Human Gene SPARC (ENST00000231061.9_7) from GENCODE V47lift37
  Description: secreted protein acidic and cysteine rich, transcript variant 1 (from RefSeq NM_003118.4)
Gencode Transcript: ENST00000231061.9_7
Gencode Gene: ENSG00000113140.11_16
Transcript (Including UTRs)
   Position: hg19 chr5:151,040,657-151,066,476 Size: 25,820 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr5:151,043,132-151,055,749 Size: 12,618 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:151,040,657-151,066,476)mRNA (may differ from genome)Protein (303 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
Human Cortex Gene ExpressionMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPRC_HUMAN
DESCRIPTION: RecName: Full=SPARC; AltName: Full=Basement-membrane protein 40; Short=BM-40; AltName: Full=Osteonectin; Short=ON; AltName: Full=Secreted protein acidic and rich in cysteine; Flags: Precursor;
FUNCTION: Appears to regulate cell growth through interactions with the extracellular matrix and cytokines. Binds calcium and copper, several types of collagen, albumin, thrombospondin, PDGF and cell membranes. There are two calcium binding sites; an acidic domain that binds 5 to 8 Ca(2+) with a low affinity and an EF-hand loop that binds a Ca(2+) ion with a high affinity.
SUBCELLULAR LOCATION: Secreted, extracellular space, extracellular matrix, basement membrane. Note=In or around the basement membrane.
DEVELOPMENTAL STAGE: Expressed at high levels in tissues undergoing morphogenesis, remodeling and wound repair.
SIMILARITY: Belongs to the SPARC family.
SIMILARITY: Contains 1 EF-hand domain.
SIMILARITY: Contains 1 follistatin-like domain.
SIMILARITY: Contains 1 Kazal-like domain.
SEQUENCE CAUTION: Sequence=AAA60993.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the C-terminal part;
WEB RESOURCE: Name=Wikipedia; Note=Osteonectin entry; URL="http://en.wikipedia.org/wiki/Osteonectin";

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: SPARC
Diseases sorted by gene-association score: osteogenesis imperfecta, type xvii* (1200), sparc-related osteogenesis imperfecta* (500), osteogenesis imperfecta, type iv* (182), clear cell chondrosarcoma (22), papillary cystadenocarcinoma (21), osteogenesis imperfecta (19), osteofibrous dysplasia (17), lateral cystocele (16), osteoblastoma (14), fibrous dysplasia (13), melorheostosis (12), fibrosarcomatous osteosarcoma (11), calcinosis (9), tooth ankylosis (9), prolapse of female genital organ (9), periosteal osteogenic sarcoma (8), osteosarcoma, somatic (8), amyloid tumor (7), gray platelet syndrome (7), chondrosarcoma (7), quebec platelet disorder (6), bone osteosarcoma (6), conventional central osteosarcoma (6), vitreoretinopathy, neovascular inflammatory (5), osseous heteroplasia, progressive (5), peripheral osteosarcoma (5), osteoporosis (2), aortic valve disease 2 (1), pulmonary fibrosis, idiopathic (1)
* = Manually curated disease association

-  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: 868.69 RPKM in Artery - Aorta
Total median expression: 11563.60 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 -13.5064-0.211 Picture PostScript Text
3' UTR -669.902475-0.271 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
IPR011992 - EF-hand-like_dom
IPR018247 - EF_Hand_1_Ca_BS
IPR003645 - Fol_N
IPR015369 - Follistatin/Osteonectin_EGF
IPR001999 - Osteonectin_CS
IPR002350 - Prot_inh_Kazal
IPR019577 - SPARC/Testican_Ca-bd-dom

Pfam Domains:
PF00050 - Kazal-type serine protease inhibitor domain
PF07648 - Kazal-type serine protease inhibitor domain
PF09289 - Follistatin/Osteonectin-like EGF domain
PF10591 - Secreted protein acidic and rich in cysteine Ca binding region

SCOP Domains:
47473 - EF-hand
57196 - EGF/Laminin
100895 - Kazal-type serine protease inhibitors

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1BMO - X-ray MuPIT 1NUB - X-ray MuPIT 1SRA - X-ray MuPIT 2V53 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P09486
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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
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005518 collagen binding
GO:0046872 metal ion binding
GO:0050840 extracellular matrix binding

Biological Process:
GO:0001503 ossification
GO:0001937 negative regulation of endothelial cell proliferation
GO:0002576 platelet degranulation
GO:0006898 receptor-mediated endocytosis
GO:0007165 signal transduction
GO:0007507 heart development
GO:0009629 response to gravity
GO:0010288 response to lead ion
GO:0010595 positive regulation of endothelial cell migration
GO:0016525 negative regulation of angiogenesis
GO:0022604 regulation of cell morphogenesis
GO:0030198 extracellular matrix organization
GO:0030324 lung development
GO:0032496 response to lipopolysaccharide
GO:0033591 response to L-ascorbic acid
GO:0034097 response to cytokine
GO:0042060 wound healing
GO:0042127 regulation of cell proliferation
GO:0043434 response to peptide hormone
GO:0043473 pigmentation
GO:0045471 response to ethanol
GO:0046686 response to cadmium ion
GO:0048839 inner ear development
GO:0051384 response to glucocorticoid
GO:0051591 response to cAMP
GO:0051592 response to calcium ion
GO:0060348 bone development
GO:0071363 cellular response to growth factor stimulus

Cellular Component:
GO:0005576 extracellular region
GO:0005604 basement membrane
GO:0005615 extracellular space
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0009986 cell surface
GO:0016363 nuclear matrix
GO:0031091 platelet alpha granule
GO:0031092 platelet alpha granule membrane
GO:0031093 platelet alpha granule lumen
GO:0031982 vesicle
GO:0071682 endocytic vesicle lumen
GO:0005739 mitochondrion
GO:0005886 plasma membrane


-  Descriptions from all associated GenBank mRNAs
  BC072457 - Homo sapiens secreted protein, acidic, cysteine-rich (osteonectin), mRNA (cDNA clone MGC:88065 IMAGE:6186685), complete cds.
LF209076 - JP 2014500723-A/16579: Polycomb-Associated Non-Coding RNAs.
LF325896 - JP 2014500723-A/133399: Polycomb-Associated Non-Coding RNAs.
BC008011 - Homo sapiens secreted protein, acidic, cysteine-rich (osteonectin), mRNA (cDNA clone MGC:15881 IMAGE:3529445), complete cds.
BC004974 - Homo sapiens secreted protein, acidic, cysteine-rich (osteonectin), mRNA (cDNA clone MGC:3651 IMAGE:2906092), complete cds.
J03040 - Human SPARC/osteonectin mRNA, complete cds.
AK126525 - Homo sapiens cDNA FLJ44561 fis, clone UTERU3008671, weakly similar to SPARC precursor.
AK096969 - Homo sapiens cDNA FLJ39650 fis, clone SMINT2005075, highly similar to SPARC PRECURSOR.
JD482390 - Sequence 463414 from Patent EP1572962.
LF325897 - JP 2014500723-A/133400: Polycomb-Associated Non-Coding RNAs.
JD528610 - Sequence 509634 from Patent EP1572962.
JD295224 - Sequence 276248 from Patent EP1572962.
LF325898 - JP 2014500723-A/133401: Polycomb-Associated Non-Coding RNAs.
JD108153 - Sequence 89177 from Patent EP1572962.
JD077008 - Sequence 58032 from Patent EP1572962.
JD453397 - Sequence 434421 from Patent EP1572962.
JD204187 - Sequence 185211 from Patent EP1572962.
JD248960 - Sequence 229984 from Patent EP1572962.
LF325899 - JP 2014500723-A/133402: Polycomb-Associated Non-Coding RNAs.
LF325900 - JP 2014500723-A/133403: Polycomb-Associated Non-Coding RNAs.
JD498594 - Sequence 479618 from Patent EP1572962.
AK299441 - Homo sapiens cDNA FLJ55667 complete cds, highly similar to Secreted protein acidic and rich in cysteine.
JD327780 - Sequence 308804 from Patent EP1572962.
JD166504 - Sequence 147528 from Patent EP1572962.
LF325901 - JP 2014500723-A/133404: Polycomb-Associated Non-Coding RNAs.
JD187742 - Sequence 168766 from Patent EP1572962.
JD292724 - Sequence 273748 from Patent EP1572962.
JD050285 - Sequence 31309 from Patent EP1572962.
JD353585 - Sequence 334609 from Patent EP1572962.
JD539642 - Sequence 520666 from Patent EP1572962.
JD222497 - Sequence 203521 from Patent EP1572962.
LF325902 - JP 2014500723-A/133405: Polycomb-Associated Non-Coding RNAs.
JD171262 - Sequence 152286 from Patent EP1572962.
JD562761 - Sequence 543785 from Patent EP1572962.
LF325903 - JP 2014500723-A/133406: Polycomb-Associated Non-Coding RNAs.
KJ892190 - Synthetic construct Homo sapiens clone ccsbBroadEn_01584 SPARC gene, encodes complete protein.
CR456799 - Homo sapiens full open reading frame cDNA clone RZPDo834D0918D for gene SPARC, secreted protein, acidic, cysteine-rich (osteonectin); complete cds, incl. stopcodon.
DQ893415 - Synthetic construct clone IMAGE:100006045; FLH199496.01X; RZPDo839E0482D secreted protein, acidic, cysteine-rich (osteonectin) (SPARC) gene, encodes complete protein.
Y00755 - Human mRNA for extracellular matrix protein BM-40.
AK315591 - Homo sapiens cDNA, FLJ96669, highly similar to Homo sapiens secreted protein, acidic, cysteine-rich (osteonectin)(SPARC), mRNA.
DQ896734 - Synthetic construct Homo sapiens clone IMAGE:100011194; FLH199402.01L; RZPDo839E0481D secreted protein, acidic, cysteine-rich (osteonectin) (SPARC) gene, encodes complete protein.
AB464190 - Synthetic construct DNA, clone: pF1KB4604, Homo sapiens SPARC gene for secreted protein, acidic, cysteine-rich, without stop codon, in Flexi system.
LF325904 - JP 2014500723-A/133407: Polycomb-Associated Non-Coding RNAs.
LF325907 - JP 2014500723-A/133410: Polycomb-Associated Non-Coding RNAs.
AY545555 - Homo sapiens cysteine-rich protein (SPARC) mRNA, partial cds.
CU678834 - Synthetic construct Homo sapiens gateway clone IMAGE:100018786 5' read SPARC mRNA.
LF325908 - JP 2014500723-A/133411: Polycomb-Associated Non-Coding RNAs.
LF325909 - JP 2014500723-A/133412: Polycomb-Associated Non-Coding RNAs.
LF325910 - JP 2014500723-A/133413: Polycomb-Associated Non-Coding RNAs.
LF325911 - JP 2014500723-A/133414: Polycomb-Associated Non-Coding RNAs.
D28381 - Homo sapiens mRNA for osteonectin, 5'UTR region.
JD261057 - Sequence 242081 from Patent EP1572962.
JD462027 - Sequence 443051 from Patent EP1572962.
JD336585 - Sequence 317609 from Patent EP1572962.
JD422793 - Sequence 403817 from Patent EP1572962.
MA561473 - JP 2018138019-A/133399: Polycomb-Associated Non-Coding RNAs.
MA561474 - JP 2018138019-A/133400: Polycomb-Associated Non-Coding RNAs.
MA561475 - JP 2018138019-A/133401: Polycomb-Associated Non-Coding RNAs.
MA561476 - JP 2018138019-A/133402: Polycomb-Associated Non-Coding RNAs.
MA561477 - JP 2018138019-A/133403: Polycomb-Associated Non-Coding RNAs.
MA561478 - JP 2018138019-A/133404: Polycomb-Associated Non-Coding RNAs.
MA561479 - JP 2018138019-A/133405: Polycomb-Associated Non-Coding RNAs.
MA561480 - JP 2018138019-A/133406: Polycomb-Associated Non-Coding RNAs.
MA561481 - JP 2018138019-A/133407: Polycomb-Associated Non-Coding RNAs.
MA561484 - JP 2018138019-A/133410: Polycomb-Associated Non-Coding RNAs.
MA561485 - JP 2018138019-A/133411: Polycomb-Associated Non-Coding RNAs.
MA561486 - JP 2018138019-A/133412: Polycomb-Associated Non-Coding RNAs.
MA561487 - JP 2018138019-A/133413: Polycomb-Associated Non-Coding RNAs.
MA561488 - JP 2018138019-A/133414: Polycomb-Associated Non-Coding RNAs.
MA444653 - JP 2018138019-A/16579: Polycomb-Associated Non-Coding RNAs.

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

Protein P09486 (Reactome details) participates in the following event(s):

R-HSA-2424243 SPARC binds Collagen type I fibril, hydroxylapatite and Ca2+
R-HSA-481007 Exocytosis of platelet alpha granule contents
R-HSA-2197770 STAB1 (FEEL-1) binds ligands
R-HSA-3000178 ECM proteoglycans
R-HSA-114608 Platelet degranulation
R-HSA-3000497 Scavenging by Class H Receptors
R-HSA-1474244 Extracellular matrix organization
R-HSA-76005 Response to elevated platelet cytosolic Ca2+
R-HSA-2173782 Binding and Uptake of Ligands by Scavenger Receptors
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-5653656 Vesicle-mediated transport
R-HSA-109582 Hemostasis

-  Other Names for This Gene
  Alternate Gene Symbols: D3DQH9, ENST00000231061.1, ENST00000231061.2, ENST00000231061.3, ENST00000231061.4, ENST00000231061.5, ENST00000231061.6, ENST00000231061.7, ENST00000231061.8, NM_003118, ON, P09486, Q6IBK4, SPRC_HUMAN, uc317dts.1, uc317dts.2
UCSC ID: ENST00000231061.9_7
RefSeq Accession: NM_003118.4
Protein: P09486 (aka SPRC_HUMAN)

-  Gene Model Information
  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.