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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 SCYL2 |
 Gene summary |
| Gene information | Gene symbol | SCYL2 | Gene ID | 55681 |
| Gene name | SCY1 like pseudokinase 2 | |
| Synonyms | CVAK104 | |
| Cytomap | 12q23.1 | |
| Type of gene | protein-coding | |
| Description | SCY1-like protein 2SCY1-like 2SCY1-like, kinase-like 2coated vesicle-associated kinase of 104 kDa | |
| Modification date | 20180519 | |
| UniProtAcc | Q6P3W7 | |
| Context | PubMed: SCYL2 [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 |
| SCYL2 | GO:0002092 | positive regulation of receptor internalization | 19643732 |
| SCYL2 | GO:0008333 | endosome to lysosome transport | 19643732 |
| SCYL2 | GO:0090090 | negative regulation of canonical Wnt signaling pathway | 19643732 |
| SCYL2 | GO:2000286 | receptor internalization involved in canonical Wnt signaling pathway | 19643732 |
| SCYL2 | GO:2000370 | positive regulation of clathrin-dependent endocytosis | 19643732 |
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Exon skipping events across known transcript of Ensembl for SCYL2 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 SCYL2 |
| 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 SCYL2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_86109 | 12 | 100661026:100661174:100676720:100676925:100685280:100685438 | 100676720:100676925 | ENSG00000136021.13 | ENST00000550067.1 |
| exon_skip_86111 | 12 | 100661161:100661570:100676720:100676925:100685280:100685438 | 100676720:100676925 | ENSG00000136021.13 | ENST00000360820.2 |
| exon_skip_86113 | 12 | 100676909:100676925:100685280:100685438:100691808:100691953 | 100685280:100685438 | ENSG00000136021.13 | ENST00000360820.2,ENST00000549687.1 |
| exon_skip_86116 | 12 | 100704821:100704971:100706209:100706431:100707199:100707316 | 100706209:100706431 | ENSG00000136021.13 | ENST00000360820.2,ENST00000549687.1 |
| exon_skip_86117 | 12 | 100706209:100706431:100707199:100707316:100708266:100708392 | 100707199:100707316 | ENSG00000136021.13 | ENST00000360820.2,ENST00000549687.1 |
| exon_skip_86119 | 12 | 100711580:100711703:100713001:100713064:100717302:100717416 | 100713001:100713064 | ENSG00000136021.13 | ENST00000550251.1 |
| exon_skip_86122 | 12 | 100717375:100717416:100720399:100720532:100722978:100723097 | 100720399:100720532 | ENSG00000136021.13 | ENST00000360820.2,ENST00000549687.1 |
| exon_skip_86123 | 12 | 100720399:100720532:100720962:100721012:100722978:100723097 | 100720962:100721012 | ENSG00000136021.13 | ENST00000548871.1 |
| exon_skip_86126 | 12 | 100729588:100729684:100731164:100731284:100732305:100732411 | 100731164:100731284 | ENSG00000136021.13 | ENST00000547735.1,ENST00000360820.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SCYL2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_86109 | 12 | 100661026:100661174:100676720:100676925:100685280:100685438 | 100676720:100676925 | ENSG00000136021.13 | ENST00000550067.1 |
| exon_skip_86111 | 12 | 100661161:100661570:100676720:100676925:100685280:100685438 | 100676720:100676925 | ENSG00000136021.13 | ENST00000360820.2 |
| exon_skip_86113 | 12 | 100676909:100676925:100685280:100685438:100691808:100691953 | 100685280:100685438 | ENSG00000136021.13 | ENST00000549687.1,ENST00000360820.2 |
| exon_skip_86117 | 12 | 100706209:100706431:100707199:100707316:100708266:100708392 | 100707199:100707316 | ENSG00000136021.13 | ENST00000549687.1,ENST00000360820.2 |
| exon_skip_86119 | 12 | 100711580:100711703:100713001:100713064:100717302:100717416 | 100713001:100713064 | ENSG00000136021.13 | ENST00000550251.1 |
| exon_skip_86122 | 12 | 100717375:100717416:100720399:100720532:100722978:100723097 | 100720399:100720532 | ENSG00000136021.13 | ENST00000549687.1,ENST00000360820.2 |
| exon_skip_86123 | 12 | 100720399:100720532:100720962:100721012:100722978:100723097 | 100720962:100721012 | ENSG00000136021.13 | ENST00000548871.1 |
| exon_skip_86126 | 12 | 100729588:100729684:100731164:100731284:100732305:100732411 | 100731164:100731284 | ENSG00000136021.13 | ENST00000360820.2,ENST00000547735.1 |
| 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 SCYL2 |
| 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 |
| ENST00000360820 | 100676720 | 100676925 | 5CDS-5UTR |
| ENST00000360820 | 100685280 | 100685438 | Frame-shift |
| ENST00000360820 | 100720399 | 100720532 | Frame-shift |
| ENST00000360820 | 100706209 | 100706431 | In-frame |
| ENST00000360820 | 100707199 | 100707316 | In-frame |
| ENST00000360820 | 100731164 | 100731284 | 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 |
| ENST00000360820 | 100676720 | 100676925 | 5CDS-5UTR |
| ENST00000360820 | 100685280 | 100685438 | Frame-shift |
| ENST00000360820 | 100720399 | 100720532 | Frame-shift |
| ENST00000360820 | 100707199 | 100707316 | In-frame |
| ENST00000360820 | 100731164 | 100731284 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SCYL2 |
| 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 |
| ENST00000360820 | 5796 | 929 | 100706209 | 100706431 | 1068 | 1289 | 210 | 284 |
| ENST00000360820 | 5796 | 929 | 100707199 | 100707316 | 1290 | 1406 | 284 | 323 |
| ENST00000360820 | 5796 | 929 | 100731164 | 100731284 | 2463 | 2582 | 675 | 715 |
| 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 |
| ENST00000360820 | 5796 | 929 | 100707199 | 100707316 | 1290 | 1406 | 284 | 323 |
| ENST00000360820 | 5796 | 929 | 100731164 | 100731284 | 2463 | 2582 | 675 | 715 |
| 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 |
| Q6P3W7 | 210 | 284 | 1 | 929 | Chain | ID=PRO_0000252446;Note=SCY1-like protein 2 |
| Q6P3W7 | 210 | 284 | 32 | 327 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q6P3W7 | 284 | 323 | 1 | 929 | Chain | ID=PRO_0000252446;Note=SCY1-like protein 2 |
| Q6P3W7 | 284 | 323 | 32 | 327 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q6P3W7 | 675 | 715 | 1 | 929 | Chain | ID=PRO_0000252446;Note=SCY1-like protein 2 |
| Q6P3W7 | 675 | 715 | 661 | 701 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q6P3W7 | 675 | 715 | 677 | 677 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163 |
| Q6P3W7 | 675 | 715 | 708 | 708 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q6P3W7 | 675 | 715 | 699 | 929 | Region | Note=Necessary for interaction with AP2 complex and clathrin%2C interaction with clathrin is necessary for its targeting to the TGN and endosomal membranes |
| 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 |
| Q6P3W7 | 284 | 323 | 1 | 929 | Chain | ID=PRO_0000252446;Note=SCY1-like protein 2 |
| Q6P3W7 | 284 | 323 | 32 | 327 | Domain | Note=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159 |
| Q6P3W7 | 675 | 715 | 1 | 929 | Chain | ID=PRO_0000252446;Note=SCY1-like protein 2 |
| Q6P3W7 | 675 | 715 | 661 | 701 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q6P3W7 | 675 | 715 | 677 | 677 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163 |
| Q6P3W7 | 675 | 715 | 708 | 708 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q6P3W7 | 675 | 715 | 699 | 929 | Region | Note=Necessary for interaction with AP2 complex and clathrin%2C interaction with clathrin is necessary for its targeting to the TGN and endosomal membranes |
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SNVs in the skipped exons for SCYL2 |
| - 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-A3A0-01 | exon_skip_86109 exon_skip_86111 | 100676721 | 100676925 | 100676894 | 100676894 | Frame_Shift_Del | T | - | p.I49fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_86113 | 100685281 | 100685438 | 100685305 | 100685305 | Frame_Shift_Del | A | - | p.K69fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_86113 | 100685281 | 100685438 | 100685305 | 100685305 | Frame_Shift_Del | A | - | p.K69fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_86113 | 100685281 | 100685438 | 100685424 | 100685424 | Frame_Shift_Del | T | - | p.P107fs |
| KIRC | TCGA-B0-5085-01 | exon_skip_86116 | 100706210 | 100706431 | 100706229 | 100706229 | Frame_Shift_Del | A | - | p.E217fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_86116 | 100706210 | 100706431 | 100706232 | 100706232 | Frame_Shift_Del | G | - | p.W218fs |
| UCEC | TCGA-BG-A0M4-01 | exon_skip_86109 exon_skip_86111 | 100676721 | 100676925 | 100676906 | 100676907 | Frame_Shift_Ins | - | A | p.T53fs |
| BRCA | TCGA-A8-A06Y-01 | exon_skip_86109 exon_skip_86111 | 100676721 | 100676925 | 100676854 | 100676854 | Nonsense_Mutation | C | T | p.R36* |
| COAD | TCGA-AZ-4315-01 | exon_skip_86113 | 100685281 | 100685438 | 100685392 | 100685392 | Nonsense_Mutation | C | T | p.R97X |
| UCEC | TCGA-AP-A056-01 | exon_skip_86113 | 100685281 | 100685438 | 100685392 | 100685392 | Nonsense_Mutation | C | T | p.R97* |
| - 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 |
| 22RV1_PROSTATE | 100676721 | 100676925 | 100676906 | 100676907 | Frame_Shift_Ins | - | A | p.TK53fs |
| CROAP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100707200 | 100707316 | 100707270 | 100707271 | Frame_Shift_Ins | - | A | p.N309fs |
| TUHR4TKB_KIDNEY | 100676721 | 100676925 | 100676779 | 100676779 | Missense_Mutation | A | G | p.T11A |
| UMUC5_URINARY_TRACT | 100676721 | 100676925 | 100676780 | 100676780 | Missense_Mutation | C | A | p.T11N |
| NCIH630_LARGE_INTESTINE | 100676721 | 100676925 | 100676786 | 100676786 | Missense_Mutation | C | T | p.T13I |
| SNU81_LARGE_INTESTINE | 100676721 | 100676925 | 100676840 | 100676840 | Missense_Mutation | A | G | p.E31G |
| HCT116_LARGE_INTESTINE | 100676721 | 100676925 | 100676875 | 100676875 | Missense_Mutation | A | G | p.N43D |
| HEC251_ENDOMETRIUM | 100685281 | 100685438 | 100685357 | 100685357 | Missense_Mutation | C | T | p.S85F |
| KYAE1_OESOPHAGUS | 100685281 | 100685438 | 100685405 | 100685405 | Missense_Mutation | T | G | p.L101R |
| HEC251_ENDOMETRIUM | 100706210 | 100706431 | 100706243 | 100706243 | Missense_Mutation | T | G | p.L222V |
| HS698T_FIBROBLAST | 100706210 | 100706431 | 100706297 | 100706297 | Missense_Mutation | T | G | p.S240A |
| LC2AD_LUNG | 100706210 | 100706431 | 100706309 | 100706309 | Missense_Mutation | G | A | p.E244K |
| RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100706210 | 100706431 | 100706335 | 100706335 | Missense_Mutation | A | C | p.L252F |
| NCIH510_LUNG | 100706210 | 100706431 | 100706354 | 100706354 | Missense_Mutation | G | C | p.V259L |
| SKN3_UPPER_AERODIGESTIVE_TRACT | 100706210 | 100706431 | 100706394 | 100706394 | Missense_Mutation | A | G | p.Q272R |
| CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 100707200 | 100707316 | 100707248 | 100707248 | Missense_Mutation | C | T | p.R301C |
| TE9_OESOPHAGUS | 100707200 | 100707316 | 100707281 | 100707281 | Missense_Mutation | C | G | p.P312A |
| PEDS015T_SOFT_TISSUE | 100707200 | 100707316 | 100707282 | 100707282 | Missense_Mutation | C | T | p.P312L |
| NCIN87_STOMACH | 100720400 | 100720532 | 100720470 | 100720470 | Missense_Mutation | A | T | p.D527V |
| LN340_CENTRAL_NERVOUS_SYSTEM | 100731165 | 100731284 | 100731198 | 100731198 | Missense_Mutation | G | A | p.A687T |
| SNU1040_LARGE_INTESTINE | 100731165 | 100731284 | 100731216 | 100731216 | Missense_Mutation | G | A | p.A693T |
| HT115_LARGE_INTESTINE | 100685281 | 100685438 | 100685392 | 100685392 | Nonsense_Mutation | C | T | p.R97* |
| NCIH1339_LUNG | 100685281 | 100685438 | 100685428 | 100685428 | Nonsense_Mutation | G | T | p.E109* |
| SNU81_LARGE_INTESTINE | 100720400 | 100720532 | 100720444 | 100720444 | Nonsense_Mutation | C | A | p.Y518* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SCYL2 |
| 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 SCYL2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SCYL2 |
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RelatedDrugs for SCYL2 |
| 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 |
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RelatedDiseases for SCYL2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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