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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 SKP1 |
Gene summary |
Gene information | Gene symbol | SKP1 | Gene ID | 6500 |
Gene name | S-phase kinase associated protein 1 | |
Synonyms | EMC19|OCP-II|OCP2|SKP1A|TCEB1L|p19A | |
Cytomap | 5q31.1 | |
Type of gene | protein-coding | |
Description | S-phase kinase-associated protein 1OCP-2RNA polymerase II elongation factor-like protein OCP2SIIIcyclin A/CDK2-associated p19cyclin-A/CDK2-associated protein p19organ of Corti protein 2organ of Corti protein IIp19skp1transcription elongation fact | |
Modification date | 20200327 | |
UniProtAcc | ||
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
SKP1 | GO:0016567 | protein ubiquitination | 15103331 |
SKP1 | GO:0031146 | SCF-dependent proteasomal ubiquitin-dependent protein catabolic process | 15103331|20347421 |
SKP1 | GO:0035518 | histone H2A monoubiquitination | 16943429 |
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Gene structures and expression levels for SKP1 |
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 |
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 SKP1 |
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_113293 | chr5 | 134173926:134174022:134174462:134174514:134176855:134176950 | 134174462:134174514 |
exon_skip_187077 | chr5 | 134157572:134157768:134158455:134158595:134160987:134161130 | 134158455:134158595 |
exon_skip_245136 | chr5 | 134167170:134167243:134173701:134173766:134173926:134174022 | 134173701:134173766 |
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 SKP1 |
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 |
ENST00000522855 | 134174462 | 134174514 | 3UTR-3UTR |
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 |
ENST00000522855 | 134174462 | 134174514 | 3UTR-3UTR |
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 |
ENST00000522855 | 134174462 | 134174514 | 3UTR-3UTR |
ENST00000353411 | 134158455 | 134158595 | In-frame |
ENST00000517625 | 134158455 | 134158595 | In-frame |
ENST00000522855 | 134158455 | 134158595 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SKP1 |
p-ENSG00000113558_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 |
ENST00000353411 | 9491 | 163 | 134158455 | 134158595 | 500 | 639 | 105 | 151 |
ENST00000517625 | 893 | 163 | 134158455 | 134158595 | 475 | 614 | 105 | 151 |
ENST00000522855 | 819 | 163 | 134158455 | 134158595 | 465 | 604 | 105 | 151 |
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 |
P63208 | 105 | 151 | 128 | 130 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1FQV |
P63208 | 105 | 151 | 128 | 130 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1FQV |
P63208 | 105 | 151 | 128 | 130 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1FQV |
P63208 | 105 | 151 | 2 | 163 | Chain | ID=PRO_0000187251;Note=S-phase kinase-associated protein 1 |
P63208 | 105 | 151 | 2 | 163 | Chain | ID=PRO_0000187251;Note=S-phase kinase-associated protein 1 |
P63208 | 105 | 151 | 2 | 163 | Chain | ID=PRO_0000187251;Note=S-phase kinase-associated protein 1 |
P63208 | 105 | 151 | 142 | 142 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:25114211;Dbxref=PMID:25114211 |
P63208 | 105 | 151 | 142 | 142 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:25114211;Dbxref=PMID:25114211 |
P63208 | 105 | 151 | 142 | 142 | Cross-link | Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1);Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:25114211;Dbxref=PMID:25114211 |
P63208 | 105 | 151 | 97 | 110 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1FS1 |
P63208 | 105 | 151 | 97 | 110 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1FS1 |
P63208 | 105 | 151 | 97 | 110 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1FS1 |
P63208 | 105 | 151 | 113 | 127 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1FS1 |
P63208 | 105 | 151 | 113 | 127 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1FS1 |
P63208 | 105 | 151 | 113 | 127 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1FS1 |
P63208 | 105 | 151 | 132 | 138 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1FS1 |
P63208 | 105 | 151 | 132 | 138 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1FS1 |
P63208 | 105 | 151 | 132 | 138 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1FS1 |
P63208 | 105 | 151 | 149 | 156 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2AST |
P63208 | 105 | 151 | 149 | 156 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2AST |
P63208 | 105 | 151 | 149 | 156 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2AST |
P63208 | 105 | 151 | 131 | 131 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692;Dbxref=PMID:20068231,PMID:21406692 |
P63208 | 105 | 151 | 131 | 131 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692;Dbxref=PMID:20068231,PMID:21406692 |
P63208 | 105 | 151 | 131 | 131 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:21406692;Dbxref=PMID:20068231,PMID:21406692 |
P63208 | 105 | 151 | 104 | 163 | Region | Note=Interaction with the F-box domain of F-box proteins;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
P63208 | 105 | 151 | 104 | 163 | Region | Note=Interaction with the F-box domain of F-box proteins;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
P63208 | 105 | 151 | 104 | 163 | Region | Note=Interaction with the F-box domain of F-box proteins;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SKP1 |
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 |
Mayo | ENST00000522855 | 134174462 | 134174514 | hsa-miR-1252-3p | chr5:134174504-134174511 | 8mer-1a | chr5:134174490-134174511 | 160.00 | -9.68 |
MSBB | ENST00000522855 | 134174462 | 134174514 | hsa-miR-1252-3p | chr5:134174504-134174511 | 8mer-1a | chr5:134174490-134174511 | 160.00 | -9.68 |
ROSMAP | ENST00000522855 | 134174462 | 134174514 | hsa-miR-1252-3p | chr5:134174504-134174511 | 8mer-1a | chr5:134174490-134174511 | 160.00 | -9.68 |
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SNVs in the skipped exons for SKP1 |
- 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 SKP1 |
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 SKP1 |
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 SKP1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SKP1 |
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 SKP1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |