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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 LCK |
 Gene summary |
| Gene information | Gene symbol | LCK | Gene ID | 3932 |
| Gene name | LCK proto-oncogene, Src family tyrosine kinase | |
| Synonyms | IMD22|LSK|YT16|p56lck|pp58lck | |
| Cytomap | 1p35.2 | |
| Type of gene | protein-coding | |
| Description | tyrosine-protein kinase LckT-lymphocyte specific protein tyrosine kinase p56lckleukocyte C-terminal Src kinaselymphocyte cell-specific protein-tyrosine kinasep56(LSTRA) protein-tyrosine kinaseproto-oncogene tyrosine-protein kinase LCKt cell-specific | |
| Modification date | 20180527 | |
| UniProtAcc | P06239 | |
| Context | PubMed: LCK [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 |
| LCK | GO:0006468 | protein phosphorylation | 214242 |
| LCK | GO:0006919 | activation of cysteine-type endopeptidase activity involved in apoptotic process | 16116473 |
| LCK | GO:0042493 | response to drug | 16116473 |
| LCK | GO:0050870 | positive regulation of T cell activation | 8943371 |
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Exon skipping events across known transcript of Ensembl for LCK 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 LCK |
| 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 LCK |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_3942 | 1 | 32716918:32716972:32739925:32740035:32740337:32740419 | 32739925:32740035 | ENSG00000182866.12 | ENST00000355928.3,ENST00000476457.1,ENST00000495610.2,ENST00000469765.1,ENST00000482949.1 |
| exon_skip_3943 | 1 | 32740337:32740419:32740593:32740684:32740921:32741020 | 32740593:32740684 | ENSG00000182866.12 | ENST00000333070.4,ENST00000373557.2,ENST00000495610.2,ENST00000469765.1,ENST00000373562.3,ENST00000336890.5 |
| exon_skip_3946 | 1 | 32741549:32741664:32741937:32742090:32742207:32742387 | 32741937:32742090 | ENSG00000182866.12 | ENST00000333070.4,ENST00000469765.1,ENST00000469956.1,ENST00000336890.5 |
| exon_skip_3948 | 1 | 32745441:32745595:32745679:32745811:32751114:32751317 | 32745679:32745811 | ENSG00000182866.12 | ENST00000333070.4,ENST00000469765.1,ENST00000373564.3,ENST00000336890.5 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LCK |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_3942 | 1 | 32716918:32716972:32739925:32740035:32740337:32740419 | 32739925:32740035 | ENSG00000182866.12 | ENST00000482949.1,ENST00000495610.2,ENST00000355928.3,ENST00000476457.1,ENST00000469765.1 |
| exon_skip_3943 | 1 | 32740337:32740419:32740593:32740684:32740921:32741020 | 32740593:32740684 | ENSG00000182866.12 | ENST00000336890.5,ENST00000495610.2,ENST00000469765.1,ENST00000373562.3,ENST00000373557.2,ENST00000333070.4 |
| exon_skip_3946 | 1 | 32741549:32741664:32741937:32742090:32742207:32742387 | 32741937:32742090 | ENSG00000182866.12 | ENST00000336890.5,ENST00000469765.1,ENST00000333070.4,ENST00000469956.1 |
| exon_skip_3948 | 1 | 32745441:32745595:32745679:32745811:32751114:32751317 | 32745679:32745811 | ENSG00000182866.12 | ENST00000336890.5,ENST00000469765.1,ENST00000333070.4,ENST00000373564.3 |
| 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 LCK |
| 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 |
| ENST00000336890 | 32740593 | 32740684 | Frame-shift |
| ENST00000336890 | 32741937 | 32742090 | In-frame |
| ENST00000336890 | 32745679 | 32745811 | 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 |
| ENST00000336890 | 32740593 | 32740684 | Frame-shift |
| ENST00000336890 | 32741937 | 32742090 | In-frame |
| ENST00000336890 | 32745679 | 32745811 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LCK |
| 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 |
| ENST00000336890 | 2134 | 509 | 32741937 | 32742090 | 770 | 922 | 210 | 261 |
| ENST00000336890 | 2134 | 509 | 32745679 | 32745811 | 1334 | 1465 | 398 | 442 |
| 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 |
| ENST00000336890 | 2134 | 509 | 32741937 | 32742090 | 770 | 922 | 210 | 261 |
| ENST00000336890 | 2134 | 509 | 32745679 | 32745811 | 1334 | 1465 | 398 | 442 |
| 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 |
| 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 |
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SNVs in the skipped exons for LCK |
| - 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-A1EG-01 | exon_skip_3942 | 32739926 | 32740035 | 32739954 | 32739954 | Frame_Shift_Del | C | - | p.H8fs |
| LIHC | TCGA-BC-A3KG-01 | exon_skip_3942 | 32739926 | 32740035 | 32740029 | 32740029 | Frame_Shift_Del | G | - | p.K33fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_3946 | 32741938 | 32742090 | 32742059 | 32742059 | Frame_Shift_Del | G | - | p.L251fs |
| LUAD | TCGA-05-4420-01 | exon_skip_3946 | 32741938 | 32742090 | 32741968 | 32741969 | Frame_Shift_Ins | - | A | p.S221fs |
| LUAD | TCGA-05-4420-01 | exon_skip_3946 | 32741938 | 32742090 | 32741968 | 32741969 | Frame_Shift_Ins | - | A | p.T221fs |
| SKCM | TCGA-Z2-AA3S-06 | exon_skip_3942 | 32739926 | 32740035 | 32739969 | 32739969 | Nonsense_Mutation | G | A | p.W13* |
| LUAD | TCGA-NJ-A4YP-01 | exon_skip_3943 | 32740594 | 32740684 | 32740623 | 32740623 | Nonsense_Mutation | G | T | p.E73* |
| HNSC | TCGA-D6-6516-01 | exon_skip_3946 | 32741938 | 32742090 | 32742008 | 32742008 | Nonsense_Mutation | G | A | p.W234* |
| SKCM | TCGA-YG-AA3N-01 | exon_skip_3946 | 32741938 | 32742090 | 32742008 | 32742008 | Nonsense_Mutation | G | A | p.W234* |
| - 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 |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32741938 | 32742090 | 32742059 | 32742059 | Frame_Shift_Del | G | - | p.L251fs |
| TCCPAN2_PANCREAS | 32740594 | 32740684 | 32740633 | 32740633 | Missense_Mutation | A | G | p.H76R |
| MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32740594 | 32740684 | 32740665 | 32740665 | Missense_Mutation | C | A | p.Q87K |
| JHUEM2_ENDOMETRIUM | 32741938 | 32742090 | 32742001 | 32742001 | Missense_Mutation | C | T | p.P232L |
| HEC108_ENDOMETRIUM | 32745680 | 32745811 | 32745724 | 32745724 | Missense_Mutation | T | A | p.Y414N |
| KOSC2_UPPER_AERODIGESTIVE_TRACT | 32745680 | 32745811 | 32745731 | 32745731 | Missense_Mutation | C | T | p.T416I |
| HEC59_ENDOMETRIUM | 32745680 | 32745811 | 32745797 | 32745797 | Missense_Mutation | G | A | p.R438H |
| MORCPR_LUNG | 32745680 | 32745811 | 32745802 | 32745802 | Missense_Mutation | C | T | p.P440S |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LCK |
| 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 LCK |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LCK |
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RelatedDrugs for LCK |
| 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 |
| P06239 | DB09079 | Nintedanib | Tyrosine-protein kinase Lck | small molecule | approved | |
| P06239 | DB01254 | Dasatinib | Tyrosine-protein kinase Lck | small molecule | approved|investigational | |
| P06239 | DB08901 | Ponatinib | Tyrosine-protein kinase Lck | small molecule | approved|investigational | |
| P06239 | DB12010 | Fostamatinib | Tyrosine-protein kinase Lck | small molecule | approved|investigational |
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RelatedDiseases for LCK |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| LCK | C4014233 | IMMUNODEFICIENCY 22 | 1 | ORPHANET;UNIPROT |
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