PDLIM7 Gene (Protein Coding)

PDZ And LIM Domain 7

GC05M177483
GIFtS:
40
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 ac... See more...

Aliases for PDLIM7 Gene

Aliases for PDLIM7 Gene

  • PDZ And LIM Domain 7 2 3 5
  • PDZ And LIM Domain 7 (Enigma) 2 3
  • PDZ And LIM Domain Protein 7 3 4
  • Protein Enigma 3 4
  • ENIGMA 2 4
  • LMP 3 4
  • Lim Mineralization Protein 3 3
  • LIM Mineralization Protein 4
  • LIM Domain Protein 3
  • 1110003B01Rik 3
  • PDLIM7 5
  • 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 Lymphoepithelioma-Like Carcinoma. Among its related pathways are GDNF-Family Ligands and Receptor Interactions and RET signaling. An important paralog of this gene is LDB3.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for PDLIM7 Gene

Genomics for PDLIM7 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for PDLIM7 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDLIM7 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PDLIM7

Top Transcription factor binding sites by QIAGEN in the PDLIM7 gene promoter:
  • AP-1
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • IRF-1

Genomic Locations for PDLIM7 Gene

Genomic Locations for PDLIM7 Gene
chr5:177,483,394-177,497,606
(GRCh38/hg38)
Size:
14,213 bases
Orientation:
Minus strand
chr5:176,910,395-176,924,607
(GRCh37/hg19)
Size:
14,213 bases
Orientation:
Minus strand

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

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  • 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; Evidence={ECO:0000305};
    Miscellaneous:
    • [Isoform 2]: Did not induce bone induction.
    • [Isoform 3]: Same activity as isoform 1 in bone nodule induction.
    • [Isoform 5]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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:
  • PDZ/DHR/GLGF domain
  • Zn-binding protein, LIM
ProtoNet:

Suggested Antigen Peptide Sequences for PDLIM7 Gene

GenScript: Design optimal peptide antigens:
  • Protein enigma (PDLI7_HUMAN)

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

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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).

Phenotypes From GWAS Catalog for PDLIM7 Gene

Gene Ontology (GO) - Molecular Function for PDLIM7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003779 actin binding IBA 21873635
GO:0005515 protein binding IEA,IPI 16189514
GO:0046872 metal ion binding IEA --
GO:0051371 muscle alpha-actinin binding IBA 21873635
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

  • Taconic Biosciences Mouse Models for PDLIM7

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDLIM7

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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
plasma membrane 2
extracellular 2
endosome 2
lysosome 2
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 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 IBA 21873635
GO:0001726 ruffle IEA --
GO:0005654 nucleoplasm 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

PathCards logo

SuperPathways 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
  • Development GDNF family signaling
1 Qiagen pathway for PDLIM7 Gene
  • GDNF-Family Ligands and Receptor Interactions

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:0007507 heart development IBA 21873635
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

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  1. Drug
No Compound Related Data Available

Transcripts for PDLIM7 Gene

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

mRNA/cDNA for PDLIM7 Gene

4 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
16 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDLIM7

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

Expression for PDLIM7 Gene

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  1. Primer
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for PDLIM7 Gene



Protein tissue co-expression partners for PDLIM7 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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(4.8)
  • Blood(4.6)
  • Heart(4.5)
  • Kidney(4.5)
  • Liver(4.4)
  • Skin(3.7)
  • Muscle(3.5)
  • Eye(2.7)
  • Bone marrow(2.6)
  • Intestine(2.6)
  • Lymph node(2.5)
  • Spleen(2.4)
  • Lung(2.4)
  • Stomach(2)
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 30 31
  • 99.49 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia PDLIM7 30 31
  • 90.23 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia -- 31
  • 90 (a)
 OneToMany
PDLIM7 30
  • 85.91 (n)
-- 31
  • 84 (a)
 OneToMany
Mouse
(Mus musculus)
 Mammalia Pdlim7 30 17 31
  • 88.4 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Pdlim7 30
  • 87.6 (n)
Oppossum
(Monodelphis domestica)
 Mammalia PDLIM7 31
  • 85 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 23 (a)
 ManyToMany
Chicken
(Gallus gallus)
 Aves PDLIM7 30 31
  • 75.28 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia PDLIM7 31
  • 77 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia Str.15717 30
Zebrafish
(Danio rerio)
 Actinopterygii pdlim7 30 31
  • 65.38 (n)
 OneToOne
zgc65907 30
Fruit Fly
(Drosophila melanogaster)
 Insecta Zasp52 31
  • 7 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea alp-1 31
  • 11 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea -- 31
  • 39 (a)
 ManyToMany
-- 31
  • 34 (a)
 ManyToMany
Species where no ortholog for PDLIM7 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for PDLIM7: view image

Paralogs for PDLIM7 Gene

Paralogs for PDLIM7 Gene

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

  • PDLI7_HUMAN
  • D6RAN1_HUMAN
  • D6RF83_HUMAN
  • D6RH06_HUMAN
  • H0Y8W6_HUMAN
  • H7BYK4_HUMAN

Pseudogenes.org Pseudogenes for PDLIM7 Gene

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

Variants for PDLIM7 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PDLIM7 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
717548 Benign: not provided 177,483,716(-) G/A NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
720469 Benign: not provided 177,484,155(-) C/A NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
724049 Benign: not provided 177,489,464(-) G/A NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
727280 Benign: not provided 177,491,068(-) C/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
733996 Benign: not provided 177,490,914(-) G/A INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for PDLIM7 Gene

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

(5) MalaCards diseases for PDLIM7 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
pleural empyema
  • abscess of pleural cavity
lymphoepithelioma-like carcinoma
  • lymphoepithelial carcinoma
pfeiffer syndrome
  • acrocephalosyndactyly, type v; acs5
mental depression
  • depression
nasopharyngeal carcinoma
  • npc
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PDLIM7

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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
  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 23
  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
  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
  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

ExternalLinks

View latest publications for PDLIM7 gene in Mastermind

Products for PDLIM7 Gene

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Sources for PDLIM7 Gene