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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 SYNJ1 |
Gene summary |
Gene information | Gene symbol | SYNJ1 | Gene ID | 8867 |
Gene name | synaptojanin 1 | |
Synonyms | EIEE53|INPP5G|PARK20 | |
Cytomap | 21q22.11 | |
Type of gene | protein-coding | |
Description | synaptojanin-1inositol 5'-phosphatase (synaptojanin 1)inositol polyphosphate-5-phosphatase Gphosphoinositide 5-phosphatasesynaptic inositol 1,4,5-trisphosphate 5-phosphatase 1synaptojanin-1, polyphosphoinositide phosphatase | |
Modification date | 20200313 | |
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 |
SYNJ1 | GO:0046856 | phosphatidylinositol dephosphorylation | 18093523 |
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Gene structures and expression levels for SYNJ1 |
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 |
CB | UP | ENST00000382491.7 | SYNJ1-202:protein_coding:SYNJ1 | 2.251938e+02 | 8.566334e-01 | 7.515780e-05 | 5.820795e-04 |
CB | UP | ENST00000418301.3 | SYNJ1-204:protein_coding:SYNJ1 | 5.694418e+00 | 9.201669e-01 | 1.040209e-04 | 7.661063e-04 |
TC | UP | ENST00000630077.2 | SYNJ1-211:protein_coding:SYNJ1 | 1.825033e+02 | 1.473136e+00 | 3.172019e-05 | 6.454590e-04 |
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 SYNJ1 |
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_105269 | chr21 | 32641896:32641966:32642095:32642133:32644968:32645006 | 32642095:32642133 |
exon_skip_106354 | chr21 | 32650184:32650346:32653288:32653366:32656687:32656902 | 32653288:32653366 |
exon_skip_121731 | chr21 | 32695226:32695282:32699838:32700105:32701961:32702047 | 32699838:32700105 |
exon_skip_159530 | chr21 | 32642095:32642133:32644968:32645006:32645646:32645710 | 32644968:32645006 |
exon_skip_186001 | chr21 | 32642095:32642133:32643410:32643457:32644968:32644999 | 32643410:32643457 |
exon_skip_188190 | chr21 | 32641896:32641966:32642095:32642133:32643410:32643457 | 32642095:32642133 |
exon_skip_190351 | chr21 | 32631778:32631801:32634861:32634884:32638908:32639072 | 32634861:32634884 |
exon_skip_192461 | chr21 | 32666433:32666573:32670288:32670372:32673340:32673531 | 32670288:32670372 |
exon_skip_220088 | chr21 | 32641896:32641966:32642095:32642133:32644968:32644999 | 32642095:32642133 |
exon_skip_230160 | chr21 | 32630990:32631801:32634861:32634884:32638908:32639125 | 32634861:32634884 |
exon_skip_240910 | chr21 | 32699838:32700105:32701961:32702047:32726772:32726917 | 32701961:32702047 |
exon_skip_26233 | chr21 | 32670288:32670372:32673340:32673531:32676332:32676355 | 32673340:32673531 |
exon_skip_262380 | chr21 | 32631778:32631801:32634861:32634881:32638908:32639072 | 32634861:32634881 |
exon_skip_262785 | chr21 | 32681496:32681648:32684038:32684119:32685748:32685917 | 32684038:32684119 |
exon_skip_288682 | chr21 | 32642095:32642133:32643410:32643457:32644968:32645006 | 32643410:32643457 |
exon_skip_33381 | chr21 | 32630990:32631801:32634861:32634881:32638908:32639125 | 32634861:32634881 |
exon_skip_63589 | chr21 | 32673340:32673531:32676332:32676355:32678645:32678801 | 32676332:32676355 |
exon_skip_79189 | chr21 | 32631778:32631801:32634861:32634881:32638908:32639125 | 32634861:32634881 |
exon_skip_88452 | chr21 | 32631778:32631801:32634861:32634884:32638908:32639125 | 32634861:32634884 |
exon_skip_90262 | chr21 | 32673340:32673531:32676332:32676355:32678645:32678688 | 32676332:32676355 |
exon_skip_92518 | chr21 | 32642095:32642133:32644968:32645006:32645646:32645703 | 32644968:32645006 |
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 |
exon_skip_63589 | Mayo_TC | 4.757500e-01 | 6.434545e-01 | -1.677045e-01 | 7.963349e-07 |
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Open reading frame (ORF) annotation in the exon skipping event for SYNJ1 |
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 |
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 |
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Infer the effects of exon skipping event on protein functional features for SYNJ1 |
p-ENSG00000159082_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 SYNJ1 |
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 SYNJ1 |
- 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 SYNJ1 |
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 SYNJ1 |
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 SYNJ1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | DAZAP1 | exon_skip_220088 | -4.570934e-01 | 1.546015e-08 |
CB | PCBP1 | exon_skip_220088 | -4.078875e-01 | 6.228422e-07 |
CB | HNRNPDL | exon_skip_220088 | 4.149642e-01 | 3.792457e-07 |
CB | NUP42 | exon_skip_220088 | 4.271125e-01 | 1.575251e-07 |
CB | SRSF2 | exon_skip_161130 | 4.141176e-01 | 3.006005e-07 |
CB | ILF2 | exon_skip_161130 | 4.033071e-01 | 6.474066e-07 |
CB | HNRNPK | exon_skip_161130 | 4.509386e-01 | 1.784925e-08 |
CB | UNK | exon_skip_161130 | 4.140187e-01 | 3.027566e-07 |
CB | PCBP2 | exon_skip_161130 | 4.014859e-01 | 7.347931e-07 |
CB | HNRNPA0 | exon_skip_161130 | 4.343289e-01 | 6.650915e-08 |
CB | HNRNPDL | exon_skip_161130 | 4.521996e-01 | 1.610609e-08 |
CB | NUP42 | exon_skip_161130 | 5.710176e-01 | 1.171594e-13 |
CB | SRSF9 | exon_skip_161130 | 4.918488e-01 | 5.098026e-10 |
FL | RBM45 | exon_skip_63589 | 4.009022e-01 | 8.296095e-09 |
FL | HNRNPL | exon_skip_63589 | 4.477123e-01 | 7.463097e-11 |
HCC | RBM3 | exon_skip_105269 | 6.215752e-01 | 1.783294e-27 |
HCC | MSI1 | exon_skip_179631 | -4.238587e-01 | 3.805011e-12 |
HCC | RBM6 | exon_skip_179631 | -4.679059e-01 | 8.696117e-15 |
HCC | RBM5 | exon_skip_179631 | -4.538613e-01 | 6.653964e-14 |
HCC | UNK | exon_skip_179631 | -4.623788e-01 | 1.958669e-14 |
HCC | SRSF11 | exon_skip_63589 | -5.361194e-01 | 1.884892e-20 |
HCC | RBM45 | exon_skip_63589 | -5.586659e-01 | 2.057725e-22 |
IFG | RBM3 | exon_skip_105269 | 5.634628e-01 | 3.356651e-03 |
IFG | PCBP4 | exon_skip_288682 | -4.064227e-01 | 3.540640e-02 |
PCC | RBM3 | exon_skip_220088 | 6.834352e-01 | 4.430141e-27 |
PCC | MSI1 | exon_skip_66088 | -4.938756e-01 | 1.048767e-12 |
PCC | RBM6 | exon_skip_66088 | -4.011362e-01 | 1.671231e-08 |
PG | IGF2BP2 | exon_skip_63589 | -4.039120e-01 | 5.159710e-08 |
PG | HNRNPL | exon_skip_63589 | 4.301508e-01 | 5.320857e-09 |
PG | NOVA1 | exon_skip_63589 | 4.574091e-01 | 4.054220e-10 |
TC | NOVA1 | exon_skip_190351 | 4.626228e-01 | 1.536561e-09 |
TC | MSI1 | exon_skip_179631 | -4.198359e-01 | 3.001083e-06 |
TC | NUP42 | exon_skip_179631 | 5.635922e-01 | 5.465215e-11 |
TC | RBM45 | exon_skip_63589 | 4.247149e-01 | 2.835766e-07 |
TC | NOVA1 | exon_skip_63589 | 7.260996e-01 | 2.188558e-23 |
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RelatedDrugs for SYNJ1 |
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 SYNJ1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |