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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 IGFBP3 |
 Gene summary |
| Gene information | Gene symbol | IGFBP3 | Gene ID | 3486 |
| Gene name | insulin like growth factor binding protein 3 | |
| Synonyms | BP-53|IBP3 | |
| Cytomap | 7p12.3 | |
| Type of gene | protein-coding | |
| Description | insulin-like growth factor-binding protein 3IBP-3IGF-binding protein 3IGFBP-3acid stable subunit of the 140 K IGF complexbinding protein 29binding protein 53growth hormone-dependent binding protein | |
| Modification date | 20180527 | |
| UniProtAcc | P17936 | |
| Context | PubMed: IGFBP3 [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 |
| IGFBP3 | GO:0001933 | negative regulation of protein phosphorylation | 17591901 |
| IGFBP3 | GO:0006468 | protein phosphorylation | 17434920 |
| IGFBP3 | GO:0014912 | negative regulation of smooth muscle cell migration | 10766744 |
| IGFBP3 | GO:0045663 | positive regulation of myoblast differentiation | 12599210 |
| IGFBP3 | GO:0048662 | negative regulation of smooth muscle cell proliferation | 10766744 |
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Exon skipping events across known transcript of Ensembl for IGFBP3 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 IGFBP3 |
| 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 IGFBP3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_475392 | 7 | 45954403:45954544:45956146:45956266:45956811:45956996 | 45956146:45956266 | ENSG00000146674.10 | ENST00000428530.1,ENST00000417621.1,ENST00000381086.5,ENST00000275521.6,ENST00000381083.4 |
| exon_skip_475399 | 7 | 45956219:45956266:45956811:45957038:45960336:45960439 | 45956811:45957038 | ENSG00000146674.10 | ENST00000381086.5,ENST00000275521.6 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for IGFBP3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_475392 | 7 | 45954403:45954544:45956146:45956266:45956811:45956996 | 45956146:45956266 | ENSG00000146674.10 | ENST00000381086.5,ENST00000275521.6,ENST00000381083.4,ENST00000428530.1,ENST00000417621.1 |
| exon_skip_475399 | 7 | 45956219:45956266:45956811:45957038:45960336:45960439 | 45956811:45957038 | ENSG00000146674.10 | ENST00000381086.5,ENST00000275521.6 |
| 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 IGFBP3 |
| 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 |
| ENST00000275521 | 45956811 | 45957038 | Frame-shift |
| ENST00000275521 | 45956146 | 45956266 | 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 |
| ENST00000275521 | 45956811 | 45957038 | Frame-shift |
| ENST00000275521 | 45956146 | 45956266 | In-frame |
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Infer the effects of exon skipping event on protein functional features for IGFBP3 |
| 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 |
| ENST00000275521 | 2279 | 291 | 45956146 | 45956266 | 765 | 884 | 210 | 250 |
| 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 |
| ENST00000275521 | 2279 | 291 | 45956146 | 45956266 | 765 | 884 | 210 | 250 |
| 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 |
| P17936 | 210 | 250 | 28 | 291 | Chain | ID=PRO_0000014378;Note=Insulin-like growth factor-binding protein 3 |
| P17936 | 210 | 250 | 213 | 240 | Disulfide bond | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00500 |
| P17936 | 210 | 250 | 210 | 285 | Domain | Note=Thyroglobulin type-1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00500 |
| P17936 | 210 | 250 | 234 | 234 | Natural variant | ID=VAR_025264;Note=G->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.4;Dbxref=dbSNP:rs35712717 |
| 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 |
| P17936 | 210 | 250 | 28 | 291 | Chain | ID=PRO_0000014378;Note=Insulin-like growth factor-binding protein 3 |
| P17936 | 210 | 250 | 213 | 240 | Disulfide bond | Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00500 |
| P17936 | 210 | 250 | 210 | 285 | Domain | Note=Thyroglobulin type-1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00500 |
| P17936 | 210 | 250 | 234 | 234 | Natural variant | ID=VAR_025264;Note=G->S;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.4;Dbxref=dbSNP:rs35712717 |
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SNVs in the skipped exons for IGFBP3 |
| - 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 |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_475392 | 45956147 | 45956266 | 45956161 | 45956161 | Frame_Shift_Del | A | - | p.Y246fs |
| STAD | TCGA-BR-4201-01 | exon_skip_475392 | 45956147 | 45956266 | 45956203 | 45956215 | Frame_Shift_Del | GACTCAGCACATT | - | p.N234fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_475399 | 45956812 | 45957038 | 45956952 | 45956953 | Frame_Shift_Ins | - | G | p.V164fs |
| UCEC | TCGA-AX-A0J0-01 | exon_skip_475392 | 45956147 | 45956266 | 45956251 | 45956251 | Nonsense_Mutation | C | A | p.E222* |
| STAD | TCGA-CG-4465-01 | exon_skip_475399 | 45956812 | 45957038 | 45957023 | 45957023 | Nonsense_Mutation | G | T | p.S140* |
| STAD | TCGA-CG-4465-01 | exon_skip_475399 | 45956812 | 45957038 | 45957023 | 45957023 | Nonsense_Mutation | G | T | p.S146X |
| - 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 |
| HS834T_FIBROBLAST | 45956147 | 45956266 | 45956256 | 45956256 | Missense_Mutation | C | T | p.R214H |
| MEWO_SKIN | 45956812 | 45957038 | 45956840 | 45956840 | Missense_Mutation | G | A | p.S201F |
| AM38_CENTRAL_NERVOUS_SYSTEM | 45956812 | 45957038 | 45956877 | 45956877 | Missense_Mutation | C | A | p.D189Y |
| MRKNU1_BREAST | 45956812 | 45957038 | 45956907 | 45956907 | Missense_Mutation | G | T | p.H179N |
| HCC2998_LARGE_INTESTINE | 45956812 | 45957038 | 45956921 | 45956921 | Missense_Mutation | A | C | p.I174S |
| GP2D_LARGE_INTESTINE | 45956812 | 45957038 | 45956943 | 45956943 | Missense_Mutation | G | A | p.P167S |
| GP5D_LARGE_INTESTINE | 45956812 | 45957038 | 45956943 | 45956943 | Missense_Mutation | G | A | p.P167S |
| GI1_CENTRAL_NERVOUS_SYSTEM | 45956812 | 45957038 | 45956967 | 45956967 | Missense_Mutation | G | A | p.R159W |
| P30OHK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 45956812 | 45957038 | 45956967 | 45956967 | Missense_Mutation | G | A | p.R159W |
| NCIBL128_MATCHED_NORMAL_TISSUE | 45956147 | 45956266 | 45956251 | 45956251 | Nonsense_Mutation | C | A | p.E216* |
| CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 45956812 | 45957038 | 45956884 | 45956884 | Nonsense_Mutation | G | C | p.Y186* |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 45956812 | 45957038 | 45956812 | 45956812 | Splice_Site | A | G | p.Y210Y |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for IGFBP3 |
| 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 IGFBP3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for IGFBP3 |
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RelatedDrugs for IGFBP3 |
| 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 |
| P17936 | DB00523 | Alitretinoin | Insulin-like growth factor-binding protein 3 | small molecule | approved|investigational | |
| P17936 | DB01277 | Mecasermin | Insulin-like growth factor-binding protein 3 | biotech | approved|investigational |
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RelatedDiseases for IGFBP3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| IGFBP3 | C0033578 | Prostatic Neoplasms | 3 | CTD_human |
| IGFBP3 | C0000786 | Spontaneous abortion | 1 | CTD_human |
| IGFBP3 | C0003873 | Rheumatoid Arthritis | 1 | CTD_human |
| IGFBP3 | C0004352 | Autistic Disorder | 1 | CTD_human |
| IGFBP3 | C0005695 | Bladder Neoplasm | 1 | CTD_human |
| IGFBP3 | C0007138 | Carcinoma, Transitional Cell | 1 | CTD_human |
| IGFBP3 | C0009404 | Colorectal Neoplasms | 1 | CTD_human |
| IGFBP3 | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| IGFBP3 | C0038356 | Stomach Neoplasms | 1 | CTD_human |
| IGFBP3 | C0151744 | Myocardial Ischemia | 1 | CTD_human |
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