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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for RYR1 |
 Gene summary |
| Gene information | Gene symbol | RYR1 | Gene ID | 6261 |
| Gene name | ryanodine receptor 1 | |
| Synonyms | CCO|MHS|MHS1|PPP1R137|RYDR|RYR|RYR-1|SKRR | |
| Cytomap | 19q13.2 | |
| Type of gene | protein-coding | |
| Description | ryanodine receptor 1central core disease of muscleprotein phosphatase 1, regulatory subunit 137ryanodine receptor 1 (skeletal)sarcoplasmic reticulum calcium release channelskeletal muscle calcium release channelskeletal muscle ryanodine receptortyp | |
| Modification date | 20200328 | |
| UniProtAcc | ||
| Context | - 28102470(Neuronal Ryanodine Receptors in Development and Aging) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| RYR1 | GO:0001666 | response to hypoxia | 19120137 |
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Gene structures and expression levels for RYR1 |
| 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. |
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ENSG00000196218
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| TC | UP | ENST00000593322.1 | RYR1-203:nonsense_mediated_decay:RYR1 | 2.435805e+01 | 9.675476e-01 | 1.760942e-04 | 2.523998e-03 |
| TC | UP | ENST00000601514.5 | RYR1-210:protein_coding:RYR1 | 2.375982e+01 | 9.105502e-01 | 6.610461e-04 | 7.157092e-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 RYR1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_104129 | chr19 | 38510660:38510781:38512072:38512132:38512245:38512483 | 38512072:38512132 |
| exon_skip_11013 | chr19 | 38516087:38516217:38517359:38517691:38519214:38519454 | 38517359:38517691 |
| exon_skip_111438 | chr19 | 38567773:38567917:38570607:38570693:38572019:38572079 | 38570607:38570693 |
| exon_skip_120971 | chr19 | 38567773:38567917:38570607:38570693:38572019:38572244 | 38570607:38570693 |
| exon_skip_124982 | chr19 | 38511571:38511610:38512072:38512132:38512245:38512483 | 38512072:38512132 |
| exon_skip_127753 | chr19 | 38535997:38536070:38536750:38536767:38537880:38537960 | 38536750:38536767 |
| exon_skip_140991 | chr19 | 38532671:38532736:38534720:38534819:38535141:38535174 | 38534720:38534819 |
| exon_skip_147743 | chr19 | 38510730:38510781:38511561:38511610:38512072:38512132 | 38511561:38511610 |
| exon_skip_162239 | chr19 | 38535316:38535392:38535997:38536070:38537880:38537960 | 38535997:38536070 |
| exon_skip_184426 | chr19 | 38575919:38575961:38577918:38578048:38578144:38578204 | 38577918:38578048 |
| exon_skip_190944 | chr19 | 38523217:38523309:38523915:38523929:38525332:38525502 | 38523915:38523929 |
| exon_skip_207147 | chr19 | 38543771:38543875:38546445:38546526:38548233:38548372 | 38546445:38546526 |
| exon_skip_210762 | chr19 | 38517359:38517691:38519214:38519454:38523028:38523115 | 38519214:38519454 |
| exon_skip_217554 | chr19 | 38523217:38523309:38523915:38523929:38525332:38525491 | 38523915:38523929 |
| exon_skip_224880 | chr19 | 38443558:38443632:38443718:38443796:38444149:38444261 | 38443718:38443796 |
| exon_skip_230232 | chr19 | 38523217:38523309:38525332:38525502:38526993:38527052 | 38525332:38525502 |
| exon_skip_24343 | chr19 | 38507712:38507827:38510498:38510565:38510660:38510781 | 38510498:38510565 |
| exon_skip_247970 | chr19 | 38523226:38523309:38523915:38523929:38525332:38525502 | 38523915:38523929 |
| exon_skip_254753 | chr19 | 38477710:38477870:38478435:38478600:38483027:38483113 | 38478435:38478600 |
| exon_skip_268970 | chr19 | 38446472:38446565:38446694:38446768:38448355:38448511 | 38446694:38446768 |
| exon_skip_284072 | chr19 | 38535316:38535392:38537880:38537960:38543347:38543435 | 38537880:38537960 |
| exon_skip_288533 | chr19 | 38467610:38467812:38468966:38469140:38469305:38469513 | 38468966:38469140 |
| exon_skip_44261 | chr19 | 38433830:38433874:38440745:38440864:38442349:38442453 | 38440745:38440864 |
| exon_skip_46448 | chr19 | 38510660:38510781:38511561:38511610:38512072:38512132 | 38511561:38511610 |
| exon_skip_68235 | chr19 | 38512245:38512483:38515026:38515107:38516087:38516217 | 38515026:38515107 |
| exon_skip_74303 | chr19 | 38580370:38580504:38584943:38585099:38585938:38586002 | 38584943:38585099 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_276817 | Mayo_CB | 4.634328e-01 | 6.042593e-01 | -1.408264e-01 | 2.777194e-05 |
| exon_skip_247970 | Mayo_TC | 1.526829e-01 | 2.732836e-01 | -1.206007e-01 | 1.987418e-06 |
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Open reading frame (ORF) annotation in the exon skipping event for RYR1 |
| 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 |
| ENST00000359596 | 38478435 | 38478600 | Frame-shift |
| ENST00000359596 | 38511561 | 38511610 | Frame-shift |
| ENST00000359596 | 38512072 | 38512132 | Frame-shift |
| ENST00000359596 | 38577918 | 38578048 | Frame-shift |
| ENST00000359596 | 38584943 | 38585099 | Frame-shift |
| ENST00000359596 | 38440745 | 38440864 | In-frame |
| ENST00000359596 | 38517359 | 38517691 | In-frame |
| ENST00000359596 | 38523915 | 38523929 | In-frame |
| ENST00000359596 | 38536750 | 38536767 | In-frame |
| ENST00000359596 | 38570607 | 38570693 | 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 |
| ENST00000359596 | 38478435 | 38478600 | Frame-shift |
| ENST00000359596 | 38511561 | 38511610 | Frame-shift |
| ENST00000359596 | 38577918 | 38578048 | Frame-shift |
| ENST00000359596 | 38584943 | 38585099 | Frame-shift |
| ENST00000359596 | 38523915 | 38523929 | In-frame |
| ENST00000359596 | 38536750 | 38536767 | In-frame |
| ENST00000359596 | 38570607 | 38570693 | 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 |
| ENST00000359596 | 38443718 | 38443796 | Frame-shift |
| ENST00000359596 | 38468966 | 38469140 | Frame-shift |
| ENST00000359596 | 38478435 | 38478600 | Frame-shift |
| ENST00000359596 | 38510498 | 38510565 | Frame-shift |
| ENST00000359596 | 38511561 | 38511610 | Frame-shift |
| ENST00000359596 | 38512072 | 38512132 | Frame-shift |
| ENST00000359596 | 38515026 | 38515107 | Frame-shift |
| ENST00000359596 | 38519214 | 38519454 | Frame-shift |
| ENST00000359596 | 38534720 | 38534819 | Frame-shift |
| ENST00000359596 | 38546445 | 38546526 | Frame-shift |
| ENST00000359596 | 38577918 | 38578048 | Frame-shift |
| ENST00000359596 | 38584943 | 38585099 | Frame-shift |
| ENST00000359596 | 38446694 | 38446768 | In-frame |
| ENST00000359596 | 38517359 | 38517691 | In-frame |
| ENST00000359596 | 38523915 | 38523929 | In-frame |
| ENST00000359596 | 38536750 | 38536767 | In-frame |
| ENST00000359596 | 38570607 | 38570693 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RYR1 |
p-ENSG00000196218_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 |
| ENST00000359596 | 15134 | 5038 | 38440745 | 38440864 | 47 | 165 | 15 | 55 |
| ENST00000359596 | 15134 | 5038 | 38517359 | 38517691 | 9687 | 10018 | 3229 | 3339 |
| ENST00000359596 | 15134 | 5038 | 38570607 | 38570693 | 13661 | 13746 | 4553 | 4582 |
| 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 |
| ENST00000359596 | 15134 | 5038 | 38570607 | 38570693 | 13661 | 13746 | 4553 | 4582 |
| 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 |
| ENST00000359596 | 15134 | 5038 | 38446694 | 38446768 | 727 | 800 | 242 | 266 |
| ENST00000359596 | 15134 | 5038 | 38517359 | 38517691 | 9687 | 10018 | 3229 | 3339 |
| ENST00000359596 | 15134 | 5038 | 38570607 | 38570693 | 13661 | 13746 | 4553 | 4582 |
| 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 |
| P21817 | 15 | 55 | 1 | 5038 | Chain | ID=PRO_0000219358;Note=Ryanodine receptor 1 |
| P21817 | 15 | 55 | 35 | 35 | Natural variant | ID=VAR_005589;Note=In MHS1%3B increases calcium-induced calcium release activity. C->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:16163667,ECO:0000269|PubMed:26115329,ECO:0000269|PubMed:9066328;Dbxref=dbSNP:rs193922747,P |
| P21817 | 15 | 55 | 40 | 40 | Natural variant | ID=VAR_071721;Note=In MHS1%3B unknown pathological significance. G->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23558838;Dbxref=PMID:23558838 |
| P21817 | 15 | 55 | 44 | 44 | Natural variant | ID=VAR_045695;Note=In CCD and MHS1. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12709367;Dbxref=dbSNP:rs193922748,PMID:12709367 |
| P21817 | 15 | 55 | 1 | 4559 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
| P21817 | 3229 | 3339 | 1 | 5038 | Chain | ID=PRO_0000219358;Note=Ryanodine receptor 1 |
| P21817 | 3229 | 3339 | 3238 | 3238 | Natural variant | ID=VAR_071746;Note=In CCD%3B unknown pathological significance. E->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23558838;Dbxref=dbSNP:rs200950673,PMID:23558838 |
| P21817 | 3229 | 3339 | 3290 | 3290 | Natural variant | ID=VAR_058574;Note=In MHS1. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19191329;Dbxref=dbSNP:rs112151058,PMID:19191329 |
| P21817 | 3229 | 3339 | 3326 | 3326 | Natural variant | ID=VAR_063848;Note=In MMDO. N->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20583297;Dbxref=dbSNP:rs367543057,PMID:20583297 |
| P21817 | 3229 | 3339 | 1 | 4559 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
| P21817 | 4553 | 4582 | 1 | 5038 | Chain | ID=PRO_0000219358;Note=Ryanodine receptor 1 |
| P21817 | 4553 | 4582 | 4558 | 4558 | Natural variant | ID=VAR_045739;Note=In CCD%3B autosomal recessive form. R->Q;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:17226826,ECO:0000269|PubMed:18253926;Dbxref=dbSNP:rs118192130,PMID:17226826,PMID:18253926 |
| P21817 | 4553 | 4582 | 1 | 4559 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
| P21817 | 4553 | 4582 | 4581 | 4641 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
| P21817 | 4553 | 4582 | 4560 | 4580 | Transmembrane | Note=Helical%3B Name%3D1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
| 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 |
| P21817 | 4553 | 4582 | 1 | 5038 | Chain | ID=PRO_0000219358;Note=Ryanodine receptor 1 |
| P21817 | 4553 | 4582 | 4558 | 4558 | Natural variant | ID=VAR_045739;Note=In CCD%3B autosomal recessive form. R->Q;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:17226826,ECO:0000269|PubMed:18253926;Dbxref=dbSNP:rs118192130,PMID:17226826,PMID:18253926 |
| P21817 | 4553 | 4582 | 1 | 4559 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
| P21817 | 4553 | 4582 | 4581 | 4641 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
| P21817 | 4553 | 4582 | 4560 | 4580 | Transmembrane | Note=Helical%3B Name%3D1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
| 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 |
| P21817 | 242 | 266 | 1 | 5038 | Chain | ID=PRO_0000219358;Note=Ryanodine receptor 1 |
| P21817 | 242 | 266 | 210 | 264 | Domain | Note=MIR 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00131 |
| P21817 | 242 | 266 | 248 | 248 | Natural variant | ID=VAR_005591;Note=In MHS1%3B unknown pathological significance%3B increases calcium-induced calcium release activity. G->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11575529,ECO:0000 |
| P21817 | 242 | 266 | 1 | 4559 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
| P21817 | 3229 | 3339 | 1 | 5038 | Chain | ID=PRO_0000219358;Note=Ryanodine receptor 1 |
| P21817 | 3229 | 3339 | 3238 | 3238 | Natural variant | ID=VAR_071746;Note=In CCD%3B unknown pathological significance. E->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:23558838;Dbxref=dbSNP:rs200950673,PMID:23558838 |
| P21817 | 3229 | 3339 | 3290 | 3290 | Natural variant | ID=VAR_058574;Note=In MHS1. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19191329;Dbxref=dbSNP:rs112151058,PMID:19191329 |
| P21817 | 3229 | 3339 | 3326 | 3326 | Natural variant | ID=VAR_063848;Note=In MMDO. N->K;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20583297;Dbxref=dbSNP:rs367543057,PMID:20583297 |
| P21817 | 3229 | 3339 | 1 | 4559 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
| P21817 | 4553 | 4582 | 1 | 5038 | Chain | ID=PRO_0000219358;Note=Ryanodine receptor 1 |
| P21817 | 4553 | 4582 | 4558 | 4558 | Natural variant | ID=VAR_045739;Note=In CCD%3B autosomal recessive form. R->Q;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:17226826,ECO:0000269|PubMed:18253926;Dbxref=dbSNP:rs118192130,PMID:17226826,PMID:18253926 |
| P21817 | 4553 | 4582 | 1 | 4559 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
| P21817 | 4553 | 4582 | 4581 | 4641 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
| P21817 | 4553 | 4582 | 4560 | 4580 | Transmembrane | Note=Helical%3B Name%3D1;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P11716 |
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3'-UTR located exon skipping events that lost miRNA binding sites in RYR1 |
| 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 RYR1 |
| - 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 RYR1 |
| 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 RYR1 |
| 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 RYR1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | CNOT4 | exon_skip_124982 | -4.354838e-01 | 1.046898e-07 |
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RelatedDrugs for RYR1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| P21817 | approved | DB00201 | Caffeine | small molecule | P21817 |
| P21817 | approved|investigational | DB01219 | Dantrolene | small molecule | P21817 |
| P21817 | approved|vet_approved | DB09085 | Tetracaine | small molecule | P21817 |
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RelatedDiseases for RYR1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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