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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 CASS4 |
Gene summary |
Gene information | Gene symbol | CASS4 | Gene ID | 57091 |
Gene name | Cas scaffold protein family member 4 | |
Synonyms | C20orf32|CAS4|HEFL|HEPL | |
Cytomap | 20q13.31 | |
Type of gene | protein-coding | |
Description | cas scaffolding protein family member 4HEF-like proteinHEF1-EFS-p130Cas-like protein | |
Modification date | 20200313 | |
UniProtAcc | Q9NQ75, | |
Context | - 30906402(Genetics of Alzheimer's Disease) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
CASS4 | GO:0061098 | positive regulation of protein tyrosine kinase activity | 18256281 |
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Gene structures and expression levels for CASS4 |
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 |
PG | UP | 3.007135e+01 | 8.642471e-01 | 1.585434e-09 | 1.403442e-07 |
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 | ENST00000434344.2 | CASS4-202:protein_coding:CASS4 | 1.501166e+01 | 9.016299e-01 | 2.484764e-08 | 4.984712e-06 |
PG | UP | ENST00000360314.7 | CASS4-201:protein_coding:CASS4 | 1.174776e+01 | 9.651423e-01 | 1.028919e-06 | 9.056628e-05 |
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 CASS4 |
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_174098 | chr20 | 56450599:56450679:56451819:56453129:56458340:56460387 | 56451819:56453129 |
exon_skip_236373 | chr20 | 56450599:56450679:56451819:56453129:56458340:56458780 | 56451819:56453129 |
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 CASS4 |
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 |
ENST00000360314 | 56451819 | 56453129 | 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 |
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 |
ENST00000360314 | 56451819 | 56453129 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CASS4 |
p-ENSG00000087589_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 |
ENST00000360314 | 2636 | 786 | 56451819 | 56453129 | 869 | 2178 | 214 | 651 |
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 |
ENST00000360314 | 2636 | 786 | 56451819 | 56453129 | 869 | 2178 | 214 | 651 |
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 |
Q9NQ75 | 214 | 651 | 215 | 651 | Alternative sequence | ID=VSP_003806;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q9NQ75 | 214 | 651 | 1 | 786 | Chain | ID=PRO_0000079425;Note=Cas scaffolding protein family member 4 |
Q9NQ75 | 214 | 651 | 274 | 277 | Compositional bias | Note=Poly-Ser |
Q9NQ75 | 214 | 651 | 373 | 429 | Compositional bias | Note=Ser-rich |
Q9NQ75 | 214 | 651 | 249 | 249 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18088087,ECO:0000244|PubMed:23186163;Dbxref=PMID:18088087,PMID:23186163 |
Q9NQ75 | 214 | 651 | 305 | 305 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18088087,ECO:0000244|PubMed:23186163;Dbxref=PMID:18088087,PMID:23186163 |
Q9NQ75 | 214 | 651 | 376 | 376 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
Q9NQ75 | 214 | 651 | 390 | 390 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
Q9NQ75 | 214 | 651 | 491 | 491 | Natural variant | ID=VAR_054084;Note=R->K;Dbxref=dbSNP:rs16979936 |
Q9NQ75 | 214 | 651 | 629 | 629 | Natural variant | ID=VAR_054085;Note=T->N;Dbxref=dbSNP:rs6069755 |
Q9NQ75 | 214 | 651 | 329 | 329 | Sequence conflict | Note=Y->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9NQ75 | 214 | 651 | 350 | 350 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9NQ75 | 214 | 651 | 488 | 488 | Sequence conflict | Note=E->A;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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 |
Q9NQ75 | 214 | 651 | 215 | 651 | Alternative sequence | ID=VSP_003806;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
Q9NQ75 | 214 | 651 | 1 | 786 | Chain | ID=PRO_0000079425;Note=Cas scaffolding protein family member 4 |
Q9NQ75 | 214 | 651 | 274 | 277 | Compositional bias | Note=Poly-Ser |
Q9NQ75 | 214 | 651 | 373 | 429 | Compositional bias | Note=Ser-rich |
Q9NQ75 | 214 | 651 | 249 | 249 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18088087,ECO:0000244|PubMed:23186163;Dbxref=PMID:18088087,PMID:23186163 |
Q9NQ75 | 214 | 651 | 305 | 305 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18088087,ECO:0000244|PubMed:23186163;Dbxref=PMID:18088087,PMID:23186163 |
Q9NQ75 | 214 | 651 | 376 | 376 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
Q9NQ75 | 214 | 651 | 390 | 390 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
Q9NQ75 | 214 | 651 | 491 | 491 | Natural variant | ID=VAR_054084;Note=R->K;Dbxref=dbSNP:rs16979936 |
Q9NQ75 | 214 | 651 | 629 | 629 | Natural variant | ID=VAR_054085;Note=T->N;Dbxref=dbSNP:rs6069755 |
Q9NQ75 | 214 | 651 | 329 | 329 | Sequence conflict | Note=Y->N;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9NQ75 | 214 | 651 | 350 | 350 | Sequence conflict | Note=Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q9NQ75 | 214 | 651 | 488 | 488 | Sequence conflict | Note=E->A;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CASS4 |
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 CASS4 |
- 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 CASS4 |
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 CASS4 |
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 CASS4 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for CASS4 |
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 CASS4 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |