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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for SNRNP200 |
 Gene summary |
| Gene information | Gene symbol | SNRNP200 | Gene ID | 23020 |
| Gene name | small nuclear ribonucleoprotein U5 subunit 200 | |
| Synonyms | ASCC3L1|BRR2|HELIC2|RP33|U5-200KD | |
| Cytomap | 2q11.2 | |
| Type of gene | protein-coding | |
| Description | U5 small nuclear ribonucleoprotein 200 kDa helicaseBRR2 homologU5 snRNP-specific 200 kDa proteinactivating signal cointegrator 1 complex subunit 3-like 1bad response to refrigeration 2 homologsmall nuclear ribonucleoprotein 200kDa (U5)small nuclear | |
| Modification date | 20180523 | |
| UniProtAcc | O75643 | |
| Context | PubMed: SNRNP200 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| SNRNP200 | GO:0000398 | mRNA splicing, via spliceosome | 8670905 |
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Exon skipping events across known transcript of Ensembl for SNRNP200 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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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Gene isoform structures and expression levels for SNRNP200 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for SNRNP200 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_341759 | 2 | 96940994:96941087:96942200:96942462:96942641:96942723 | 96942200:96942462 | ENSG00000144028.10 | ENST00000429650.1 |
| exon_skip_341760 | 2 | 96940994:96941087:96942641:96942723:96942818:96942979 | 96942641:96942723 | ENSG00000144028.10 | ENST00000323853.5,ENST00000497539.1 |
| exon_skip_341763 | 2 | 96943276:96943453:96943544:96943688:96943974:96944096 | 96943544:96943688 | ENSG00000144028.10 | ENST00000323853.5,ENST00000429650.1,ENST00000497539.1 |
| exon_skip_341766 | 2 | 96944546:96944736:96945188:96945297:96947551:96947660 | 96945188:96945297 | ENSG00000144028.10 | ENST00000323853.5,ENST00000429650.1,ENST00000497539.1 |
| exon_skip_341770 | 2 | 96945188:96945297:96947551:96947660:96948938:96949090 | 96947551:96947660 | ENSG00000144028.10 | ENST00000323853.5,ENST00000429650.1,ENST00000497539.1 |
| exon_skip_341773 | 2 | 96949550:96949742:96950095:96950259:96950917:96951078 | 96950095:96950259 | ENSG00000144028.10 | ENST00000429650.1 |
| exon_skip_341775 | 2 | 96949550:96949742:96950095:96950323:96950917:96951078 | 96950095:96950323 | ENSG00000144028.10 | ENST00000323853.5 |
| exon_skip_341777 | 2 | 96953176:96953295:96953600:96953707:96954400:96954484 | 96953600:96953707 | ENSG00000144028.10 | ENST00000480615.1,ENST00000323853.5 |
| exon_skip_341779 | 2 | 96963374:96963458:96964021:96964158:96964340:96964440 | 96964021:96964158 | ENSG00000144028.10 | ENST00000323853.5,ENST00000349783.5 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SNRNP200 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_341759 | 2 | 96940994:96941087:96942200:96942462:96942641:96942723 | 96942200:96942462 | ENSG00000144028.10 | ENST00000429650.1 |
| exon_skip_341760 | 2 | 96940994:96941087:96942641:96942723:96942818:96942979 | 96942641:96942723 | ENSG00000144028.10 | ENST00000323853.5,ENST00000497539.1 |
| exon_skip_341763 | 2 | 96943276:96943453:96943544:96943688:96943974:96944096 | 96943544:96943688 | ENSG00000144028.10 | ENST00000323853.5,ENST00000497539.1,ENST00000429650.1 |
| exon_skip_341766 | 2 | 96944546:96944736:96945188:96945297:96947551:96947660 | 96945188:96945297 | ENSG00000144028.10 | ENST00000323853.5,ENST00000497539.1,ENST00000429650.1 |
| exon_skip_341770 | 2 | 96945188:96945297:96947551:96947660:96948938:96949090 | 96947551:96947660 | ENSG00000144028.10 | ENST00000323853.5,ENST00000497539.1,ENST00000429650.1 |
| exon_skip_341773 | 2 | 96949550:96949742:96950095:96950259:96950917:96951078 | 96950095:96950259 | ENSG00000144028.10 | ENST00000429650.1 |
| exon_skip_341775 | 2 | 96949550:96949742:96950095:96950323:96950917:96951078 | 96950095:96950323 | ENSG00000144028.10 | ENST00000323853.5 |
| exon_skip_341777 | 2 | 96953176:96953295:96953600:96953707:96954400:96954484 | 96953600:96953707 | ENSG00000144028.10 | ENST00000323853.5,ENST00000480615.1 |
| exon_skip_341779 | 2 | 96963374:96963458:96964021:96964158:96964340:96964440 | 96964021:96964158 | ENSG00000144028.10 | ENST00000323853.5,ENST00000349783.5 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for SNRNP200 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000323853 | 96942641 | 96942723 | Frame-shift |
| ENST00000323853 | 96945188 | 96945297 | Frame-shift |
| ENST00000323853 | 96947551 | 96947660 | Frame-shift |
| ENST00000323853 | 96953600 | 96953707 | Frame-shift |
| ENST00000323853 | 96964021 | 96964158 | Frame-shift |
| ENST00000323853 | 96943544 | 96943688 | In-frame |
| ENST00000323853 | 96950095 | 96950323 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000323853 | 96942641 | 96942723 | Frame-shift |
| ENST00000323853 | 96945188 | 96945297 | Frame-shift |
| ENST00000323853 | 96947551 | 96947660 | Frame-shift |
| ENST00000323853 | 96953600 | 96953707 | Frame-shift |
| ENST00000323853 | 96964021 | 96964158 | Frame-shift |
| ENST00000323853 | 96943544 | 96943688 | In-frame |
| ENST00000323853 | 96950095 | 96950323 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SNRNP200 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA 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 |
| ENST00000323853 | 7182 | 2136 | 96950095 | 96950323 | 4243 | 4470 | 1388 | 1464 |
| ENST00000323853 | 7182 | 2136 | 96943544 | 96943688 | 5689 | 5832 | 1870 | 1918 |
| Loci of skipped exons in GTEx 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 |
| ENST00000323853 | 7182 | 2136 | 96950095 | 96950323 | 4243 | 4470 | 1388 | 1464 |
| ENST00000323853 | 7182 | 2136 | 96943544 | 96943688 | 5689 | 5832 | 1870 | 1918 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| 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 |
| O75643 | 1388 | 1464 | 561 | 2071 | Alternative sequence | ID=VSP_026622;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| O75643 | 1388 | 1464 | 1405 | 1407 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1423 | 1427 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1449 | 1453 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1 | 2136 | Chain | ID=PRO_0000102087;Note=U5 small nuclear ribonucleoprotein 200 kDa helicase |
| O75643 | 1388 | 1464 | 1337 | 1512 | Domain | Note=Helicase ATP-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| O75643 | 1388 | 1464 | 1383 | 1397 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1412 | 1421 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1429 | 1436 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1443 | 1446 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1456 | 1460 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1464 | 1479 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1428 | 1428 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| O75643 | 1388 | 1464 | 1454 | 1457 | Motif | Note=DEVH box |
| O75643 | 1388 | 1464 | 1398 | 1400 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1437 | 1441 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1870 | 1918 | 561 | 2071 | Alternative sequence | ID=VSP_026622;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| O75643 | 1870 | 1918 | 1875 | 1877 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2Q0Z |
| O75643 | 1870 | 1918 | 1 | 2136 | Chain | ID=PRO_0000102087;Note=U5 small nuclear ribonucleoprotein 200 kDa helicase |
| O75643 | 1870 | 1918 | 1812 | 2124 | Domain | Note=SEC63 2 |
| O75643 | 1870 | 1918 | 1865 | 1874 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2Q0Z |
| O75643 | 1870 | 1918 | 1887 | 1899 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2Q0Z |
| O75643 | 1870 | 1918 | 1906 | 1932 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2Q0Z |
| Lost protein functional features of individual exon skipping events in GTEx. |
| 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 |
| O75643 | 1388 | 1464 | 561 | 2071 | Alternative sequence | ID=VSP_026622;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| O75643 | 1388 | 1464 | 1405 | 1407 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1423 | 1427 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1449 | 1453 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1 | 2136 | Chain | ID=PRO_0000102087;Note=U5 small nuclear ribonucleoprotein 200 kDa helicase |
| O75643 | 1388 | 1464 | 1337 | 1512 | Domain | Note=Helicase ATP-binding 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00541 |
| O75643 | 1388 | 1464 | 1383 | 1397 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1412 | 1421 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1429 | 1436 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1443 | 1446 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1456 | 1460 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1464 | 1479 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1428 | 1428 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| O75643 | 1388 | 1464 | 1454 | 1457 | Motif | Note=DEVH box |
| O75643 | 1388 | 1464 | 1398 | 1400 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1388 | 1464 | 1437 | 1441 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4F92 |
| O75643 | 1870 | 1918 | 561 | 2071 | Alternative sequence | ID=VSP_026622;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| O75643 | 1870 | 1918 | 1875 | 1877 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2Q0Z |
| O75643 | 1870 | 1918 | 1 | 2136 | Chain | ID=PRO_0000102087;Note=U5 small nuclear ribonucleoprotein 200 kDa helicase |
| O75643 | 1870 | 1918 | 1812 | 2124 | Domain | Note=SEC63 2 |
| O75643 | 1870 | 1918 | 1865 | 1874 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2Q0Z |
| O75643 | 1870 | 1918 | 1887 | 1899 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2Q0Z |
| O75643 | 1870 | 1918 | 1906 | 1932 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2Q0Z |
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SNVs in the skipped exons for SNRNP200 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
SNRNP200_KIRP_exon_skip_341775_psi_boxplot.png |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_341760 | 96942642 | 96942723 | 96942670 | 96942670 | Frame_Shift_Del | C | - | p.G2049fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_341763 | 96943545 | 96943688 | 96943670 | 96943670 | Frame_Shift_Del | G | - | p.H1877fs |
| LUAD | TCGA-MP-A4TF-01 | exon_skip_341770 | 96947552 | 96947660 | 96947605 | 96947605 | Frame_Shift_Del | A | - | p.A1658fs |
| KIRP | TCGA-B3-A6W5-01 | exon_skip_341775 | 96950096 | 96950323 | 96950320 | 96950340 | Frame_Shift_Del | ATACCTGGCGGGCAGAGGAGG | - | p.1389_1390del |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_341779 | 96964022 | 96964158 | 96964113 | 96964113 | Frame_Shift_Del | T | - | p.K343fs |
| STAD | TCGA-HF-7132-01 | exon_skip_341763 | 96943545 | 96943688 | 96943574 | 96943574 | Nonsense_Mutation | G | A | p.Q1909* |
| STAD | TCGA-HF-7132-01 | exon_skip_341763 | 96943545 | 96943688 | 96943574 | 96943574 | Nonsense_Mutation | G | A | p.Q1909X |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-B3-A6W5-01 |
| Cancer type: KIRP | |
| ESID: exon_skip_341775 | |
| Skipped exon start: 96950096 | |
| Skipped exon end: 96950323 | |
| Mutation start: 96950320 | |
| Mutation end: 96950340 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: ATACCTGGCGGGCAGAGGAGG | |
| Mutation seq: - | |
| AAchange: p.1389_1390del | |
exon_skip_341775_KIRP_TCGA-B3-A6W5-01.png | |
| - 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 |
| IGR39_SKIN | 96943545 | 96943688 | 96943668 | 96943668 | Frame_Shift_Del | G | - | p.H1877fs |
| IGR37_SKIN | 96943545 | 96943688 | 96943668 | 96943668 | Frame_Shift_Del | G | - | p.H1877fs |
| NCIH2081_LUNG | 96945189 | 96945297 | 96945206 | 96945209 | Frame_Shift_Del | ACAT | - | p.MC1705fs |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 96945189 | 96945297 | 96945238 | 96945239 | Frame_Shift_Del | AA | - | p.L1695fs |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 96945189 | 96945297 | 96945243 | 96945244 | Frame_Shift_Ins | - | GC | p.R1693fs |
| NCIH650_LUNG | 96942642 | 96942723 | 96942678 | 96942678 | Missense_Mutation | T | A | p.E2046D |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96943545 | 96943688 | 96943586 | 96943586 | Missense_Mutation | T | C | p.S1905G |
| HUCCT1_BILIARY_TRACT | 96943545 | 96943688 | 96943593 | 96943593 | Missense_Mutation | C | A | p.M1902I |
| NCIH1869_LUNG | 96943545 | 96943688 | 96943593 | 96943593 | Missense_Mutation | C | A | p.M1902I |
| FARAGE_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96943545 | 96943688 | 96943672 | 96943672 | Missense_Mutation | G | A | p.P1876L |
| KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96945189 | 96945297 | 96945221 | 96945221 | Missense_Mutation | G | A | p.R1701C |
| SNU324_PANCREAS | 96945189 | 96945297 | 96945251 | 96945251 | Missense_Mutation | C | T | p.A1691T |
| DU145_PROSTATE | 96950096 | 96950323 | 96950245 | 96950245 | Missense_Mutation | C | T | p.D1415N |
| DU145_PROSTATE | 96950096 | 96950259 | 96950245 | 96950245 | Missense_Mutation | C | T | p.D1415N |
| RL952_ENDOMETRIUM | 96950096 | 96950323 | 96950257 | 96950257 | Missense_Mutation | C | T | p.E1411K |
| RL952_ENDOMETRIUM | 96950096 | 96950259 | 96950257 | 96950257 | Missense_Mutation | C | T | p.E1411K |
| NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96950096 | 96950323 | 96950275 | 96950275 | Missense_Mutation | C | T | p.V1405M |
| BICR56_UPPER_AERODIGESTIVE_TRACT | 96953601 | 96953707 | 96953611 | 96953611 | Missense_Mutation | C | T | p.D1119N |
| MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 96964022 | 96964158 | 96964093 | 96964093 | Missense_Mutation | T | C | p.M350V |
| HELA_CERVIX | 96953601 | 96953707 | 96953706 | 96953706 | Splice_Site | G | A | p.S1087L |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SNRNP200 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SNRNP200 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SNRNP200 |
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RelatedDrugs for SNRNP200 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for SNRNP200 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SNRNP200 | C1835895 | RETINITIS PIGMENTOSA 33 (disorder) | 5 | CTD_human;UNIPROT |
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