Human Gene HSPG2 (uc009vqe.1) Description and Page Index
  Description: Homo sapiens heparan sulfate proteoglycan 2 (HSPG2), mRNA.
RefSeq Summary (NM_005529): This gene encodes the perlecan protein, which consists of a core protein to which three long chains of glycosaminoglycans (heparan sulfate or chondroitin sulfate) are attached. The perlecan protein is a large multidomain proteoglycan that binds to and cross-links many extracellular matrix components and cell-surface molecules. It has been shown that this protein interacts with laminin, prolargin, collagen type IV, FGFBP1, FBLN2, FGF7 and transthyretin, etc., and it plays essential roles in multiple biological activities. Perlecan is a key component of the vascular extracellular matrix, where it helps to maintain the endothelial barrier function. It is a potent inhibitor of smooth muscle cell proliferation and is thus thought to help maintain vascular homeostasis. It can also promote growth factor (e.g., FGF2) activity and thus stimulate endothelial growth and re-generation. It is a major component of basement membranes, where it is involved in the stabilization of other molecules as well as being involved with glomerular permeability to macromolecules and cell adhesion. Mutations in this gene cause Schwartz-Jampel syndrome type 1, Silverman-Handmaker type of dyssegmental dysplasia, and tardive dyskinesia. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2014].
Transcript (Including UTRs)
   Position: hg19 chr1:22,213,708-22,222,803 Size: 9,096 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr1:22,213,919-22,222,731 Size: 8,813 Coding Exon Count: 5 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:22,213,708-22,222,803)mRNA (may differ from genome)Protein (215 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsGeneNetworkHGNC
LynxMGIPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HSPG2
CDC HuGE Published Literature: HSPG2
Positive Disease Associations: periodontitis
Related Studies:
  1. periodontitis
    Suzuki A 2004, Single nucleotide polymorphisms associated with aggressive periodontitis and severe chronic periodontitis in Japanese., Biochemical and biophysical research communications. 2004 May;317(3):887-92. [PubMed 15081423]
    These appear to be good candidates as genetic factors for future study.

-  MalaCards Disease Associations
  MalaCards Gene Search: HSPG2
Diseases sorted by gene-association score: schwartz-jampel syndrome, type 1* (1684), dyssegmental dysplasia, silverman-handmaker type* (1390), gas gangrene (24), tardive dyskinesia (20), myotonia (18), hyperglobulinemic purpura (15), sjogren's syndrome (14), sialadenitis (11), hypersensitivity syndrome, carbamazepine-induced (11), dacryoadenitis (11), pseudomembranous conjunctivitis (10), keratoconjunctivitis sicca (9), mixed connective tissue disease (8), functional colonic disease (7), urbach-wiethe disease (7), aplasia of lacrimal and salivary glands (7), blepharospasm (7), xerophthalmia (6), eyelid disease (6), salivary gland disease (6), colonic pseudo-obstruction (6), skeletal dysplasias (5), hemometra (5), cenani-lenz syndactyly syndrome (5), lacrimal apparatus disease (5), kniest dysplasia (4), exanthem (4), muscular dystrophy-dystroglycanopathy , type b, 6 (4), behcet syndrome (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 80.29 RPKM in Artery - Tibial
Total median expression: 1126.11 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -20.1072-0.279 Picture PostScript Text
3' UTR -32.90126-0.261 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
  ModBase Predicted Comparative 3D Structure on Q5SZI5
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 orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  M85289 - Human heparan sulfate proteoglycan (HSPG2) mRNA, complete cds.
X62515 - H.sapiens mRNA for basement membrane heparan sulfate proteoglycan.
AF479675 - Homo sapiens perlecan variant miniperl mRNA, complete cds; alternatively spliced.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04512 - ECM-receptor interaction

-  Other Names for This Gene
  Alternate Gene Symbols: AF479675, Q5SZI5, Q5SZI5_HUMAN, RP11-132G19.2-003
UCSC ID: uc009vqe.1
RefSeq Accession: NM_005529
Protein: Q5SZI5

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AF479675.1
exon count: 6CDS single in 3' UTR: no RNA size: 831
ORF size: 648CDS single in intron: no Alignment % ID: 99.76
txCdsPredict score: 1360.00frame shift in genome: no % Coverage: 99.64
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.