|
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 SSBP4 |
Gene summary |
Gene information | Gene symbol | SSBP4 | Gene ID | 170463 |
Gene name | single stranded DNA binding protein 4 | |
Synonyms | - | |
Cytomap | 19p13.11 | |
Type of gene | protein-coding | |
Description | single-stranded DNA-binding protein 4 | |
Modification date | 20200313 | |
UniProtAcc | A0A024R7K9, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
Top |
Gene structures and expression levels for SSBP4 |
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 | DOWN | ENST00000599699.2 | SSBP4-206:protein_coding:SSBP4 | 4.810513e+01 | -8.592281e-01 | 2.215047e-09 | 8.445242e-08 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SSBP4 |
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_148969 | chr19 | 18432559:18432604:18432700:18432735:18432829:18432844 | 18432700:18432735 |
exon_skip_149362 | chr19 | 18430841:18430930:18431647:18431706:18432000:18432023 | 18431647:18431706 |
exon_skip_165430 | chr19 | 18419649:18419707:18425909:18426083:18427351:18427423 | 18425909:18426083 |
exon_skip_169952 | chr19 | 18431647:18431706:18431793:18431862:18432000:18432023 | 18431793:18431862 |
exon_skip_19038 | chr19 | 18419624:18419707:18425909:18426083:18427351:18427423 | 18425909:18426083 |
exon_skip_22329 | chr19 | 18430841:18430930:18431647:18431706:18431793:18431838 | 18431647:18431706 |
exon_skip_225995 | chr19 | 18431813:18431862:18432000:18432070:18432147:18432174 | 18432000:18432070 |
exon_skip_229378 | chr19 | 18432200:18432214:18432559:18432735:18432829:18432883 | 18432559:18432735 |
exon_skip_233715 | chr19 | 18430841:18430930:18431353:18431418:18431647:18431705 | 18431353:18431418 |
exon_skip_243627 | chr19 | 18431353:18431418:18431647:18431706:18431793:18431838 | 18431647:18431706 |
exon_skip_273397 | chr19 | 18431672:18431706:18431793:18431862:18432000:18432023 | 18431793:18431862 |
exon_skip_276117 | chr19 | 18432973:18433043:18433135:18433213:18433585:18433613 | 18433135:18433213 |
exon_skip_35544 | chr19 | 18432559:18432604:18432700:18432735:18432829:18432883 | 18432700:18432735 |
exon_skip_49359 | chr19 | 18427351:18427423:18427752:18427813:18427898:18427982 | 18427752:18427813 |
exon_skip_52781 | chr19 | 18432067:18432070:18432147:18432214:18432559:18432579 | 18432147:18432214 |
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 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for SSBP4 |
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 |
ENST00000270061 | 18427752 | 18427813 | Frame-shift |
ENST00000270061 | 18431793 | 18431862 | Frame-shift |
ENST00000270061 | 18433135 | 18433213 | Frame-shift |
ENST00000270061 | 18431353 | 18431418 | In-frame |
ENST00000270061 | 18431647 | 18431706 | In-frame |
ENST00000270061 | 18432700 | 18432735 | 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 |
ENST00000270061 | 18427752 | 18427813 | Frame-shift |
ENST00000270061 | 18431793 | 18431862 | Frame-shift |
ENST00000270061 | 18431353 | 18431418 | In-frame |
ENST00000270061 | 18431647 | 18431706 | 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 |
ENST00000270061 | 18427752 | 18427813 | Frame-shift |
ENST00000270061 | 18431793 | 18431862 | Frame-shift |
ENST00000270061 | 18432000 | 18432070 | Frame-shift |
ENST00000270061 | 18432147 | 18432214 | Frame-shift |
ENST00000270061 | 18433135 | 18433213 | Frame-shift |
ENST00000270061 | 18431353 | 18431418 | In-frame |
ENST00000270061 | 18431647 | 18431706 | In-frame |
ENST00000270061 | 18432700 | 18432735 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for SSBP4 |
p-ENSG00000130511_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 |
ENST00000270061 | 1785 | 385 | 18431647 | 18431706 | 731 | 789 | 145 | 165 |
ENST00000270061 | 1785 | 385 | 18432700 | 18432735 | 1046 | 1080 | 250 | 262 |
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 |
ENST00000270061 | 1785 | 385 | 18431647 | 18431706 | 731 | 789 | 145 | 165 |
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 |
ENST00000270061 | 1785 | 385 | 18431647 | 18431706 | 731 | 789 | 145 | 165 |
ENST00000270061 | 1785 | 385 | 18432700 | 18432735 | 1046 | 1080 | 250 | 262 |
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 |
Q9BWG4 | 145 | 165 | 1 | 385 | Chain | ID=PRO_0000123832;Note=Single-stranded DNA-binding protein 4 |
Q9BWG4 | 145 | 165 | 125 | 279 | Compositional bias | Note=Pro-rich |
Q9BWG4 | 250 | 262 | 1 | 385 | Chain | ID=PRO_0000123832;Note=Single-stranded DNA-binding protein 4 |
Q9BWG4 | 250 | 262 | 125 | 279 | Compositional bias | Note=Pro-rich |
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 |
Q9BWG4 | 145 | 165 | 1 | 385 | Chain | ID=PRO_0000123832;Note=Single-stranded DNA-binding protein 4 |
Q9BWG4 | 145 | 165 | 125 | 279 | Compositional bias | Note=Pro-rich |
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 |
Q9BWG4 | 145 | 165 | 1 | 385 | Chain | ID=PRO_0000123832;Note=Single-stranded DNA-binding protein 4 |
Q9BWG4 | 145 | 165 | 125 | 279 | Compositional bias | Note=Pro-rich |
Q9BWG4 | 250 | 262 | 1 | 385 | Chain | ID=PRO_0000123832;Note=Single-stranded DNA-binding protein 4 |
Q9BWG4 | 250 | 262 | 125 | 279 | Compositional bias | Note=Pro-rich |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in SSBP4 |
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 |
Top |
SNVs in the skipped exons for SSBP4 |
- 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 |
Top |
AD stage-associated exon skippint events for SSBP4 |
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 |
ADstage | ROSMAP | HCC | exon_skip_49359 | -3.408295e-01 | 7.490000e-09 | chr19 | + | 18427351 | 18427423 | 18427752 | 18427813 | 18427898 | 18427982 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SSBP4 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for SSBP4 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | RBM3 | exon_skip_49359 | 4.782549e-01 | 1.822525e-10 |
CB | PCBP1 | exon_skip_49359 | -4.790952e-01 | 1.676375e-10 |
CB | TRA2A | exon_skip_49359 | -6.073474e-01 | 2.111477e-17 |
CB | RBM45 | exon_skip_49359 | 6.974069e-01 | 1.748264e-24 |
DLPFC | RBM3 | exon_skip_49359 | 4.513454e-01 | 1.440155e-18 |
HCC | RBM3 | exon_skip_49359 | 6.175070e-01 | 4.325184e-30 |
IFG | RBM3 | exon_skip_49359 | 5.373607e-01 | 3.190182e-03 |
PCC | RBM3 | exon_skip_49359 | 4.811177e-01 | 7.432704e-14 |
PG | RBM3 | exon_skip_49359 | 4.825398e-01 | 1.783280e-10 |
Top |
RelatedDrugs for SSBP4 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for SSBP4 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |