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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 LYN |
 Gene summary |
| Gene information | Gene symbol | LYN | Gene ID | 4067 |
| Gene name | LYN proto-oncogene, Src family tyrosine kinase | |
| Synonyms | JTK8|p53Lyn|p56Lyn | |
| Cytomap | 8q12.1 | |
| Type of gene | protein-coding | |
| Description | tyrosine-protein kinase Lynlck/Yes-related novel protein tyrosine kinasev-yes-1 Yamaguchi sarcoma viral related oncogene homolog | |
| Modification date | 20180523 | |
| UniProtAcc | P07948 | |
| Context | PubMed: LYN [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 |
| LYN | GO:0006468 | protein phosphorylation | 11517336 |
| LYN | GO:0006974 | cellular response to DNA damage stimulus | 10891478|11517336 |
| LYN | GO:0018108 | peptidyl-tyrosine phosphorylation | 7682714|11782428 |
| LYN | GO:0046777 | protein autophosphorylation | 7682714 |
| LYN | GO:0051272 | positive regulation of cellular component movement | 16467205 |
| LYN | GO:0070304 | positive regulation of stress-activated protein kinase signaling cascade | 10891478 |
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Exon skipping events across known transcript of Ensembl for LYN 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 LYN |
| 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 LYN |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_483603 | 8 | 56792393:56792662:56854413:56854487:56859006:56859052 | 56854413:56854487 | ENSG00000254087.3 | ENST00000520220.2 |
| exon_skip_483610 | 8 | 56854413:56854487:56859006:56859052:56860176:56860282 | 56859006:56859052 | ENSG00000254087.3 | ENST00000520220.2 |
| exon_skip_483611 | 8 | 56854413:56854550:56859006:56859052:56860176:56860282 | 56859006:56859052 | ENSG00000254087.3 | ENST00000520050.1,ENST00000519728.1 |
| exon_skip_483612 | 8 | 56860176:56860282:56863017:56863116:56863239:56863307 | 56863017:56863116 | ENSG00000254087.3 | ENST00000520050.1,ENST00000520220.2,ENST00000519728.1 |
| exon_skip_483614 | 8 | 56866390:56866543:56879273:56879456:56882275:56882352 | 56879273:56879456 | ENSG00000254087.3 | ENST00000520220.2,ENST00000519728.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LYN |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_483603 | 8 | 56792393:56792662:56854413:56854487:56859006:56859052 | 56854413:56854487 | ENSG00000254087.3 | ENST00000520220.2 |
| exon_skip_483610 | 8 | 56854413:56854487:56859006:56859052:56860176:56860282 | 56859006:56859052 | ENSG00000254087.3 | ENST00000520220.2 |
| exon_skip_483611 | 8 | 56854413:56854550:56859006:56859052:56860176:56860282 | 56859006:56859052 | ENSG00000254087.3 | ENST00000519728.1,ENST00000520050.1 |
| exon_skip_483612 | 8 | 56860176:56860282:56863017:56863116:56863239:56863307 | 56863017:56863116 | ENSG00000254087.3 | ENST00000519728.1,ENST00000520220.2,ENST00000520050.1 |
| exon_skip_483614 | 8 | 56866390:56866543:56879273:56879456:56882275:56882352 | 56879273:56879456 | ENSG00000254087.3 | ENST00000519728.1,ENST00000520220.2 |
| 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 LYN |
| 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 |
| ENST00000519728 | 56859006 | 56859052 | Frame-shift |
| ENST00000519728 | 56863017 | 56863116 | In-frame |
| ENST00000519728 | 56879273 | 56879456 | 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 |
| ENST00000519728 | 56859006 | 56859052 | Frame-shift |
| ENST00000519728 | 56863017 | 56863116 | In-frame |
| ENST00000519728 | 56879273 | 56879456 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LYN |
| 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 |
| ENST00000519728 | 2314 | 512 | 56863017 | 56863116 | 581 | 679 | 95 | 127 |
| ENST00000519728 | 2314 | 512 | 56879273 | 56879456 | 1087 | 1269 | 263 | 324 |
| 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 |
| ENST00000519728 | 2314 | 512 | 56863017 | 56863116 | 581 | 679 | 95 | 127 |
| ENST00000519728 | 2314 | 512 | 56879273 | 56879456 | 1087 | 1269 | 263 | 324 |
| 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 |
| P07948 | 95 | 127 | 89 | 95 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1W1F |
| P07948 | 95 | 127 | 97 | 104 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1W1F |
| P07948 | 95 | 127 | 110 | 114 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1W1F |
| P07948 | 95 | 127 | 118 | 120 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1W1F |
| P07948 | 95 | 127 | 2 | 512 | Chain | ID=PRO_0000088129;Note=Tyrosine-protein kinase Lyn |
| P07948 | 95 | 127 | 63 | 123 | Domain | Note=SH3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00192 |
| P07948 | 95 | 127 | 105 | 107 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1W1F |
| P07948 | 95 | 127 | 115 | 117 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1W1F |
| P07948 | 263 | 324 | 260 | 266 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XY1 |
| P07948 | 263 | 324 | 270 | 277 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XY1 |
| P07948 | 263 | 324 | 305 | 309 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XY1 |
| P07948 | 263 | 324 | 311 | 320 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XY1 |
| P07948 | 263 | 324 | 275 | 275 | Binding site | Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| P07948 | 263 | 324 | 2 | 512 | Chain | ID=PRO_0000088129;Note=Tyrosine-protein kinase Lyn |
| P07948 | 263 | 324 | 247 | 501 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| P07948 | 263 | 324 | 284 | 296 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XY1 |
| P07948 | 263 | 324 | 306 | 306 | Modified residue | Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19369195;Dbxref=PMID:19369195 |
| P07948 | 263 | 324 | 316 | 316 | Modified residue | Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19369195;Dbxref=PMID:19369195 |
| P07948 | 263 | 324 | 275 | 275 | Mutagenesis | Note=Loss of activity and no effect on localization to the cell membrane. Abundant localization in the nucleus%3B when associated with A-2 and A-3. K->A;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11435302,ECO |
| P07948 | 263 | 324 | 275 | 275 | Mutagenesis | Note=Loss of kinase activity. K->L%2CR;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11435302,ECO:0000269|PubMed:11517336,ECO:0000269|PubMed:15173188,ECO:0000269|PubMed:18817770;Dbxref=PMID:11435302,PMID:1151733 |
| P07948 | 263 | 324 | 267 | 269 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XY1 |
| 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 |
| P07948 | 95 | 127 | 89 | 95 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1W1F |
| P07948 | 95 | 127 | 97 | 104 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1W1F |
| P07948 | 95 | 127 | 110 | 114 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1W1F |
| P07948 | 95 | 127 | 118 | 120 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1W1F |
| P07948 | 95 | 127 | 2 | 512 | Chain | ID=PRO_0000088129;Note=Tyrosine-protein kinase Lyn |
| P07948 | 95 | 127 | 63 | 123 | Domain | Note=SH3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00192 |
| P07948 | 95 | 127 | 105 | 107 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1W1F |
| P07948 | 95 | 127 | 115 | 117 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1W1F |
| P07948 | 263 | 324 | 260 | 266 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XY1 |
| P07948 | 263 | 324 | 270 | 277 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XY1 |
| P07948 | 263 | 324 | 305 | 309 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XY1 |
| P07948 | 263 | 324 | 311 | 320 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XY1 |
| P07948 | 263 | 324 | 275 | 275 | Binding site | Note=ATP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| P07948 | 263 | 324 | 2 | 512 | Chain | ID=PRO_0000088129;Note=Tyrosine-protein kinase Lyn |
| P07948 | 263 | 324 | 247 | 501 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| P07948 | 263 | 324 | 284 | 296 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XY1 |
| P07948 | 263 | 324 | 306 | 306 | Modified residue | Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19369195;Dbxref=PMID:19369195 |
| P07948 | 263 | 324 | 316 | 316 | Modified residue | Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19369195;Dbxref=PMID:19369195 |
| P07948 | 263 | 324 | 275 | 275 | Mutagenesis | Note=Loss of activity and no effect on localization to the cell membrane. Abundant localization in the nucleus%3B when associated with A-2 and A-3. K->A;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11435302,ECO |
| P07948 | 263 | 324 | 275 | 275 | Mutagenesis | Note=Loss of kinase activity. K->L%2CR;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11435302,ECO:0000269|PubMed:11517336,ECO:0000269|PubMed:15173188,ECO:0000269|PubMed:18817770;Dbxref=PMID:11435302,PMID:1151733 |
| P07948 | 263 | 324 | 267 | 269 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5XY1 |
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SNVs in the skipped exons for LYN |
| - 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-G3-A3CJ-01 | exon_skip_483611 exon_skip_483610 | 56859007 | 56859052 | 56859023 | 56859023 | Frame_Shift_Del | T | - | p.L30fs |
| HNSC | TCGA-F7-A624-01 | exon_skip_483612 | 56863018 | 56863116 | 56863054 | 56863054 | Frame_Shift_Del | A | - | p.T86fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_483612 | 56863018 | 56863116 | 56863054 | 56863054 | Frame_Shift_Del | A | - | p.T86fs |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_483612 | 56863018 | 56863116 | 56863054 | 56863054 | Frame_Shift_Del | A | - | p.T107fs |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_483612 | 56863018 | 56863116 | 56863054 | 56863054 | Frame_Shift_Del | A | - | p.T86fs |
| UCEC | TCGA-AP-A0LT-01 | exon_skip_483612 | 56863018 | 56863116 | 56863054 | 56863054 | Frame_Shift_Del | A | - | p.T107fs |
| HNSC | TCGA-CR-7370-01 | exon_skip_483614 | 56879274 | 56879456 | 56879420 | 56879420 | Nonsense_Mutation | G | T | p.E292* |
| HNSC | TCGA-CR-7370-01 | exon_skip_483614 | 56879274 | 56879456 | 56879420 | 56879420 | Nonsense_Mutation | G | T | p.E313* |
| LUSC | TCGA-66-2754-01 | exon_skip_483614 | 56879274 | 56879456 | 56879273 | 56879273 | Splice_Site | G | T | p.G264_splice |
| - 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 |
| SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 56863018 | 56863116 | 56863054 | 56863054 | Frame_Shift_Del | A | - | p.T107fs |
| KM12_LARGE_INTESTINE | 56863018 | 56863116 | 56863054 | 56863054 | Frame_Shift_Del | A | - | p.T107fs |
| KMS12BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 56854414 | 56854487 | 56854490 | 56854492 | In_Frame_Del | ACG | - | p.R25del |
| FARAGE_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 56859007 | 56859052 | 56859010 | 56859010 | Missense_Mutation | C | G | p.P46A |
| MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 56859007 | 56859052 | 56859023 | 56859023 | Missense_Mutation | T | C | p.L50P |
| NCIH1155_LUNG | 56863018 | 56863116 | 56863085 | 56863085 | Missense_Mutation | G | A | p.V118M |
| SNUC1_LARGE_INTESTINE | 56863018 | 56863116 | 56863098 | 56863098 | Missense_Mutation | A | T | p.N122I |
| MFE319_ENDOMETRIUM | 56879274 | 56879456 | 56879296 | 56879296 | Missense_Mutation | G | T | p.K271N |
| SKNDZ_AUTONOMIC_GANGLIA | 56879274 | 56879456 | 56879303 | 56879303 | Missense_Mutation | G | T | p.V274L |
| NCIH524_LUNG | 56879274 | 56879456 | 56879309 | 56879309 | Missense_Mutation | A | T | p.T276S |
| LS411N_LARGE_INTESTINE | 56879274 | 56879456 | 56879394 | 56879394 | Missense_Mutation | G | A | p.R304K |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LYN |
| 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 LYN |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LYN |
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RelatedDrugs for LYN |
| 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 |
| P07948 | DB06616 | Bosutinib | Tyrosine-protein kinase Lyn | small molecule | approved | |
| P07948 | DB09079 | Nintedanib | Tyrosine-protein kinase Lyn | small molecule | approved | |
| P07948 | DB01254 | Dasatinib | Tyrosine-protein kinase Lyn | small molecule | approved|investigational | |
| P07948 | DB08901 | Ponatinib | Tyrosine-protein kinase Lyn | small molecule | approved|investigational | |
| P07948 | DB12010 | Fostamatinib | Tyrosine-protein kinase Lyn | small molecule | approved|investigational |
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RelatedDiseases for LYN |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| LYN | C0019693 | HIV Infections | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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