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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 RBPMS |
Gene summary |
Gene information | Gene symbol | RBPMS | Gene ID | 11030 |
Gene name | RNA binding protein, mRNA processing factor | |
Synonyms | HERMES | |
Cytomap | 8p12 | |
Type of gene | protein-coding | |
Description | RNA-binding protein with multiple splicingRNA binding protein with multiple splicingheart and RRM expressed sequence | |
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 |
RBPMS | GO:0010862 | positive regulation of pathway-restricted SMAD protein phosphorylation | 17099224 |
RBPMS | GO:0060391 | positive regulation of SMAD protein signal transduction | 17099224 |
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Gene structures and expression levels for RBPMS |
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 | ENST00000519647.5 | RBPMS-207:protein_coding:RBPMS | 2.035386e+00 | 1.774321e+00 | 5.986004e-04 | 1.002981e-02 |
TC | UP | ENST00000520161.5 | RBPMS-209:protein_coding:RBPMS | 1.096749e+01 | 1.194422e+00 | 7.743630e-04 | 8.114442e-03 |
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 RBPMS |
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_247707 | chr8 | 30479330:30479377:30504286:30504436:30544494:30544556 | 30504286:30504436 |
exon_skip_25105 | chr8 | 30504286:30504436:30544494:30544624:30547292:30547483 | 30544494:30544624 |
exon_skip_276628 | chr8 | 30544494:30544624:30545164:30545220:30547292:30547483 | 30545164:30545220 |
exon_skip_55787 | chr8 | 30558887:30558956:30566257:30566360:30570637:30570700 | 30566257:30566360 |
exon_skip_75675 | chr8 | 30504286:30504436:30537578:30537723:30544494:30544556 | 30537578:30537723 |
exon_skip_81185 | chr8 | 30544494:30544624:30549500:30549585:30558887:30558956 | 30549500:30549585 |
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 RBPMS |
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 |
ENST00000397323 | 30566257 | 30566360 | 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 |
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 |
ENST00000397323 | 30566257 | 30566360 | 3UTR-3UTR |
ENST00000320203 | 30504286 | 30504436 | Frame-shift |
ENST00000397323 | 30504286 | 30504436 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for RBPMS |
p-ENSG00000157110_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 RBPMS |
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 | ENST00000397323 | 30566257 | 30566360 | hsa-miR-7156-3p | chr8:30566276-30566283 | 8mer-1a | chr8:30566272-30566291 | 147.00 | -24.13 |
Mayo | ENST00000397323 | 30566257 | 30566360 | hsa-miR-4699-5p | chr8:30566306-30566313 | 8mer-1a | chr8:30566291-30566313 | 159.00 | -17.91 |
Mayo | ENST00000397323 | 30566257 | 30566360 | hsa-miR-4773 | chr8:30566335-30566342 | 8mer-1a | chr8:30566322-30566346 | 162.00 | -15.53 |
Mayo | ENST00000397323 | 30566257 | 30566360 | hsa-miR-3925-5p | chr8:30566326-30566333 | 8mer-1a | chr8:30566322-30566346 | 162.00 | -15.53 |
Mayo | ENST00000397323 | 30566257 | 30566360 | hsa-miR-3674 | chr8:30566339-30566346 | 8mer-1a | chr8:30566322-30566346 | 162.00 | -15.53 |
ROSMAP | ENST00000397323 | 30566257 | 30566360 | hsa-miR-7156-3p | chr8:30566276-30566283 | 8mer-1a | chr8:30566272-30566291 | 147.00 | -24.13 |
ROSMAP | ENST00000397323 | 30566257 | 30566360 | hsa-miR-4699-5p | chr8:30566306-30566313 | 8mer-1a | chr8:30566291-30566313 | 159.00 | -17.91 |
ROSMAP | ENST00000397323 | 30566257 | 30566360 | hsa-miR-4773 | chr8:30566335-30566342 | 8mer-1a | chr8:30566322-30566346 | 162.00 | -15.53 |
ROSMAP | ENST00000397323 | 30566257 | 30566360 | hsa-miR-3925-5p | chr8:30566326-30566333 | 8mer-1a | chr8:30566322-30566346 | 162.00 | -15.53 |
ROSMAP | ENST00000397323 | 30566257 | 30566360 | hsa-miR-3674 | chr8:30566339-30566346 | 8mer-1a | chr8:30566322-30566346 | 162.00 | -15.53 |
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SNVs in the skipped exons for RBPMS |
- 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 RBPMS |
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 RBPMS |
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 RBPMS |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for RBPMS |
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 RBPMS |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |