Human Gene GPC5 (uc010tif.2)
  Description: Homo sapiens glypican 5 (GPC5), mRNA.
RefSeq Summary (NM_004466): 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].
Transcript (Including UTRs)
   Position: hg19 chr13:92,050,935-93,519,487 Size: 1,468,553 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr13:92,051,301-93,518,692 Size: 1,467,392 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:92,050,935-93,519,487)mRNA (may differ from genome)Protein (572 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GPC5_HUMAN
DESCRIPTION: RecName: Full=Glypican-5; Contains: RecName: Full=Secreted glypican-5; Flags: Precursor;
FUNCTION: Cell surface proteoglycan that bears heparan sulfate (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor, GPI-anchor; Extracellular side (By similarity).
SUBCELLULAR LOCATION: Secreted glypican-5: Secreted, extracellular space (By similarity).
TISSUE SPECIFICITY: In adult, primarily expressed in the brain. Also detected in fetal brain, lung and liver.
SIMILARITY: Belongs to the glypican family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): GPC5
CDC HuGE Published Literature: GPC5
Positive Disease Associations: Body Mass Index , Body Weight , Cholesterol, HDL , Coronary Artery Disease , Docosahexaenoic Acids , Echocardiography , Glucose , height , Hip , HIV-1 , Lung Neoplasms , Mental Competency , Monocyte Chemoattractant Protein-1 , multiple sclerosis , Nephrotic Syndrome , Platelet Aggregation , serum metabolites , Stroke
Related Studies:
  1. Body Mass Index
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  2. Body Weight
    , , . [PubMed 0]
  3. Cholesterol, HDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: GPC5
Diseases sorted by gene-association score: simpson-golabi-behmel syndrome (5), tetralogy of fallot (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.82 RPKM in Brain - Caudate (basal ganglia)
Total median expression: 54.88 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -171.90366-0.470 Picture PostScript Text
3' UTR -155.52795-0.196 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001863 - Glypican
IPR019803 - Glypican_CS

Pfam Domains:
PF01153 - Glypican

ModBase Predicted Comparative 3D Structure on P78333
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details  Gene Details  
Gene Sorter  Gene Sorter  
  EnsemblFlyBase  
  Protein SequenceProtein Sequence  
  AlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0043395 heparan sulfate proteoglycan binding

Biological Process:
GO:0001523 retinoid metabolic process
GO:0006024 glycosaminoglycan biosynthetic process
GO:0006027 glycosaminoglycan catabolic process
GO:0009966 regulation of signal transduction

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005796 Golgi lumen
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0031225 anchored component of membrane
GO:0043202 lysosomal lumen
GO:0046658 anchored component of plasma membrane


-  Descriptions from all associated GenBank mRNAs
  BC039730 - Homo sapiens glypican 5, mRNA (cDNA clone MGC:47702 IMAGE:5744533), complete cds.
AK312815 - Homo sapiens cDNA, FLJ93248, Homo sapiens glypican 5 (GPC5), mRNA.
BC030584 - Homo sapiens cDNA clone IMAGE:4826683, containing frame-shift errors.
AF001462 - Homo sapiens glypican-5 (GPC5) mRNA, complete cds.
U66033 - Human glypican-5 (GPC5) mRNA, complete cds.
CU691756 - Synthetic construct Homo sapiens gateway clone IMAGE:100020891 5' read GPC5 mRNA.
JF432362 - Synthetic construct Homo sapiens clone IMAGE:100073555 glypican 5 (GPC5) gene, encodes complete protein.
KJ891168 - Synthetic construct Homo sapiens clone ccsbBroadEn_00562 GPC5 gene, encodes complete protein.
JD487385 - Sequence 468409 from Patent EP1572962.
JD358700 - Sequence 339724 from Patent EP1572962.
JD544477 - Sequence 525501 from Patent EP1572962.
JD439411 - Sequence 420435 from Patent EP1572962.
JD294896 - Sequence 275920 from Patent EP1572962.
JD230630 - Sequence 211654 from Patent EP1572962.
JD536878 - Sequence 517902 from Patent EP1572962.
JD464297 - Sequence 445321 from Patent EP1572962.
JD376870 - Sequence 357894 from Patent EP1572962.
JD214516 - Sequence 195540 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P78333 (Reactome details) participates in the following event(s):

R-HSA-5362427 Hh-Np binds GPC5
R-HSA-1878002 XYLTs transfer Xyl to core protein
R-HSA-1889955 B3GATs transfer GlcA to tetrasaccharide linker
R-HSA-1889978 B3GALT6 transfers Gal to the tetrasaccharide linker
R-HSA-2022919 EXT1:EXT2 transfers GlcNAc to the terminal GlcA residue
R-HSA-1889981 B4GALT7 transfers Gal group to xylosyl-unit of the tetrasaccharide linker
R-HSA-2076419 HS6STs sulfate GlcN at C6 in heparan sulfate/heparin
R-HSA-2022887 NDST1-4 N-deacetylates GlcNAc residues in heparan
R-HSA-2076392 EXT1:EXT2 transfers GlcA to heparan
R-HSA-2076371 GLCE epimerises more GlcA to IdoA as sulfate content rises
R-HSA-2076508 HS2ST1 sulfates IdoA at C2 in heparan sulfate
R-HSA-2024100 GLCE epimerises GlcA to IdoA
R-HSA-2022856 EXT1:EXT2 transfers GlcNAc to heparan
R-HSA-2022851 EXT1:EXT2 transfer GlcNAc to the heparan chain
R-HSA-2022860 NDST1-4 can sulfate a glucosamine residue in heparan to form heparan sulfate (HS)
R-HSA-2076383 HS3ST1 sulfates GlcN at C3 in heparan sulfate
R-HSA-2076611 HS3STs sulfate GlcN at C3 in heparan sulfate
R-HSA-1678694 Heparanase 2 (HPSE2) cleaves heparan sulfate from its proteoglycan (plasma membrane)
R-HSA-1667005 Heparanase (HPSE) cleaves heparan sulfate from its proteoglycan (lysosome)
R-HSA-5362553 NOTUM releases Hh-Np:GPC5 from the plasma membrane
R-HSA-2423785 CR:atREs binds apoE and HSPG
R-HSA-2429643 NREH hydrolyses atREs (HSPG:apoE) to atROL and FAs
R-HSA-2404131 LRPs transport extracellular CR:atREs:HSPG:apoE to cytosol
R-HSA-5362798 Release of Hh-Np from the secreting cell
R-HSA-1971475 A tetrasaccharide linker sequence is required for GAG synthesis
R-HSA-3560801 Defective B3GAT3 causes JDSSDHD
R-HSA-2022928 HS-GAG biosynthesis
R-HSA-3656253 Defective EXT1 causes exostoses 1, TRPS2 and CHDS
R-HSA-3656237 Defective EXT2 causes exostoses 2
R-HSA-4420332 Defective B3GALT6 causes EDSP2 and SEMDJL1
R-HSA-3560783 Defective B4GALT7 causes EDS, progeroid type
R-HSA-2024096 HS-GAG degradation
R-HSA-5358346 Hedgehog ligand biogenesis
R-HSA-1638091 Heparan sulfate/heparin (HS-GAG) metabolism
R-HSA-1793185 Chondroitin sulfate/dermatan sulfate metabolism
R-HSA-3560782 Diseases associated with glycosaminoglycan metabolism
R-HSA-975634 Retinoid metabolism and transport
R-HSA-5358351 Signaling by Hedgehog
R-HSA-1630316 Glycosaminoglycan metabolism
R-HSA-3781865 Diseases of glycosylation
R-HSA-2187338 Visual phototransduction
R-HSA-6806667 Metabolism of fat-soluble vitamins
R-HSA-162582 Signal Transduction
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1643685 Disease
R-HSA-418594 G alpha (i) signalling events
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-1430728 Metabolism
R-HSA-388396 GPCR downstream signalling
R-HSA-372790 Signaling by GPCR

-  Other Names for This Gene
  Alternate Gene Symbols: B2R726, GPC5_HUMAN, NM_004466, NP_004457, O60436, P78333, Q9BX27
UCSC ID: uc010tif.2
RefSeq Accession: NM_004466
Protein: P78333 (aka GPC5_HUMAN)
CCDS: CCDS9468.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004466.4
exon count: 8CDS single in 3' UTR: no RNA size: 2904
ORF size: 1719CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2771.00frame shift in genome: no % Coverage: 99.17
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.