

GeneCards Summary for PDLIM7 Gene

PDLIM7 (PDZ And LIM Domain 7) is a Protein Coding gene. Diseases associated with PDLIM7 include Pleural Empyema and Dental Pulp Calcification. Among its related pathways are Developmental Biology and GDNF-Family Ligands and Receptor Interactions. An important paralog of this gene is LDB3.

UniProtKB/Swiss-Prot for PDLIM7 Gene

  • May function as a scaffold on which the coordinated assembly of proteins can occur. May play a role as an adapter that, via its PDZ domain, localizes LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Involved in both of the two fundamental mechanisms of bone formation, direct bone formation (e.g. embryonic flat bones mandible and cranium), and endochondral bone formation (e.g. embryonic long bone development). Plays a role during fracture repair. Involved in BMP6 signaling pathway (By similarity).

Gene Wiki entry for PDLIM7 Gene

Additional gene information for PDLIM7 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDLIM7 Gene

Genomics for PDLIM7 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for PDLIM7 Gene

Promoters and enhancers for PDLIM7 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH05I177492 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 584.7 +2.1 2121 6.7 HDGF SMAD1 ARNT SIN3A ZNF2 YY1 SLC30A9 POLR2B ZNF213 ZNF143 PDLIM7 ENSG00000248996 RMND5B GC05P176931
GH05I177499 Enhancer 1.3 Ensembl ENCODE dbSUPER 34.5 -3.2 -3192 2.2 ATF1 FOXA2 RB1 ARNT ZSCAN4 ARID4B SIN3A ZNF2 ZNF48 RAD21 PDLIM7 ENSG00000248996 DOK3 GC05P176931
GH05I177507 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 11 -12.2 -12238 4.8 HDGF PKNOX1 TCF12 ZNF121 GLIS2 RUNX3 NCOA1 ZNF592 SMARCA4 ZNF184 DOK3 LOC105377750 PDLIM7 DDX41 GC05P176931
GH05I177490 Enhancer 0.7 ENCODE dbSUPER 28.8 +8.1 8144 0.2 CTCF ZFHX2 POLR2A KLF9 ZBTB33 EGR2 PDLIM7 DBN1 ENSG00000248996 GC05P176931
GH05I177542 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.8 -48.4 -48384 6.3 PKNOX1 FOXA2 ARID4B SIN3A ETS1 YY1 ATF7 FOS RXRA REST DOK3 LOC105377750 DDX41 TMED9 PDLIM7 MXD3 DBN1 RAB24 GRK6 NSD1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PDLIM7 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDLIM7 gene promoter:

Genomic Locations for PDLIM7 Gene

Genomic Locations for PDLIM7 Gene
chr5:177,483,394-177,497,619
(GRCh38/hg38)
Size:
14,226 bases
Orientation:
Minus strand
chr5:176,910,395-176,924,607
(GRCh37/hg19)

Genomic View for PDLIM7 Gene

Genes around PDLIM7 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDLIM7 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDLIM7 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PDLIM7 Gene

Proteins for PDLIM7 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for PDLIM7 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NR12-PDLI7_HUMAN
    Recommended name:
    PDZ and LIM domain protein 7
    Protein Accession:
    Q9NR12
    Secondary Accessions:
    • Q14250
    • Q5XG82
    • Q6NVZ5
    • Q96C91
    • Q9BXB8
    • Q9BXB9

    Protein attributes for PDLIM7 Gene

    Size:
    457 amino acids
    Molecular mass:
    49845 Da
    Quaternary structure:
    • Binds via its LIM zinc-binding 3 domain (LIM 3) to endocytic codes of INSR, but not with those of IGF1R, LDLR, TFRC, or EGFR. Interacts with various PKC isoforms through the LIM zinc-binding domains. Binds to RET in a phosphorylation-independent manner via its LIM zinc-binding domain 2 (LIM 2). Probably part of a complex with SHC and the RET dimer. Interacts with TPM2. Interacts with TBX4 and TBX5 (By similarity).
    SequenceCaution:
    • Sequence=AAC37565.1; Type=Frameshift; Positions=103, 128, 161, 183, 195, 245; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PDLIM7 Gene

    Alternative splice isoforms for PDLIM7 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDLIM7 Gene

Protein Expression for PDLIM7 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PDLIM7 Gene

No Post-translational modifications

Other Protein References for PDLIM7 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PDLIM7 Gene

Domains & Families for PDLIM7 Gene

Gene Families for PDLIM7 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PDLIM7 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PDLIM7 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NR12

UniProtKB/Swiss-Prot:

PDLI7_HUMAN :
  • The LIM zinc-binding 2 (LIM 2) domain interacts with TBX4.
Domain:
  • The LIM zinc-binding 2 (LIM 2) domain interacts with TBX4.
  • The LIM zinc-binding 3 (LIM 3) domain provides the structural basis for recognition of tyrosine-containing tight turn structures. This domain is necessary and sufficient for interaction with TBX5 (By similarity).
  • Anchored to cell periphery via its N-terminal PDZ domain.
genes like me logo Genes that share domains with PDLIM7: view

Function for PDLIM7 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for PDLIM7 Gene

UniProtKB/Swiss-Prot Function:
May function as a scaffold on which the coordinated assembly of proteins can occur. May play a role as an adapter that, via its PDZ domain, localizes LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Involved in both of the two fundamental mechanisms of bone formation, direct bone formation (e.g. embryonic flat bones mandible and cranium), and endochondral bone formation (e.g. embryonic long bone development). Plays a role during fracture repair. Involved in BMP6 signaling pathway (By similarity).

Gene Ontology (GO) - Molecular Function for PDLIM7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PDLIM7: view
genes like me logo Genes that share phenotypes with PDLIM7: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDLIM7 Gene

Localization for PDLIM7 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDLIM7 Gene

Cytoplasm. Cytoplasm, cytoskeleton. Note=Colocalizes with RET to the cell periphery and in some cytoskeletal components. Colocalizes with TPM2 near the Z line in muscle. Colocalizes with TBX4 and TBX5 to actin filaments (By similarity). {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PDLIM7 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 5
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (4)
  • Focal adhesion sites (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PDLIM7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001725 stress fiber IEA --
GO:0001726 ruffle IEA --
GO:0005634 nucleus IDA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with PDLIM7: view

Pathways & Interactions for PDLIM7 Gene

genes like me logo Genes that share pathways with PDLIM7: view

Pathways by source for PDLIM7 Gene

3 Reactome pathways for PDLIM7 Gene
1 GeneGo (Thomson Reuters) pathway for PDLIM7 Gene
1 Qiagen pathway for PDLIM7 Gene

Gene Ontology (GO) - Biological Process for PDLIM7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001503 ossification IEA --
GO:0006898 receptor-mediated endocytosis TAS 7929196
GO:0007275 multicellular organism development IEA --
GO:0007411 axon guidance TAS --
GO:0030036 actin cytoskeleton organization IEA --
genes like me logo Genes that share ontologies with PDLIM7: view

No data available for SIGNOR curated interactions for PDLIM7 Gene

Drugs & Compounds for PDLIM7 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for PDLIM7 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PDLIM7 Gene

(6) REFSEQ mRNAs :
(10) Additional mRNA sequences :
(403) Selected AceView cDNA sequences:
(16) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PDLIM7 Gene

PDZ and LIM domain 7 (enigma):
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDLIM7 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b · 5c · 5d ^ 6a · 6b · 6c ^ 7a · 7b · 7c · 7d ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^
SP1: - - - - - - - - - -
SP2: - - - - - - - - - - -
SP3: - - - - - - - - - - -
SP4: - - - - - - - - - - -
SP5: - - - - - - - -
SP6: - - - - - -
SP7: - -
SP8:
SP9: - - - -
SP10: - -
SP11: - - -
SP12:
SP13:

ExUns: 12a · 12b ^ 13 ^ 14
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for PDLIM7 Gene

GeneLoc Exon Structure for
PDLIM7
ECgene alternative splicing isoforms for
PDLIM7

Expression for PDLIM7 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDLIM7 Gene

mRNA expression in normal human tissues for PDLIM7 Gene
mRNA expression by BioGPS for PDLIM7 GenemRNA expression by GTEx for PDLIM7 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PDLIM7 Gene

This gene is overexpressed in Colon - Sigmoid (x4.4) and Artery - Aorta (x4.2).

Protein differential expression in normal tissues from HIPED for PDLIM7 Gene

This gene is overexpressed in Urinary Bladder (10.2), Bone marrow stromal cell (9.3), Colon muscle (6.9), Prostate (6.7), and Rectum (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PDLIM7 Gene



Protein tissue co-expression partners for PDLIM7 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDLIM7 Gene:

PDLIM7

SOURCE GeneReport for Unigene cluster for PDLIM7 Gene:

Hs.533040

mRNA Expression by UniProt/SwissProt for PDLIM7 Gene:

Q9NR12-PDLI7_HUMAN
Tissue specificity: Isoform 1 and isoform 2 are expressed ubiquitously, however, isoform 2 predominates in skeletal muscle, isoform 1 is more abundant in lung, spleen, leukocytes and fetal liver.

Evidence on tissue expression from TISSUES for PDLIM7 Gene

  • Nervous system(4.7)
  • Blood(4.5)
  • Heart(4.4)
  • Kidney(4.3)
  • Liver(4.2)
  • Muscle(3.1)
  • Skin(2.9)
  • Eye(2.4)
  • Bone marrow(2.2)
  • Lymph node(2.2)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with PDLIM7: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PDLIM7 Gene

Orthologs for PDLIM7 Gene

This gene was present in the common ancestor of animals.

Orthologs for PDLIM7 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PDLIM7 33 34
  • 99.49 (n)
cow
(Bos Taurus)
 Mammalia PDLIM7 33 34
  • 90.23 (n)
dog
(Canis familiaris)
 Mammalia -- 34
  • 90 (a)
 OneToMany
PDLIM7 33
  • 85.91 (n)
-- 34
  • 84 (a)
 OneToMany
mouse
(Mus musculus)
 Mammalia Pdlim7 33 16 34
  • 88.4 (n)
rat
(Rattus norvegicus)
 Mammalia Pdlim7 33
  • 87.6 (n)
oppossum
(Monodelphis domestica)
 Mammalia PDLIM7 34
  • 85 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia -- 34
  • 23 (a)
 ManyToMany
chicken
(Gallus gallus)
 Aves PDLIM7 33 34
  • 75.28 (n)
lizard
(Anolis carolinensis)
 Reptilia PDLIM7 34
  • 77 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia Str.15717 33
zebrafish
(Danio rerio)
 Actinopterygii pdlim7 33 34
  • 65.38 (n)
zgc65907 33
fruit fly
(Drosophila melanogaster)
 Insecta Zasp52 34
  • 7 (a)
 OneToMany
worm
(Caenorhabditis elegans)
 Secernentea alp-1 34
  • 11 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 39 (a)
 ManyToMany
-- 34
  • 34 (a)
 ManyToMany
Species where no ortholog for PDLIM7 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PDLIM7 Gene

ENSEMBL:
Gene Tree for PDLIM7 (if available)
TreeFam:
Gene Tree for PDLIM7 (if available)

Paralogs for PDLIM7 Gene

Paralogs for PDLIM7 Gene

(10) SIMAP similar genes for PDLIM7 Gene using alignment to 6 proteins:

Pseudogenes.org Pseudogenes for PDLIM7 Gene

genes like me logo Genes that share paralogs with PDLIM7: view

Variants for PDLIM7 Gene

Sequence variations from dbSNP and Humsavar for PDLIM7 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
VAR_036193 A breast cancer sample p.Lys450Asn
rs1000066525 -- 177,494,353(-) C/G intron_variant
rs1000104763 -- 177,486,593(-) T/C/G genic_downstream_transcript_variant, intron_variant
rs1000129710 -- 177,494,052(-) G/C intron_variant
rs1000295178 -- 177,484,909(-) C/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PDLIM7 Gene

Variant ID Type Subtype PubMed ID
nsv1161311 CNV duplication 26073780

Variation tolerance for PDLIM7 Gene

Residual Variation Intolerance Score: 85% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.81; 66.96% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDLIM7 Gene

Human Gene Mutation Database (HGMD)
PDLIM7
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDLIM7

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDLIM7 Gene

Disorders for PDLIM7 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PDLIM7 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
pleural empyema
  • abscess of pleural cavity
dental pulp calcification
  • pulp calcification
bare lymphocyte syndrome, type i
  • bls, type i
pharynx cancer
  • pharyngeal cancer
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PDLIM7

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PDLIM7: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDLIM7 Gene

Publications for PDLIM7 Gene

  1. Overexpressed LIM mineralization proteins do not require LIM domains to induce bone. (PMID: 11874232) Liu Y … Titus L (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2002) 2 3 4 58
  2. Modeling and analysis of molecularinteraction between Smurf1-WW2 domain and various isoforms of LIM mineralization protein. (PMID: 17510966) Sangadala S … Reddy BV (Proteins 2007) 3 22 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. The PDZ domain of the LIM protein enigma binds to beta-tropomyosin. (PMID: 10359609) Guy PM … Gill GN (Molecular biology of the cell 1999) 3 4 58
  5. Shc and Enigma are both required for mitogenic signaling by Ret/ptc2. (PMID: 9528800) Durick K … Taylor SS (Molecular and cellular biology 1998) 3 4 58

Products for PDLIM7 Gene

Sources for PDLIM7 Gene

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