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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for CYLD |
Gene summary |
Gene information | Gene symbol | CYLD | Gene ID | 1540 |
Gene name | CYLD lysine 63 deubiquitinase | |
Synonyms | BRSS|CDMT|CYLD1|CYLDI|EAC|MFT|MFT1|SBS|TEM|USPL2 | |
Cytomap | 16q12.1 | |
Type of gene | protein-coding | |
Description | ubiquitin carboxyl-terminal hydrolase CYLDcylindromatosis (turban tumor syndrome)deubiquitinating enzyme CYLDprobable ubiquitin carboxyl-terminal hydrolase CYLDubiquitin specific peptidase like 2ubiquitin thioesterase CYLDubiquitin thiolesterase CYL | |
Modification date | 20200329 | |
UniProtAcc | A0A024R6Q9, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
CYLD | GO:0010803 | regulation of tumor necrosis factor-mediated signaling pathway | 26997266|27458237|27591049 |
CYLD | GO:0016579 | protein deubiquitination | 29291351 |
CYLD | GO:0032088 | negative regulation of NF-kappaB transcription factor activity | 18313383 |
CYLD | GO:0045087 | innate immune response | 26997266 |
CYLD | GO:0046329 | negative regulation of JNK cascade | 29291351 |
CYLD | GO:0050727 | regulation of inflammatory response | 27591049 |
CYLD | GO:0060544 | regulation of necroptotic process | 27458237 |
CYLD | GO:0070536 | protein K63-linked deubiquitination | 18313383|18636086|26997266|27458237|27591049|29291351 |
CYLD | GO:1901223 | negative regulation of NIK/NF-kappaB signaling | 18313383 |
CYLD | GO:1903753 | negative regulation of p38MAPK cascade | 29291351 |
CYLD | GO:1990108 | protein linear deubiquitination | 26997266|27458237|27591049 |
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Gene structures and expression levels for CYLD |
Skipped exons in the ROSMAP, MSBB, and Mayo 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. |
Differentially expressed gene analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
PG | UP | ENST00000564634.5 | CYLD-208:protein_coding:CYLD | 2.979836e+00 | 1.254424e+00 | 2.096279e-03 | 2.470988e-02 |
CB | UP | ENST00000398568.6 | CYLD-202:protein_coding:CYLD | 5.926137e+01 | 1.588993e+00 | 4.780307e-11 | 3.428003e-09 |
CB | DOWN | ENST00000568744.1 | CYLD-213:retained_intron:CYLD | 9.359955e+00 | -9.167479e-01 | 1.405586e-07 | 2.832464e-06 |
CB | UP | ENST00000566679.6 | CYLD-211:protein_coding:CYLD | 1.212853e+00 | 1.292386e+00 | 4.250940e-03 | 1.722425e-02 |
TC | UP | ENST00000398568.6 | CYLD-202:protein_coding:CYLD | 7.058566e+01 | 1.119834e+00 | 1.606523e-07 | 8.988985e-06 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for CYLD |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_142497 | chr16 | 50754319:50754424:50775166:50775174:50776179:50776277 | 50775166:50775174 |
exon_skip_155801 | chr16 | 50742762:50742841:50744730:50744866:50749576:50749798 | 50744730:50744866 |
exon_skip_173674 | chr16 | 50779695:50780044:50781246:50781411:50782325:50782466 | 50781246:50781411 |
exon_skip_212848 | chr16 | 50786855:50786946:50787786:50787852:50791558:50791690 | 50787786:50787852 |
exon_skip_222094 | chr16 | 50779736:50780044:50781246:50781411:50782325:50782466 | 50781246:50781411 |
exon_skip_234884 | chr16 | 50779665:50780044:50781246:50781411:50782325:50782466 | 50781246:50781411 |
exon_skip_49401 | chr16 | 50787786:50787852:50791558:50791690:50792597:50792705 | 50791558:50791690 |
exon_skip_50415 | chr16 | 50784329:50784451:50786855:50786946:50787786:50787852 | 50786855:50786946 |
Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for CYLD |
Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000311559 | 50744730 | 50744866 | 5UTR-5UTR |
ENST00000311559 | 50781246 | 50781411 | Frame-shift |
ENST00000427738 | 50781246 | 50781411 | Frame-shift |
ENST00000311559 | 50786855 | 50786946 | Frame-shift |
ENST00000427738 | 50786855 | 50786946 | Frame-shift |
ENST00000311559 | 50775166 | 50775174 | In-frame |
ENST00000427738 | 50775166 | 50775174 | In-frame |
Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000311559 | 50744730 | 50744866 | 5UTR-5UTR |
ENST00000311559 | 50781246 | 50781411 | Frame-shift |
ENST00000427738 | 50781246 | 50781411 | Frame-shift |
ENST00000311559 | 50786855 | 50786946 | Frame-shift |
ENST00000427738 | 50786855 | 50786946 | Frame-shift |
ENST00000311559 | 50787786 | 50787852 | Frame-shift |
ENST00000427738 | 50787786 | 50787852 | Frame-shift |
ENST00000311559 | 50775166 | 50775174 | In-frame |
ENST00000427738 | 50775166 | 50775174 | In-frame |
Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000311559 | 50744730 | 50744866 | 5UTR-5UTR |
ENST00000311559 | 50781246 | 50781411 | Frame-shift |
ENST00000427738 | 50781246 | 50781411 | Frame-shift |
ENST00000311559 | 50786855 | 50786946 | Frame-shift |
ENST00000427738 | 50786855 | 50786946 | Frame-shift |
ENST00000311559 | 50787786 | 50787852 | Frame-shift |
ENST00000427738 | 50787786 | 50787852 | Frame-shift |
ENST00000311559 | 50791558 | 50791690 | Frame-shift |
ENST00000427738 | 50791558 | 50791690 | Frame-shift |
ENST00000311559 | 50775166 | 50775174 | In-frame |
ENST00000427738 | 50775166 | 50775174 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CYLD |
p-ENSG00000083799_img4.png |
Loci of skipped exons in ROSMAP 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 |
Loci of skipped exons in MSBB 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 |
Loci of skipped exons in Mayo 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 |
Lost protein functional features of individual exon skipping events in ROSMAP. |
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 MSBB. |
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 Mayo. |
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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3'-UTR located exon skipping events that lost miRNA binding sites in CYLD |
3'-UTR exon skipping evnets lost miRNA binding. |
Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for CYLD |
- Differential PSIs between mutated versus non-mutated samples. |
- Depth of Coverage in the skipped exon of the mutated samples. |
- Sashimi plot in the skipped exon of the mutated samples. |
- Non-synonymous mutations located in the skipped exons. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
- 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 |
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AD stage-associated exon skippint events for CYLD |
Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CYLD |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for CYLD |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | TARDBP | exon_skip_50415 | -4.280506e-01 | 4.655786e-08 |
CB | TRA2A | exon_skip_50415 | -5.573685e-01 | 1.281805e-13 |
CB | FUBP1 | exon_skip_50415 | -4.614789e-01 | 2.789058e-09 |
CB | DAZAP1 | exon_skip_160034 | -4.798544e-01 | 3.036422e-10 |
CB | TARDBP | exon_skip_160034 | -4.921385e-01 | 9.035124e-11 |
CB | ELAVL1 | exon_skip_160034 | -4.095419e-01 | 1.334372e-07 |
CB | U2AF2 | exon_skip_160034 | -5.715676e-01 | 9.816853e-15 |
CB | PCBP1 | exon_skip_160034 | -4.817189e-01 | 2.533958e-10 |
CB | PCBP4 | exon_skip_160034 | 4.719082e-01 | 6.485609e-10 |
CB | TRA2A | exon_skip_160034 | -5.222410e-01 | 3.748212e-12 |
CB | FUBP1 | exon_skip_160034 | -4.947618e-01 | 6.930728e-11 |
CB | HNRNPA2B1 | exon_skip_160034 | -4.982122e-01 | 4.873335e-11 |
CB | NUP42 | exon_skip_160034 | 4.182420e-01 | 6.759278e-08 |
CB | PTBP1 | exon_skip_160034 | -5.183181e-01 | 5.776890e-12 |
HCC | DAZAP1 | exon_skip_155801 | 4.872270e-01 | 2.524460e-17 |
HCC | SFPQ | exon_skip_155801 | 5.310513e-01 | 7.869877e-21 |
HCC | KHDRBS2 | exon_skip_155801 | -4.095555e-01 | 3.195110e-12 |
HCC | SF1 | exon_skip_155801 | 4.129307e-01 | 2.036125e-12 |
IFG | DAZAP1 | exon_skip_155801 | 6.334138e-01 | 2.967039e-04 |
IFG | RBMS3 | exon_skip_155801 | 4.782129e-01 | 1.005317e-02 |
IFG | SFPQ | exon_skip_155801 | 5.051653e-01 | 6.108248e-03 |
IFG | CNOT4 | exon_skip_155801 | 4.732153e-01 | 1.097986e-02 |
IFG | RC3H1 | exon_skip_155801 | 4.325634e-01 | 2.150493e-02 |
IFG | SF1 | exon_skip_155801 | 5.015630e-01 | 6.543878e-03 |
IFG | FUBP3 | exon_skip_155801 | 4.938006e-01 | 7.572476e-03 |
IFG | KHSRP | exon_skip_155801 | 4.275755e-01 | 2.323225e-02 |
STG | KHDRBS2 | exon_skip_155801 | -4.049858e-01 | 2.137646e-04 |
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RelatedDrugs for CYLD |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for CYLD |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |