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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 RB1 |
Gene summary |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
RB1 | GO:0043550 | regulation of lipid kinase activity | 16286473 |
RB1 | GO:0045892 | negative regulation of transcription, DNA-templated | 10783144|12065415|19223331 |
RB1 | GO:2000679 | positive regulation of transcription regulatory region DNA binding | 25100735 |
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Gene structures and expression levels for RB1 |
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 | ENST00000322153.11 | IL12RB1-201:protein_coding:IL12RB1 | 2.916351e+00 | 8.627284e-01 | 2.829158e-04 | 5.875725e-03 |
PG | UP | ENST00000396315.5 | LILRB1-202:protein_coding:LILRB1 | 1.563007e+00 | 1.825910e+00 | 3.143635e-03 | 3.289640e-02 |
CB | UP | ENST00000530086.1 | ARRB1-207:retained_intron:ARRB1 | 7.502050e+00 | 1.411047e+00 | 6.590636e-12 | 6.953499e-10 |
CB | DOWN | ENST00000611804.1 | BDKRB1-204:protein_coding:BDKRB1 | 4.001514e+01 | -1.070958e+00 | 6.546795e-06 | 7.360959e-05 |
CB | UP | ENST00000525036.1 | RB1-205:retained_intron:RB1 | 1.570767e+00 | 8.389414e-01 | 3.492687e-03 | 1.462438e-02 |
CB | UP | ENST00000348831.9 | ADARB1-201:protein_coding:ADARB1 | 1.108523e+03 | 8.585712e-01 | 3.552827e-03 | 1.483162e-02 |
CB | UP | ENST00000449478.1 | ADARB1-206:protein_coding:ADARB1 | 2.878576e+00 | 1.695039e+00 | 9.889710e-03 | 3.443250e-02 |
CB | DOWN | ENST00000396332.8 | LILRB1-206:protein_coding:LILRB1 | 1.037354e+00 | -2.014798e+00 | 1.543823e-02 | 4.937400e-02 |
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 RB1 |
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_125328 | chr13 | 48367494:48367603:48368527:48368604:48373405:48373492 | 48368527:48368604 |
exon_skip_129539 | chr13 | 48345080:48345199:48347825:48347863:48348956:48349023 | 48347825:48347863 |
exon_skip_149673 | chr13 | 48364894:48364971:48367494:48367603:48368527:48368604 | 48367494:48367603 |
exon_skip_211811 | chr13 | 48465205:48465368:48473360:48473390:48476701:48476843 | 48473360:48473390 |
exon_skip_231350 | chr13 | 48459700:48459833:48463731:48463835:48464998:48465111 | 48463731:48463835 |
exon_skip_240417 | chr13 | 48303775:48304049:48307280:48307406:48342599:48342714 | 48307280:48307406 |
exon_skip_252290 | chr13 | 48476701:48476843:48477355:48477404:48479998:48480339 | 48477355:48477404 |
exon_skip_26102 | chr13 | 48376918:48377034:48379594:48379650:48380053:48380084 | 48379594:48379650 |
exon_skip_279842 | chr13 | 48373405:48373492:48376918:48377034:48379594:48379650 | 48376918:48377034 |
exon_skip_28591 | chr13 | 48459688:48459833:48463731:48463835:48464998:48465111 | 48463731:48463835 |
exon_skip_99937 | chr13 | 48360017:48360127:48362815:48362957:48364894:48364971 | 48362815:48362957 |
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 RB1 |
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 |
ENST00000267163 | 48463731 | 48463835 | 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 |
ENST00000267163 | 48362815 | 48362957 | Frame-shift |
ENST00000267163 | 48367494 | 48367603 | Frame-shift |
ENST00000267163 | 48473360 | 48473390 | Frame-shift |
ENST00000267163 | 48477355 | 48477404 | Frame-shift |
ENST00000267163 | 48347825 | 48347863 | In-frame |
ENST00000267163 | 48368527 | 48368604 | In-frame |
ENST00000267163 | 48376918 | 48377034 | In-frame |
ENST00000267163 | 48379594 | 48379650 | In-frame |
ENST00000267163 | 48463731 | 48463835 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RB1 |
p-ENSG00000139687_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 |
ENST00000267163 | 4810 | 928 | 48463731 | 48463835 | 2295 | 2398 | 702 | 737 |
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 |
ENST00000267163 | 4810 | 928 | 48347825 | 48347863 | 689 | 726 | 167 | 179 |
ENST00000267163 | 4810 | 928 | 48368527 | 48368604 | 1238 | 1314 | 350 | 375 |
ENST00000267163 | 4810 | 928 | 48376918 | 48377034 | 1404 | 1519 | 405 | 444 |
ENST00000267163 | 4810 | 928 | 48379594 | 48379650 | 1521 | 1576 | 444 | 463 |
ENST00000267163 | 4810 | 928 | 48463731 | 48463835 | 2295 | 2398 | 702 | 737 |
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 |
P06400 | 702 | 737 | 731 | 733 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1N4M |
P06400 | 702 | 737 | 2 | 928 | Chain | ID=PRO_0000167836;Note=Retinoblastoma-associated protein |
P06400 | 702 | 737 | 700 | 714 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2R7G |
P06400 | 702 | 737 | 721 | 728 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2R7G |
P06400 | 702 | 737 | 737 | 740 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2R7G |
P06400 | 702 | 737 | 706 | 706 | Natural variant | ID=VAR_005586;Note=In RB. C->Y |
P06400 | 702 | 737 | 712 | 712 | Natural variant | ID=VAR_005587;Note=In RB. C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10671068;Dbxref=dbSNP:rs137853296,PMID:10671068 |
P06400 | 702 | 737 | 373 | 771 | Region | Note=Pocket%3B binds T and E1A |
P06400 | 702 | 737 | 640 | 771 | Region | Note=Domain B |
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 |
P06400 | 167 | 179 | 2 | 928 | Chain | ID=PRO_0000167836;Note=Retinoblastoma-associated protein |
P06400 | 167 | 179 | 142 | 172 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2QDJ |
P06400 | 167 | 179 | 173 | 173 | Natural variant | ID=VAR_069376;Note=Y->H;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23033978;Dbxref=PMID:23033978 |
P06400 | 350 | 375 | 2 | 928 | Chain | ID=PRO_0000167836;Note=Retinoblastoma-associated protein |
P06400 | 350 | 375 | 347 | 353 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2QDJ |
P06400 | 350 | 375 | 356 | 356 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18220336,ECO:0000244|PubMed:23186163;Dbxref=PMID:18220336,PMID:23186163 |
P06400 | 350 | 375 | 373 | 373 | Modified residue | Note=Phosphothreonine%3B by CDK1;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:19690332,ECO:0000244|PubMed:23186163,ECO:0000269|PubMed:1756735;Dbxref=PMID:19690332,PMID:23186163,PMID:1756735 |
P06400 | 350 | 375 | 358 | 358 | Natural variant | ID=VAR_010046;Note=In RB. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8776589;Dbxref=PMID:8776589 |
P06400 | 350 | 375 | 358 | 358 | Natural variant | ID=VAR_005575;Note=In RB. R->Q;Dbxref=dbSNP:rs767011440 |
P06400 | 350 | 375 | 373 | 771 | Region | Note=Pocket%3B binds T and E1A |
P06400 | 350 | 375 | 373 | 579 | Region | Note=Domain A |
P06400 | 405 | 444 | 407 | 409 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2R7G |
P06400 | 405 | 444 | 2 | 928 | Chain | ID=PRO_0000167836;Note=Retinoblastoma-associated protein |
P06400 | 405 | 444 | 398 | 405 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2R7G |
P06400 | 405 | 444 | 412 | 434 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2R7G |
P06400 | 405 | 444 | 436 | 438 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2R7G |
P06400 | 405 | 444 | 439 | 468 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2R7G |
P06400 | 405 | 444 | 436 | 436 | Natural variant | ID=VAR_019379;Note=Q->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|Ref.7;Dbxref=dbSNP:rs4151534 |
P06400 | 405 | 444 | 373 | 771 | Region | Note=Pocket%3B binds T and E1A |
P06400 | 405 | 444 | 373 | 579 | Region | Note=Domain A |
P06400 | 444 | 463 | 2 | 928 | Chain | ID=PRO_0000167836;Note=Retinoblastoma-associated protein |
P06400 | 444 | 463 | 439 | 468 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2R7G |
P06400 | 444 | 463 | 447 | 447 | Natural variant | ID=VAR_010048;Note=In RB. K->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9140452;Dbxref=PMID:9140452 |
P06400 | 444 | 463 | 457 | 457 | Natural variant | ID=VAR_005576;Note=In RB. M->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8346255;Dbxref=PMID:8346255 |
P06400 | 444 | 463 | 373 | 771 | Region | Note=Pocket%3B binds T and E1A |
P06400 | 444 | 463 | 373 | 579 | Region | Note=Domain A |
P06400 | 702 | 737 | 731 | 733 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1N4M |
P06400 | 702 | 737 | 2 | 928 | Chain | ID=PRO_0000167836;Note=Retinoblastoma-associated protein |
P06400 | 702 | 737 | 700 | 714 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2R7G |
P06400 | 702 | 737 | 721 | 728 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2R7G |
P06400 | 702 | 737 | 737 | 740 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2R7G |
P06400 | 702 | 737 | 706 | 706 | Natural variant | ID=VAR_005586;Note=In RB. C->Y |
P06400 | 702 | 737 | 712 | 712 | Natural variant | ID=VAR_005587;Note=In RB. C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10671068;Dbxref=dbSNP:rs137853296,PMID:10671068 |
P06400 | 702 | 737 | 373 | 771 | Region | Note=Pocket%3B binds T and E1A |
P06400 | 702 | 737 | 640 | 771 | Region | Note=Domain B |
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3'-UTR located exon skipping events that lost miRNA binding sites in RB1 |
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 RB1 |
- 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 RB1 |
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 RB1 |
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 RB1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for RB1 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
P06400 | approved|investigational | DB00030 | Insulin Human | biotech | P06400 |
P06400 | approved | DB00071 | Insulin Pork | biotech | P06400 |
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RelatedDiseases for RB1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |