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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 RPAP2 |
 Gene summary |
| Gene information | Gene symbol | RPAP2 | Gene ID | 79871 |
| Gene name | RNA polymerase II associated protein 2 | |
| Synonyms | C1orf82|Rtr1 | |
| Cytomap | 1p22.1 | |
| Type of gene | protein-coding | |
| Description | putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 | |
| Modification date | 20180523 | |
| UniProtAcc | Q8IXW5 | |
| Context | PubMed: RPAP2 [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 |
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Exon skipping events across known transcript of Ensembl for RPAP2 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 RPAP2 |
| 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 RPAP2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_7826 | 1 | 92765750:92765796:92767032:92767147:92769533:92769632 | 92767032:92767147 | ENSG00000122484.8 | ENST00000610020.1 |
| exon_skip_7827 | 1 | 92769840:92769906:92772744:92772833:92786155:92786191 | 92772744:92772833 | ENSG00000122484.8 | ENST00000610020.1,ENST00000484158.1 |
| exon_skip_7830 | 1 | 92786155:92786191:92789001:92789932:92798947:92799030 | 92789001:92789932 | ENSG00000122484.8 | ENST00000610020.1 |
| exon_skip_7833 | 1 | 92801903:92801984:92811402:92811471:92846280:92846430 | 92811402:92811471 | ENSG00000122484.8 | ENST00000477322.1,ENST00000610020.1 |
| exon_skip_7840 | 1 | 92811402:92811471:92846280:92846430:92852567:92852790 | 92846280:92846430 | ENSG00000122484.8 | ENST00000477322.1,ENST00000610020.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RPAP2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_7821 | 1 | 92764641:92764703:92765750:92765796:92769533:92769632 | 92765750:92765796 | ENSG00000122484.8 | ENST00000484158.1 |
| exon_skip_7826 | 1 | 92765750:92765796:92767032:92767147:92769533:92769632 | 92767032:92767147 | ENSG00000122484.8 | ENST00000610020.1 |
| exon_skip_7827 | 1 | 92769840:92769906:92772744:92772833:92786155:92786191 | 92772744:92772833 | ENSG00000122484.8 | ENST00000610020.1,ENST00000484158.1 |
| exon_skip_7830 | 1 | 92786155:92786191:92789001:92789932:92798947:92799030 | 92789001:92789932 | ENSG00000122484.8 | ENST00000610020.1 |
| exon_skip_7833 | 1 | 92801903:92801984:92811402:92811471:92846280:92846430 | 92811402:92811471 | ENSG00000122484.8 | ENST00000610020.1,ENST00000477322.1 |
| exon_skip_7840 | 1 | 92811402:92811471:92846280:92846430:92852567:92852790 | 92846280:92846430 | ENSG00000122484.8 | ENST00000610020.1,ENST00000477322.1 |
| 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 RPAP2 |
| 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 |
| ENST00000610020 | 92767032 | 92767147 | Frame-shift |
| ENST00000610020 | 92772744 | 92772833 | Frame-shift |
| ENST00000610020 | 92789001 | 92789932 | Frame-shift |
| ENST00000610020 | 92811402 | 92811471 | In-frame |
| ENST00000610020 | 92846280 | 92846430 | 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 |
| ENST00000610020 | 92767032 | 92767147 | Frame-shift |
| ENST00000610020 | 92772744 | 92772833 | Frame-shift |
| ENST00000610020 | 92789001 | 92789932 | Frame-shift |
| ENST00000610020 | 92811402 | 92811471 | In-frame |
| ENST00000610020 | 92846280 | 92846430 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RPAP2 |
| 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 |
| ENST00000610020 | 17010 | 612 | 92811402 | 92811471 | 1729 | 1797 | 540 | 562 |
| ENST00000610020 | 17010 | 612 | 92846280 | 92846430 | 1798 | 1947 | 563 | 612 |
| 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 |
| ENST00000610020 | 17010 | 612 | 92811402 | 92811471 | 1729 | 1797 | 540 | 562 |
| ENST00000610020 | 17010 | 612 | 92846280 | 92846430 | 1798 | 1947 | 563 | 612 |
| 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 |
| Q8IXW5 | 540 | 562 | 2 | 612 | Chain | ID=PRO_0000250648;Note=Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 |
| Q8IXW5 | 563 | 612 | 563 | 596 | Alternative sequence | ID=VSP_020680;Note=In isoform 2. LLTPILGIQKHSQEGMVFTRFLDTLLEELHLKNE->FLLNVKTRIKTFMMIYFHLMNS;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8IXW5 | 563 | 612 | 597 | 612 | Alternative sequence | ID=VSP_020681;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8IXW5 | 563 | 612 | 2 | 612 | Chain | ID=PRO_0000250648;Note=Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 |
| 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 |
| Q8IXW5 | 540 | 562 | 2 | 612 | Chain | ID=PRO_0000250648;Note=Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 |
| Q8IXW5 | 563 | 612 | 563 | 596 | Alternative sequence | ID=VSP_020680;Note=In isoform 2. LLTPILGIQKHSQEGMVFTRFLDTLLEELHLKNE->FLLNVKTRIKTFMMIYFHLMNS;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8IXW5 | 563 | 612 | 597 | 612 | Alternative sequence | ID=VSP_020681;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q8IXW5 | 563 | 612 | 2 | 612 | Chain | ID=PRO_0000250648;Note=Putative RNA polymerase II subunit B1 CTD phosphatase RPAP2 |
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SNVs in the skipped exons for RPAP2 |
| - 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. |
RPAP2_CESC_exon_skip_7830_psi_boxplot.png |
RPAP2_LIHC_exon_skip_7830_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 |
| COAD | TCGA-CM-6171-01 | exon_skip_7827 | 92772745 | 92772833 | 92772747 | 92772747 | Frame_Shift_Del | T | - | p.S134fs |
| UCEC | TCGA-DI-A0WH-01 | exon_skip_7827 | 92772745 | 92772833 | 92772747 | 92772747 | Frame_Shift_Del | T | - | p.S134fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_7830 | 92789002 | 92789932 | 92789045 | 92789045 | Frame_Shift_Del | A | - | p.K190fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_7830 | 92789002 | 92789932 | 92789208 | 92789208 | Frame_Shift_Del | A | - | p.Q244fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_7830 | 92789002 | 92789932 | 92789563 | 92789563 | Frame_Shift_Del | A | - | p.G362fs |
| COAD | TCGA-D5-6540-01 | exon_skip_7840 | 92846281 | 92846430 | 92846371 | 92846371 | Frame_Shift_Del | A | - | p.L593fs |
| HNSC | TCGA-F7-A624-01 | exon_skip_7840 | 92846281 | 92846430 | 92846371 | 92846371 | Frame_Shift_Del | A | - | p.L593fs |
| BLCA | TCGA-ZF-AA4N-01 | exon_skip_7827 | 92772745 | 92772833 | 92772769 | 92772769 | Nonsense_Mutation | C | T | p.Q142* |
| READ | TCGA-F5-6814-01 | exon_skip_7827 | 92772745 | 92772833 | 92772826 | 92772826 | Nonsense_Mutation | G | T | p.E161X |
| CESC | TCGA-IR-A3LK-01 | exon_skip_7830 | 92789002 | 92789932 | 92789379 | 92789379 | Nonsense_Mutation | C | A | p.S301* |
| LIHC | TCGA-DD-A3A9-01 | exon_skip_7830 | 92789002 | 92789932 | 92789745 | 92789745 | Nonsense_Mutation | G | A | p.W423* |
| LIHC | TCGA-DD-A3A9-01 | exon_skip_7830 | 92789002 | 92789932 | 92789745 | 92789745 | Nonsense_Mutation | G | A | p.W423X |
| COAD | TCGA-AZ-4315-01 | exon_skip_7833 | 92811403 | 92811471 | 92811447 | 92811447 | Nonsense_Mutation | T | G | p.L555X |
| UCEC | TCGA-AX-A05T-01 | exon_skip_7840 | 92846281 | 92846430 | 92846378 | 92846378 | Nonsense_Mutation | G | T | p.E596* |
| ESCA | TCGA-LN-A4A8-01 | exon_skip_7840 | 92846281 | 92846430 | 92846387 | 92846387 | Nonsense_Mutation | G | T | p.E599* |
| ESCA | TCGA-LN-A4A8-01 | exon_skip_7840 | 92846281 | 92846430 | 92846387 | 92846387 | Nonsense_Mutation | G | T | p.E599X |
| STAD | TCGA-CG-4305-01 | exon_skip_7826 | 92767033 | 92767147 | 92767148 | 92767148 | Splice_Site | G | A | . |
| STAD | TCGA-CG-4305-01 | exon_skip_7826 | 92767033 | 92767147 | 92767148 | 92767148 | Splice_Site | G | A | p.C78_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-IR-A3LK-01 |
| Cancer type: CESC | |
| ESID: exon_skip_7830 | |
| Skipped exon start: 92789002 | |
| Skipped exon end: 92789932 | |
| Mutation start: 92789379 | |
| Mutation end: 92789379 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: C | |
| Mutation seq: A | |
| AAchange: p.S301* | |
exon_skip_129969_CESC_TCGA-IR-A3LK-01.png | |
exon_skip_131474_CESC_TCGA-IR-A3LK-01.png | |
exon_skip_435729_CESC_TCGA-IR-A3LK-01.png | |
exon_skip_457524_CESC_TCGA-IR-A3LK-01.png | |
exon_skip_63491_CESC_TCGA-IR-A3LK-01.png | |
exon_skip_71523_CESC_TCGA-IR-A3LK-01.png | |
exon_skip_7830_CESC_TCGA-IR-A3LK-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 |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 92789002 | 92789932 | 92789630 | 92789630 | Frame_Shift_Del | T | - | p.F385fs |
| YD15_SALIVARY_GLAND | 92789002 | 92789932 | 92789867 | 92789867 | Frame_Shift_Del | A | - | p.R464fs |
| HEC108_ENDOMETRIUM | 92789002 | 92789932 | 92789892 | 92789892 | Frame_Shift_Del | T | - | p.V472fs |
| SNU81_LARGE_INTESTINE | 92767033 | 92767147 | 92767066 | 92767066 | Missense_Mutation | G | T | p.K51N |
| LC2AD_LUNG | 92772745 | 92772833 | 92772787 | 92772787 | Missense_Mutation | G | C | p.E148Q |
| MEWO_SKIN | 92789002 | 92789932 | 92789010 | 92789010 | Missense_Mutation | C | T | p.S178F |
| MKN1_STOMACH | 92789002 | 92789932 | 92789109 | 92789109 | Missense_Mutation | C | T | p.T211I |
| SAS_UPPER_AERODIGESTIVE_TRACT | 92789002 | 92789932 | 92789109 | 92789109 | Missense_Mutation | C | T | p.T211I |
| HCC1569_BREAST | 92789002 | 92789932 | 92789126 | 92789126 | Missense_Mutation | A | G | p.S217G |
| NCIH1693_LUNG | 92789002 | 92789932 | 92789181 | 92789181 | Missense_Mutation | C | T | p.S235L |
| NCIH1819_LUNG | 92789002 | 92789932 | 92789181 | 92789181 | Missense_Mutation | C | T | p.S235L |
| HEC251_ENDOMETRIUM | 92789002 | 92789932 | 92789187 | 92789187 | Missense_Mutation | A | C | p.N237T |
| NCIH650_LUNG | 92789002 | 92789932 | 92789206 | 92789206 | Missense_Mutation | C | G | p.H243Q |
| HT115_LARGE_INTESTINE | 92789002 | 92789932 | 92789256 | 92789256 | Missense_Mutation | A | G | p.H260R |
| ZR751_BREAST | 92789002 | 92789932 | 92789263 | 92789263 | Missense_Mutation | C | A | p.D262E |
| YMB1E_BREAST | 92789002 | 92789932 | 92789263 | 92789263 | Missense_Mutation | C | A | p.D262E |
| SNU182_LIVER | 92789002 | 92789932 | 92789369 | 92789369 | Missense_Mutation | C | G | p.Q298E |
| FU97_STOMACH | 92789002 | 92789932 | 92789386 | 92789386 | Missense_Mutation | C | A | p.S303R |
| HEC59_ENDOMETRIUM | 92789002 | 92789932 | 92789433 | 92789433 | Missense_Mutation | A | G | p.Y319C |
| SNU1040_LARGE_INTESTINE | 92789002 | 92789932 | 92789454 | 92789454 | Missense_Mutation | T | C | p.L326P |
| HS683_CENTRAL_NERVOUS_SYSTEM | 92789002 | 92789932 | 92789462 | 92789462 | Missense_Mutation | A | T | p.I329L |
| KYSE30_OESOPHAGUS | 92789002 | 92789932 | 92789477 | 92789477 | Missense_Mutation | G | A | p.A334T |
| SNU1196_BILIARY_TRACT | 92789002 | 92789932 | 92789478 | 92789478 | Missense_Mutation | C | G | p.A334G |
| SKMES1_LUNG | 92789002 | 92789932 | 92789495 | 92789495 | Missense_Mutation | A | C | p.K340Q |
| HCT15_LARGE_INTESTINE | 92789002 | 92789932 | 92789697 | 92789697 | Missense_Mutation | T | G | p.L407R |
| HCC2450_LUNG | 92789002 | 92789932 | 92789746 | 92789746 | Missense_Mutation | G | C | p.W423C |
| SNU410_PANCREAS | 92789002 | 92789932 | 92789757 | 92789757 | Missense_Mutation | A | C | p.Q427P |
| SNU245_BILIARY_TRACT | 92789002 | 92789932 | 92789799 | 92789799 | Missense_Mutation | C | G | p.T441R |
| HCT15_LARGE_INTESTINE | 92789002 | 92789932 | 92789867 | 92789867 | Missense_Mutation | A | G | p.R464G |
| NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 92811403 | 92811471 | 92811455 | 92811455 | Missense_Mutation | A | G | p.M558V |
| SNU324_PANCREAS | 92846281 | 92846430 | 92846326 | 92846326 | Missense_Mutation | G | T | p.M578I |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 92767033 | 92767147 | 92767034 | 92767034 | Splice_Site | A | G | p.K41E |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RPAP2 |
| 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 RPAP2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RPAP2 |
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RelatedDrugs for RPAP2 |
| 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 RPAP2 |
| 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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