GPC1 Gene (Protein Coding)

Glypican 1

GC02P240435
GIFtS:
43
Cell surface heparan sulfate proteoglycans are composed of a membrane-associated protein core substituted with a variable number of heparan sulfate chains. Members of the glypican-related integral membrane proteoglycan family (GRIPS) contain a core protein anchored to the cytoplasmic membrane via a glycosyl phosphatidylinositol linkage. These proteins may play a role in the co... See more...

Aliases for GPC1 Gene

Aliases for GPC1 Gene

  • Glypican 1 2 3 5
  • Glypican Proteoglycan 1 2 3
  • Glypican-1 3 4
  • Glypican 2 3
  • Epididymis Secretory Sperm Binding Protein 3
  • GPC1 5

External Ids for GPC1 Gene

Previous GeneCards Identifiers for GPC1 Gene

  • GC02M240071
  • GC02M240913
  • GC02P241394
  • GC02P241695
  • GC02P241095
  • GC02P241023
  • GC02P233131
  • GC02P241378

Summaries for GPC1 Gene

Entrez Gene Summary for GPC1 Gene

  • Cell surface heparan sulfate proteoglycans are composed of a membrane-associated protein core substituted with a variable number of heparan sulfate chains. Members of the glypican-related integral membrane proteoglycan family (GRIPS) contain a core protein anchored to the cytoplasmic membrane via a glycosyl phosphatidylinositol linkage. These proteins may play a role in the control of cell division and growth regulation. [provided by RefSeq, Jul 2008]

GeneCards Summary for GPC1 Gene

GPC1 (Glypican 1) is a Protein Coding gene. Diseases associated with GPC1 include Biliary Atresia, Extrahepatic and Simpson-Golabi-Behmel Syndrome, Type 1. Among its related pathways are Signaling by GPCR and Cell surface interactions at the vascular wall. Gene Ontology (GO) annotations related to this gene include copper ion binding and fibroblast growth factor binding. An important paralog of this gene is GPC6.

UniProtKB/Swiss-Prot Summary for GPC1 Gene

  • Cell surface proteoglycan that bears heparan sulfate. Binds, via the heparan sulfate side chains, alpha-4 (V) collagen and participates in Schwann cell myelination (By similarity). May act as a catalyst in increasing the rate of conversion of prion protein PRPN(C) to PRNP(Sc) via associating (via the heparan sulfate side chains) with both forms of PRPN, targeting them to lipid rafts and facilitating their interaction. Required for proper skeletal muscle differentiation by sequestering FGF2 in lipid rafts preventing its binding to receptors (FGFRs) and inhibiting the FGF-mediated signaling.

Gene Wiki entry for GPC1 Gene

Additional gene information for GPC1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GPC1 Gene

Genomics for GPC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for GPC1 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 GPC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GPC1

Genomic Locations for GPC1 Gene

Genomic Locations for GPC1 Gene
chr2:240,435,663-240,468,076
(GRCh38/hg38)
Size:
32,414 bases
Orientation:
Plus strand
chr2:241,375,088-241,407,495
(GRCh37/hg19)
Size:
32,408 bases
Orientation:
Plus strand

Genomic View for GPC1 Gene

Genes around GPC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GPC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GPC1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for GPC1 Gene

Proteins for GPC1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for GPC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P35052-GPC1_HUMAN
    Recommended name:
    Glypican-1
    Protein Accession:
    P35052
    Secondary Accessions:
    • B3KTD1
    • Q53QM4

    Protein attributes for GPC1 Gene

    Size:
    558 amino acids
    Molecular mass:
    61680 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for GPC1 Gene

    Alternative splice isoforms for GPC1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GPC1 Gene

Protein Expression for GPC1 Gene

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

Post-translational modifications for GPC1 Gene

  • S-nitrosylated in a Cu(2+)-dependent manner. Nitric acid (NO) is released from the nitrosylated cysteines by ascorbate or by some other reducing agent, in a Cu(2+) or Zn(2+) dependent manner. This free nitric oxide is then capable of cleaving the heparan sulfate side chains.
  • N- and O-glycosylated. N-glycosylation is mainly of the complex type containing sialic acid. O-glycosylated with heparan sulfate. The heparan sulfate chains can be cleaved either by the action of heparanase or, degraded by a deaminative process that uses nitric oxide (NO) released from the S-nitrosylated cysteines. This process is triggered by ascorbate, or by some other reducing agent, in a Cu(2+)- or Zn(2+) dependent manner. Cu(2+) ions are provided by ceruloproteins such as APP, PRNP or CP which associate with GCP1 in intracellular compartments or lipid rafts.
  • This cell-associated glypican is further processed to give rise to a medium-released species.
  • Glycosylation at Asn79, Asn116, Ser486, Ser488, Ser490, Thr512, and Thr515
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect

Other Protein References for GPC1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for GPC1 Gene

Domains & Families for GPC1 Gene

Gene Families for GPC1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for GPC1 Gene

InterPro:
Blocks:
  • Glypican
ProtoNet:

Suggested Antigen Peptide Sequences for GPC1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ39319 fis, clone OCBBF2014576, highly similar to GLYPICAN-1 (B3KTD1_HUMAN)
  • Glypican-1 (GPC1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P35052

UniProtKB/Swiss-Prot:

GPC1_HUMAN :
  • Belongs to the glypican family.
Family:
  • Belongs to the glypican family.
genes like me logo Genes that share domains with GPC1: view

Function for GPC1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
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  6. Cell Line

Molecular function for GPC1 Gene

UniProtKB/Swiss-Prot Function:
Cell surface proteoglycan that bears heparan sulfate. Binds, via the heparan sulfate side chains, alpha-4 (V) collagen and participates in Schwann cell myelination (By similarity). May act as a catalyst in increasing the rate of conversion of prion protein PRPN(C) to PRNP(Sc) via associating (via the heparan sulfate side chains) with both forms of PRPN, targeting them to lipid rafts and facilitating their interaction. Required for proper skeletal muscle differentiation by sequestering FGF2 in lipid rafts preventing its binding to receptors (FGFRs) and inhibiting the FGF-mediated signaling.
GENATLAS Biochemistry:
glypican 1,62kDa,integral membrane (heparan sulfate) proteoglycan,potentially,involved in cell adhesion,cell growth histogenesis of nervous central system,receptor of SLIT1 and SLIT3

Phenotypes From GWAS Catalog for GPC1 Gene

Gene Ontology (GO) - Molecular Function for GPC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005507 copper ion binding IDA 12732622
GO:0017134 fibroblast growth factor binding IBA,ISS --
GO:0043236 laminin binding IEA,ISS --
genes like me logo Genes that share ontologies with GPC1: view
genes like me logo Genes that share phenotypes with GPC1: view

Human Phenotype Ontology for GPC1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for GPC1 Gene

MGI Knock Outs for GPC1:
  • Gpc1 Gpc1<tm1.1Alan>

Animal Model Products

  • Taconic Biosciences Mouse Models for GPC1

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GPC1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for GPC1 Gene

Localization for GPC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GPC1 Gene

Cell membrane. Lipid-anchor, GPI-anchor. Extracellular side. Endosome. Note=S-nitrosylated form recycled in endosomes. Localizes to CAV1-containing vesicles close to the cell surface. Cleavage of heparan sulfate side chains takes place mainly in late endosomes. Associates with both forms of PRNP in lipid rafts. Colocalizes with APP in perinuclear compartments and with CP in intracellular compartments. Associates with fibrillar APP amyloid-beta peptides in lipid rafts in Alzheimer disease brains.
[Secreted glypican-1]: Secreted, extracellular space.

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 GPC1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endosome 5
nucleus 4
cytosol 4
lysosome 4
golgi apparatus 4
cytoskeleton 2
endoplasmic reticulum 2
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GPC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region HDA,IBA 21873635
GO:0005615 extracellular space TAS 2148568
GO:0005654 nucleoplasm IDA --
GO:0005768 endosome IEA --
GO:0005796 Golgi lumen TAS --
genes like me logo Genes that share ontologies with GPC1: view

Pathways & Interactions for GPC1 Gene

genes like me logo Genes that share pathways with GPC1: view

SIGNOR curated interactions for GPC1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for GPC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001523 retinoid metabolic process TAS --
GO:0006024 glycosaminoglycan biosynthetic process TAS --
GO:0006027 glycosaminoglycan catabolic process TAS --
GO:0007411 axon guidance TAS --
GO:0009966 regulation of signal transduction IEA --
genes like me logo Genes that share ontologies with GPC1: view

Drugs & Compounds for GPC1 Gene

Products:

  1. Drug

(1) Drugs for GPC1 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Triethylenetetramine Approved, Investigational Pharma Transporter, substrate 0
genes like me logo Genes that share compounds with GPC1: view

Transcripts for GPC1 Gene

Products:

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

mRNA/cDNA for GPC1 Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
9 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 GPC1

Alternative Splicing Database (ASD) splice patterns (SP) for GPC1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b · 7c ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14
SP1: - - - - - -
SP2: - - - - -
SP3: -
SP4:
SP5: - - -
SP6: - -
SP7:
SP8: -

Relevant External Links for GPC1 Gene

GeneLoc Exon Structure for
GPC1

Expression for GPC1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GPC1 Gene

mRNA expression in normal human tissues for GPC1 Gene
mRNA expression by GTEx for GPC1 GenemRNA expression by BioGPS for GPC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for GPC1 Gene

This gene is overexpressed in Amniocyte (11.4) and Testis (9.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GPC1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GPC1

SOURCE GeneReport for Unigene cluster for GPC1 Gene:

Hs.328232

Evidence on tissue expression from TISSUES for GPC1 Gene

  • Nervous system(4.9)
  • Lung(4.5)
  • Skin(3.3)
  • Muscle(3.1)
  • Heart(3)
  • Liver(2.5)
  • Kidney(2.5)
  • Intestine(2.5)
  • Eye(2.4)
  • Pancreas(2.3)
  • Blood(2.3)
  • Adrenal gland(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for GPC1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • skeletal muscle
  • urinary
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • head
  • mouth
  • salivary gland
Thorax:
  • breast
  • esophagus
Abdomen:
  • biliary tract
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • liver
  • small intestine
  • spleen
Pelvis:
  • testicle
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • nail
  • toe
  • upper limb
General:
  • blood vessel
  • coagulation system
  • skin
genes like me logo Genes that share expression patterns with GPC1: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for GPC1 Gene

Orthologs for GPC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for GPC1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia GPC1 30
  • 91.33 (n)
Cow
(Bos Taurus)
 Mammalia GPC1 30 31
  • 88.64 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia GPC1 30 31
  • 87.88 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Gpc1 30 17 31
  • 86.95 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Gpc1 30
  • 86.32 (n)
Oppossum
(Monodelphis domestica)
 Mammalia GPC1 31
  • 75 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia GPC1 31
  • 62 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves GPC1 30 31
  • 67.39 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia GPC1 31
  • 60 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia gpc1 30
  • 61.72 (n)
Zebrafish
(Danio rerio)
 Actinopterygii gpc1a 30 31
  • 60.97 (n)
 OneToMany
GPC1 (2 of 3) 31
  • 52 (a)
 OneToMany
gpc1b 31
  • 50 (a)
 OneToMany
zgc63947 30
Fruit Fly
(Drosophila melanogaster)
 Insecta dlp 31
  • 22 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea gpn-1 31
  • 20 (a)
 OneToMany
Species where no ortholog for GPC1 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 Squirt (Ciona savignyi)
  • 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 GPC1 Gene

ENSEMBL:
Gene Tree for GPC1 (if available)
TreeFam:
Gene Tree for GPC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GPC1: view image

Paralogs for GPC1 Gene

Paralogs for GPC1 Gene

(3) SIMAP similar genes for GPC1 Gene using alignment to 7 proteins:

  • GPC1_HUMAN
  • B3KTD1_HUMAN
  • C9J4Y6_HUMAN
  • H7BZE9_HUMAN
  • H7BZL4_HUMAN
  • H7C024_HUMAN
  • H7C410_HUMAN
genes like me logo Genes that share paralogs with GPC1: view

Variants for GPC1 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GPC1 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
725099 Likely Benign: not provided 240,462,311(+) G/A MISSENSE_VARIANT
747734 Likely Benign: not provided 240,465,626(+) C/T SYNONYMOUS_VARIANT
781829 Benign: not provided 240,465,497(+) C/T SYNONYMOUS_VARIANT
790521 Benign: not provided 240,462,246(+) C/T SYNONYMOUS_VARIANT
VAR_036044 A breast cancer sample p.Ala337Asp

Additional dbSNP identifiers (rs#s) for GPC1 Gene

Structural Variations from Database of Genomic Variants (DGV) for GPC1 Gene

Variant ID Type Subtype PubMed ID
dgv7359n54 CNV loss 21841781
esv1000024 CNV deletion 20482838
esv1515337 CNV insertion 17803354
esv2721931 CNV deletion 23290073
esv2721932 CNV deletion 23290073
esv2721933 CNV deletion 23290073
esv2759119 CNV gain 17122850
esv3594796 CNV gain 21293372
esv3594798 CNV gain 21293372
nsv1071663 CNV deletion 25765185
nsv1122025 CNV deletion 24896259
nsv1126584 CNV deletion 24896259
nsv460157 CNV loss 19166990
nsv460158 CNV loss 19166990
nsv473084 CNV novel sequence insertion 20440878
nsv508899 CNV insertion 20534489
nsv516179 CNV loss 19592680
nsv584809 CNV gain 21841781
nsv584810 CNV loss 21841781
nsv584811 CNV loss 21841781
nsv819854 CNV gain 19587683
nsv834585 CNV loss 17160897
nsv955288 CNV deletion 24416366
nsv997288 CNV gain 25217958

Variation tolerance for GPC1 Gene

Residual Variation Intolerance Score: 80% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GPC1 Gene

Human Gene Mutation Database (HGMD)
GPC1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GPC1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GPC1 Gene

Disorders for GPC1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for GPC1 Gene - From: Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search GPC1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

GPC1_HUMAN
  • Note=Associates (via the heparan sulfate side chains) with fibrillar APP amyloid-beta peptides in primitive and classic amyloid plaques and may be involved in the deposition of these senile plaques in the Alzheimer disease (AD) brain (PubMed:15084524). {ECO:0000269 PubMed:15084524}.
  • Note=Misprocessing of GPC1 is found in fibroblasts of patients with Niemann-Pick Type C1 disease. This is due to the defective deaminative degradation of heparan sulfate chains (PubMed:16645004). {ECO:0000269 PubMed:16645004}.

Additional Disease Information for GPC1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with GPC1: view

No data available for Genatlas for GPC1 Gene

Publications for GPC1 Gene

  1. Crystal structure of N-glycosylated human glypican-1 core protein: structure of two loops evolutionarily conserved in vertebrate glypican-1. (PMID: 22351761) Svensson G … Logan DT (The Journal of biological chemistry 2012) 3 4
  2. The structural role of N-linked glycans on human glypican-1. (PMID: 21932778) Svensson G … Mani K (Biochemistry 2011) 3 4
  3. S-Nitrosylation of secreted recombinant human glypican-1. (PMID: 19479373) Svensson G … Mani K (Glycoconjugate journal 2009) 3 4
  4. A genome-wide association study of schizophrenia using brain activation as a quantitative phenotype. (PMID: 19023125) Potkin SG … FBIRN (Schizophrenia bulletin 2009) 3 41
  5. Common genetic variants in pre-microRNAs were associated with increased risk of breast cancer in Chinese women. (PMID: 18634034) Hu Z … Shen H (Human mutation 2009) 3 41

ExternalLinks

View latest publications for GPC1 gene in Mastermind

Products for GPC1 Gene

Sources for GPC1 Gene