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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 XRN2 |
 Gene summary |
| Gene information | Gene symbol | XRN2 | Gene ID | 22803 |
| Gene name | 5'-3' exoribonuclease 2 | |
| Synonyms | - | |
| Cytomap | 20p11.22 | |
| Type of gene | protein-coding | |
| Description | 5'-3' exoribonuclease 2DHP proteinDhm1-like protein | |
| Modification date | 20180519 | |
| UniProtAcc | Q9H0D6 | |
| Context | PubMed: XRN2 [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 |
| XRN2 | GO:0000738 | DNA catabolic process, exonucleolytic | 15565158 |
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Exon skipping events across known transcript of Ensembl for XRN2 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 XRN2 |
| 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 XRN2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_349560 | 20 | 21307127:21307239:21309196:21309308:21311118:21311177 | 21309196:21309308 | ENSG00000088930.6 | ENST00000539513.1,ENST00000377191.3,ENST00000430571.2 |
| exon_skip_349564 | 20 | 21309196:21309308:21311118:21311177:21311253:21311343 | 21311118:21311177 | ENSG00000088930.6 | ENST00000539513.1,ENST00000377191.3,ENST00000430571.2 |
| exon_skip_349565 | 20 | 21312920:21313078:21314181:21314256:21314341:21314475 | 21314181:21314256 | ENSG00000088930.6 | ENST00000539513.1,ENST00000377191.3,ENST00000430571.2 |
| exon_skip_349573 | 20 | 21314181:21314256:21314341:21314475:21314574:21314632 | 21314341:21314475 | ENSG00000088930.6 | ENST00000539513.1,ENST00000377191.3,ENST00000430571.2 |
| exon_skip_349580 | 20 | 21314574:21314632:21314715:21314823:21319681:21319726 | 21314715:21314823 | ENSG00000088930.6 | ENST00000539513.1,ENST00000377191.3,ENST00000430571.2 |
| exon_skip_349585 | 20 | 21328783:21328891:21328978:21329068:21330026:21330099 | 21328978:21329068 | ENSG00000088930.6 | ENST00000539513.1,ENST00000377191.3,ENST00000430571.2 |
| exon_skip_349589 | 20 | 21336717:21336815:21337223:21337303:21338373:21338430 | 21337223:21337303 | ENSG00000088930.6 | ENST00000539513.1,ENST00000377191.3,ENST00000430571.2 |
| exon_skip_349594 | 20 | 21337223:21337303:21338373:21338430:21346058:21346127 | 21338373:21338430 | ENSG00000088930.6 | ENST00000539513.1,ENST00000377191.3,ENST00000430571.2 |
| exon_skip_349598 | 20 | 21346210:21346342:21349100:21349228:21362631:21362695 | 21349100:21349228 | ENSG00000088930.6 | ENST00000539513.1,ENST00000377191.3,ENST00000430571.2 |
| exon_skip_349600 | 20 | 21362631:21362695:21367505:21367644:21369910:21370263 | 21367505:21367644 | ENSG00000088930.6 | ENST00000539513.1,ENST00000377191.3,ENST00000430571.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for XRN2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_349560 | 20 | 21307127:21307239:21309196:21309308:21311118:21311177 | 21309196:21309308 | ENSG00000088930.6 | ENST00000377191.3,ENST00000430571.2,ENST00000539513.1 |
| exon_skip_349564 | 20 | 21309196:21309308:21311118:21311177:21311253:21311343 | 21311118:21311177 | ENSG00000088930.6 | ENST00000377191.3,ENST00000430571.2,ENST00000539513.1 |
| exon_skip_349565 | 20 | 21312920:21313078:21314181:21314256:21314341:21314475 | 21314181:21314256 | ENSG00000088930.6 | ENST00000377191.3,ENST00000430571.2,ENST00000539513.1 |
| exon_skip_349573 | 20 | 21314181:21314256:21314341:21314475:21314574:21314632 | 21314341:21314475 | ENSG00000088930.6 | ENST00000377191.3,ENST00000430571.2,ENST00000539513.1 |
| exon_skip_349580 | 20 | 21314574:21314632:21314715:21314823:21319681:21319726 | 21314715:21314823 | ENSG00000088930.6 | ENST00000377191.3,ENST00000430571.2,ENST00000539513.1 |
| exon_skip_349585 | 20 | 21328783:21328891:21328978:21329068:21330026:21330099 | 21328978:21329068 | ENSG00000088930.6 | ENST00000377191.3,ENST00000430571.2,ENST00000539513.1 |
| exon_skip_349589 | 20 | 21336717:21336815:21337223:21337303:21338373:21338430 | 21337223:21337303 | ENSG00000088930.6 | ENST00000377191.3,ENST00000430571.2,ENST00000539513.1 |
| exon_skip_349594 | 20 | 21337223:21337303:21338373:21338430:21346058:21346127 | 21338373:21338430 | ENSG00000088930.6 | ENST00000377191.3,ENST00000430571.2,ENST00000539513.1 |
| exon_skip_349598 | 20 | 21346210:21346342:21349100:21349228:21362631:21362695 | 21349100:21349228 | ENSG00000088930.6 | ENST00000377191.3,ENST00000430571.2,ENST00000539513.1 |
| exon_skip_349600 | 20 | 21362631:21362695:21367505:21367644:21369910:21370263 | 21367505:21367644 | ENSG00000088930.6 | ENST00000377191.3,ENST00000430571.2,ENST00000539513.1 |
| 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 XRN2 |
| 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 |
| ENST00000377191 | 21309196 | 21309308 | Frame-shift |
| ENST00000377191 | 21311118 | 21311177 | Frame-shift |
| ENST00000377191 | 21314341 | 21314475 | Frame-shift |
| ENST00000377191 | 21337223 | 21337303 | Frame-shift |
| ENST00000377191 | 21349100 | 21349228 | Frame-shift |
| ENST00000377191 | 21367505 | 21367644 | Frame-shift |
| ENST00000377191 | 21314181 | 21314256 | In-frame |
| ENST00000377191 | 21314715 | 21314823 | In-frame |
| ENST00000377191 | 21328978 | 21329068 | In-frame |
| ENST00000377191 | 21338373 | 21338430 | 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 |
| ENST00000377191 | 21309196 | 21309308 | Frame-shift |
| ENST00000377191 | 21311118 | 21311177 | Frame-shift |
| ENST00000377191 | 21314341 | 21314475 | Frame-shift |
| ENST00000377191 | 21337223 | 21337303 | Frame-shift |
| ENST00000377191 | 21349100 | 21349228 | Frame-shift |
| ENST00000377191 | 21367505 | 21367644 | Frame-shift |
| ENST00000377191 | 21314181 | 21314256 | In-frame |
| ENST00000377191 | 21314715 | 21314823 | In-frame |
| ENST00000377191 | 21328978 | 21329068 | In-frame |
| ENST00000377191 | 21338373 | 21338430 | In-frame |
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Infer the effects of exon skipping event on protein functional features for XRN2 |
| 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 |
| ENST00000377191 | 3452 | 950 | 21314181 | 21314256 | 954 | 1028 | 286 | 311 |
| ENST00000377191 | 3452 | 950 | 21314715 | 21314823 | 1221 | 1328 | 375 | 411 |
| ENST00000377191 | 3452 | 950 | 21328978 | 21329068 | 1869 | 1958 | 591 | 621 |
| ENST00000377191 | 3452 | 950 | 21338373 | 21338430 | 2294 | 2350 | 733 | 751 |
| 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 |
| ENST00000377191 | 3452 | 950 | 21314181 | 21314256 | 954 | 1028 | 286 | 311 |
| ENST00000377191 | 3452 | 950 | 21314715 | 21314823 | 1221 | 1328 | 375 | 411 |
| ENST00000377191 | 3452 | 950 | 21328978 | 21329068 | 1869 | 1958 | 591 | 621 |
| ENST00000377191 | 3452 | 950 | 21338373 | 21338430 | 2294 | 2350 | 733 | 751 |
| 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 |
| Q9H0D6 | 286 | 311 | 1 | 950 | Chain | ID=PRO_0000071396;Note=5'-3' exoribonuclease 2 |
| Q9H0D6 | 286 | 311 | 286 | 286 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9DBR1 |
| Q9H0D6 | 375 | 411 | 1 | 950 | Chain | ID=PRO_0000071396;Note=5'-3' exoribonuclease 2 |
| Q9H0D6 | 591 | 621 | 1 | 950 | Chain | ID=PRO_0000071396;Note=5'-3' exoribonuclease 2 |
| Q9H0D6 | 733 | 751 | 1 | 950 | Chain | ID=PRO_0000071396;Note=5'-3' exoribonuclease 2 |
| Q9H0D6 | 733 | 751 | 743 | 743 | Natural variant | ID=VAR_027516;Note=R->M;Dbxref=dbSNP:rs6137324 |
| Q9H0D6 | 733 | 751 | 737 | 737 | Sequence conflict | Note=S->A;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| Q9H0D6 | 286 | 311 | 1 | 950 | Chain | ID=PRO_0000071396;Note=5'-3' exoribonuclease 2 |
| Q9H0D6 | 286 | 311 | 286 | 286 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9DBR1 |
| Q9H0D6 | 375 | 411 | 1 | 950 | Chain | ID=PRO_0000071396;Note=5'-3' exoribonuclease 2 |
| Q9H0D6 | 591 | 621 | 1 | 950 | Chain | ID=PRO_0000071396;Note=5'-3' exoribonuclease 2 |
| Q9H0D6 | 733 | 751 | 1 | 950 | Chain | ID=PRO_0000071396;Note=5'-3' exoribonuclease 2 |
| Q9H0D6 | 733 | 751 | 743 | 743 | Natural variant | ID=VAR_027516;Note=R->M;Dbxref=dbSNP:rs6137324 |
| Q9H0D6 | 733 | 751 | 737 | 737 | Sequence conflict | Note=S->A;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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SNVs in the skipped exons for XRN2 |
| - 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. |
XRN2_STAD_exon_skip_349580_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 |
| LUAD | TCGA-95-7944-01 | exon_skip_349598 | 21349101 | 21349228 | 21349164 | 21349164 | Frame_Shift_Del | T | - | p.T840fs |
| LIHC | TCGA-DD-A3A1-01 | exon_skip_349600 | 21367506 | 21367644 | 21367550 | 21367550 | Frame_Shift_Del | A | - | p.Q898fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_349600 | 21367506 | 21367644 | 21367553 | 21367553 | Frame_Shift_Del | C | - | p.T899fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_349600 | 21367506 | 21367644 | 21367597 | 21367597 | Frame_Shift_Del | G | - | p.G914fs |
| CESC | TCGA-EK-A2PL-01 | exon_skip_349560 | 21309197 | 21309308 | 21309246 | 21309246 | Nonsense_Mutation | C | G | p.S122* |
| READ | TCGA-AG-A002-01 | exon_skip_349565 | 21314182 | 21314256 | 21314218 | 21314218 | Nonsense_Mutation | G | T | p.G299X |
| BRCA | TCGA-A8-A084-01 | exon_skip_349573 | 21314342 | 21314475 | 21314348 | 21314348 | Nonsense_Mutation | G | T | p.E314* |
| CESC | TCGA-IR-A3LL-01 | exon_skip_349573 | 21314342 | 21314475 | 21314412 | 21314412 | Nonsense_Mutation | G | A | p.W335* |
| STAD | TCGA-BR-6452-01 | exon_skip_349580 | 21314716 | 21314823 | 21314803 | 21314803 | Nonsense_Mutation | A | T | p.K405* |
| LUSC | TCGA-18-3409-01 | exon_skip_349598 | 21349101 | 21349228 | 21349207 | 21349207 | Nonsense_Mutation | C | T | p.Q855* |
| STAD | TCGA-BR-8589-01 | exon_skip_349580 | 21314716 | 21314823 | 21314715 | 21314715 | Splice_Site | G | A | . |
| STAD | TCGA-BR-8589-01 | exon_skip_349580 | 21314716 | 21314823 | 21314715 | 21314715 | Splice_Site | G | A | p.G376_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-BR-8589-01 |
| Cancer type: STAD | |
| ESID: exon_skip_349580 | |
| Skipped exon start: 21314716 | |
| Skipped exon end: 21314823 | |
| Mutation start: 21314715 | |
| Mutation end: 21314715 | |
| Mutation type: Splice_Site | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: . | |
| Sample: TCGA-BR-8589-01 |
| Cancer type: STAD | |
| ESID: exon_skip_349580 | |
| Skipped exon start: 21314716 | |
| Skipped exon end: 21314823 | |
| Mutation start: 21314715 | |
| Mutation end: 21314715 | |
| Mutation type: Splice_Site | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.G376_splice | |
exon_skip_349580_STAD_TCGA-BR-8589-01.png | |
exon_skip_463530_STAD_TCGA-BR-8589-01.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 |
| HEC1A_ENDOMETRIUM | 21309197 | 21309308 | 21309225 | 21309225 | Missense_Mutation | G | A | p.R115H |
| HEC1_ENDOMETRIUM | 21309197 | 21309308 | 21309225 | 21309225 | Missense_Mutation | G | A | p.R115H |
| HEC1B_ENDOMETRIUM | 21309197 | 21309308 | 21309225 | 21309225 | Missense_Mutation | G | A | p.R115H |
| SW48_LARGE_INTESTINE | 21309197 | 21309308 | 21309240 | 21309240 | Missense_Mutation | G | T | p.R120M |
| AU565_BREAST | 21311119 | 21311177 | 21311134 | 21311134 | Missense_Mutation | C | T | p.P148L |
| SKBR3_BREAST | 21311119 | 21311177 | 21311134 | 21311134 | Missense_Mutation | C | T | p.P148L |
| SKNDZ_AUTONOMIC_GANGLIA | 21314182 | 21314256 | 21314237 | 21314237 | Missense_Mutation | G | C | p.R305P |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 21314182 | 21314256 | 21314252 | 21314252 | Missense_Mutation | G | A | p.R310H |
| BICR6_UPPER_AERODIGESTIVE_TRACT | 21314342 | 21314475 | 21314391 | 21314391 | Missense_Mutation | T | G | p.V328G |
| LN464_CENTRAL_NERVOUS_SYSTEM | 21314342 | 21314475 | 21314414 | 21314414 | Missense_Mutation | G | C | p.V336L |
| ACN_AUTONOMIC_GANGLIA | 21314342 | 21314475 | 21314414 | 21314414 | Missense_Mutation | G | C | p.V336L |
| LXF289_LUNG | 21328979 | 21329068 | 21329025 | 21329025 | Missense_Mutation | G | C | p.G607A |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 21328979 | 21329068 | 21329042 | 21329042 | Missense_Mutation | T | A | p.S613T |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 21338374 | 21338430 | 21338424 | 21338424 | Missense_Mutation | T | C | p.V750A |
| GT3TKB_STOMACH | 21349101 | 21349228 | 21349219 | 21349220 | Missense_Mutation | CT | TA | p.L859Y |
| RERFLCAI_LUNG | 21349101 | 21349228 | 21349219 | 21349219 | Missense_Mutation | C | T | p.L859F |
| RERFLCAI_LUNG | 21349101 | 21349228 | 21349220 | 21349220 | Missense_Mutation | T | A | p.L859H |
| OCILY3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 21349101 | 21349228 | 21349223 | 21349223 | Missense_Mutation | T | C | p.M860T |
| ISTSL2_LUNG | 21367506 | 21367644 | 21367519 | 21367519 | Missense_Mutation | G | C | p.E888Q |
| NCIH358_LUNG | 21367506 | 21367644 | 21367630 | 21367630 | Missense_Mutation | C | T | p.R925C |
| HEC251_ENDOMETRIUM | 21314342 | 21314475 | 21314354 | 21314354 | Nonsense_Mutation | G | T | p.E316* |
| OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 21338374 | 21338430 | 21338430 | 21338430 | Splice_Site | G | A | p.S752N |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for XRN2 |
| 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 |
| exon_skip_349565 | 20 | 21312920:21313078:21314181:21314256:21314341:21314475 | 21314181:21314256 | ENST00000539513.1,ENST00000377191.3,ENST00000430571.2 | LGG | rs62217928 | chr20:21314176 | T/G | 3.12e-04 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for XRN2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for XRN2 |
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RelatedDrugs for XRN2 |
| 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 XRN2 |
| 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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