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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for SPARC |
 Gene summary |
| Gene information | Gene symbol | SPARC | Gene ID | 6678 |
| Gene name | secreted protein acidic and cysteine rich | |
| Synonyms | BM-40|OI17|ON | |
| Cytomap | 5q33.1 | |
| Type of gene | protein-coding | |
| Description | SPARCbasement-membrane protein 40secreted protein, acidic, cysteine-rich (osteonectin) | |
| Modification date | 20180523 | |
| UniProtAcc | P09486 | |
| Context | PubMed: SPARC [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| SPARC | GO:0001937 | negative regulation of endothelial cell proliferation | 12867428 |
| SPARC | GO:0010595 | positive regulation of endothelial cell migration | 12867428 |
| SPARC | GO:0016525 | negative regulation of angiogenesis | 12867428 |
| SPARC | GO:0022604 | regulation of cell morphogenesis | 15389586 |
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Exon skipping events across known transcript of Ensembl for SPARC from UCSC genome browser |
| Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Gene isoform structures and expression levels for SPARC |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for SPARC |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_445706 | 5 | 151043647:151043796:151045921:151046070:151047027:151047145 | 151045921:151046070 | ENSG00000113140.6 | ENST00000231061.4,ENST00000520687.1 |
| exon_skip_445708 | 5 | 151046037:151046070:151047027:151047161:151049224:151049345 | 151047027:151047161 | ENSG00000113140.6 | ENST00000538026.1,ENST00000231061.4,ENST00000521569.1 |
| exon_skip_445710 | 5 | 151051133:151051255:151052689:151052777:151054172:151054232 | 151052689:151052777 | ENSG00000113140.6 | ENST00000231061.4,ENST00000539687.1 |
| exon_skip_445713 | 5 | 151052738:151052777:151054172:151054235:151055692:151055762 | 151054172:151054235 | ENSG00000113140.6 | ENST00000522348.1,ENST00000231061.4,ENST00000539687.1,ENST00000521327.1 |
| exon_skip_445719 | 5 | 151054172:151054235:151055692:151055762:151066425:151066474 | 151055692:151055762 | ENSG00000113140.6 | ENST00000521327.1 |
| exon_skip_445721 | 5 | 151055692:151055762:151058634:151058860:151066425:151066524 | 151058634:151058860 | ENSG00000113140.6 | ENST00000522348.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SPARC |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_445708 | 5 | 151046037:151046070:151047027:151047161:151049224:151049345 | 151047027:151047161 | ENSG00000113140.6 | ENST00000231061.4,ENST00000538026.1,ENST00000521569.1 |
| exon_skip_445710 | 5 | 151051133:151051255:151052689:151052777:151054172:151054232 | 151052689:151052777 | ENSG00000113140.6 | ENST00000231061.4,ENST00000539687.1 |
| exon_skip_445713 | 5 | 151052738:151052777:151054172:151054235:151055692:151055762 | 151054172:151054235 | ENSG00000113140.6 | ENST00000231061.4,ENST00000539687.1,ENST00000521327.1,ENST00000522348.1 |
| exon_skip_445719 | 5 | 151054172:151054235:151055692:151055762:151066425:151066474 | 151055692:151055762 | ENSG00000113140.6 | ENST00000521327.1 |
| exon_skip_445721 | 5 | 151055692:151055762:151058634:151058860:151066425:151066524 | 151058634:151058860 | ENSG00000113140.6 | ENST00000522348.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for SPARC |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000231061 | 151045921 | 151046070 | Frame-shift |
| ENST00000231061 | 151047027 | 151047161 | Frame-shift |
| ENST00000231061 | 151052689 | 151052777 | Frame-shift |
| ENST00000231061 | 151054172 | 151054235 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000231061 | 151047027 | 151047161 | Frame-shift |
| ENST00000231061 | 151052689 | 151052777 | Frame-shift |
| ENST00000231061 | 151054172 | 151054235 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SPARC |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000231061 | 3718 | 303 | 151054172 | 151054235 | 372 | 434 | 19 | 40 |
| Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| ENST00000231061 | 3718 | 303 | 151054172 | 151054235 | 372 | 434 | 19 | 40 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| P09486 | 19 | 40 | 18 | 303 | Chain | ID=PRO_0000020304;Note=SPARC |
| P09486 | 19 | 40 | 22 | 69 | Compositional bias | Note=Asp/Glu-rich (acidic%3B binds calcium) |
| P09486 | 19 | 40 | 19 | 19 | Natural variant | ID=VAR_050431;Note=P->S;Dbxref=dbSNP:rs6874468 |
| Lost protein functional features of individual exon skipping events in GTEx. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| P09486 | 19 | 40 | 18 | 303 | Chain | ID=PRO_0000020304;Note=SPARC |
| P09486 | 19 | 40 | 22 | 69 | Compositional bias | Note=Asp/Glu-rich (acidic%3B binds calcium) |
| P09486 | 19 | 40 | 19 | 19 | Natural variant | ID=VAR_050431;Note=P->S;Dbxref=dbSNP:rs6874468 |
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SNVs in the skipped exons for SPARC |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| UCEC | TCGA-B5-A0JY-01 | exon_skip_445710 | 151052690 | 151052777 | 151052711 | 151052711 | Nonsense_Mutation | C | A | p.E63* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_445710 | 151052690 | 151052777 | 151052738 | 151052738 | Nonsense_Mutation | C | A | p.E54* |
| UCS | TCGA-ND-A4WC-01 | exon_skip_445710 | 151052690 | 151052777 | 151052738 | 151052738 | Nonsense_Mutation | C | A | p.E54X |
| UCEC | TCGA-AP-A059-01 | exon_skip_445710 | 151052690 | 151052777 | 151052741 | 151052741 | Nonsense_Mutation | C | A | p.G53* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| IGROV1_OVARY | 151047028 | 151047161 | 151047152 | 151047152 | Frame_Shift_Del | G | - | p.P154fs |
| ISHIKAWAHERAKLIO02ER_ENDOMETRIUM | 151047028 | 151047161 | 151047152 | 151047152 | Frame_Shift_Del | G | - | p.P154fs |
| OVK18_OVARY | 151047028 | 151047161 | 151047119 | 151047120 | Frame_Shift_Ins | - | T | p.L165fs |
| IGROV1_OVARY | 151045922 | 151046070 | 151045967 | 151045967 | Missense_Mutation | G | T | p.P230H |
| UMUC1_URINARY_TRACT | 151045922 | 151046070 | 151046004 | 151046004 | Missense_Mutation | G | A | p.R218W |
| BC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 151045922 | 151046070 | 151046004 | 151046004 | Missense_Mutation | G | A | p.R218W |
| LS411N_LARGE_INTESTINE | 151047028 | 151047161 | 151047047 | 151047047 | Missense_Mutation | G | A | p.T189I |
| KM12_LARGE_INTESTINE | 151047028 | 151047161 | 151047063 | 151047063 | Missense_Mutation | C | T | p.D184N |
| CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 151052690 | 151052777 | 151052704 | 151052704 | Missense_Mutation | T | A | p.E65V |
| SKGT2_STOMACH | 151052690 | 151052777 | 151052750 | 151052750 | Missense_Mutation | C | T | p.V50M |
| MDAMB468_BREAST | 151052690 | 151052777 | 151052771 | 151052771 | Missense_Mutation | C | G | p.V43L |
| HT55_LARGE_INTESTINE | 151055693 | 151055762 | 151055727 | 151055727 | Missense_Mutation | A | T | p.L8H |
| SNU81_LARGE_INTESTINE | 151055693 | 151055762 | 151055728 | 151055728 | Missense_Mutation | G | T | p.L8I |
| HEC59_ENDOMETRIUM | 151047028 | 151047161 | 151047029 | 151047029 | Splice_Site | C | T | p.R195Q |
| SW48_LARGE_INTESTINE | 151052690 | 151052777 | 151052776 | 151052776 | Splice_Site | A | G | p.V41A |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SPARC |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SPARC |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SPARC |
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RelatedDrugs for SPARC |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P09486 | DB11348 | Calcium Phosphate | SPARC | small molecule | approved | |
| P09486 | DB11093 | Calcium Citrate | SPARC | small molecule | approved|investigational |
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RelatedDiseases for SPARC |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SPARC | C0023893 | Liver Cirrhosis, Experimental | 2 | CTD_human |
| SPARC | C0009375 | Colonic Neoplasms | 1 | CTD_human |
| SPARC | C0009404 | Colorectal Neoplasms | 1 | CTD_human |
| SPARC | C0019158 | Hepatitis | 1 | CTD_human |
| SPARC | C0020429 | Hyperalgesia | 1 | CTD_human |
| SPARC | C0022658 | Kidney Diseases | 1 | CTD_human |
| SPARC | C0023467 | Leukemia, Myelocytic, Acute | 1 | CTD_human |
| SPARC | C0023890 | Liver Cirrhosis | 1 | CTD_human |
| SPARC | C0024031 | Low Back Pain | 1 | CTD_human |
| SPARC | C0026764 | Multiple Myeloma | 1 | CTD_human |
| SPARC | C0027540 | Necrosis | 1 | CTD_human |
| SPARC | C0027659 | Neoplasms, Experimental | 1 | CTD_human |
| SPARC | C0029434 | Osteogenesis Imperfecta | 1 | CTD_human |
| SPARC | C0041948 | Uremia | 1 | CTD_human |
| SPARC | C0043094 | Weight Gain | 1 | CTD_human |
| SPARC | C0151744 | Myocardial Ischemia | 1 | CTD_human |
| SPARC | C0158266 | Intervertebral Disc Degeneration | 1 | CTD_human |
| SPARC | C0206686 | Adrenocortical carcinoma | 1 | CTD_human |
| SPARC | C0919267 | ovarian neoplasm | 1 | CTD_human |
| SPARC | C4225301 | OSTEOGENESIS IMPERFECTA, TYPE XVII | 1 | UNIPROT |
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