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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 XYLB |
 Gene summary |
| Gene information | Gene symbol | XYLB | Gene ID | 9942 |
| Gene name | xylulokinase | |
| Synonyms | - | |
| Cytomap | 3p22.2 | |
| Type of gene | protein-coding | |
| Description | xylulose kinaseD-xylulokinasexylulokinase homolog (H. influenzae) | |
| Modification date | 20180523 | |
| UniProtAcc | O75191 | |
| Context | PubMed: XYLB [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 |
| XYLB | GO:0005997 | xylulose metabolic process | 23179721 |
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Exon skipping events across known transcript of Ensembl for XYLB 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 XYLB |
| 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 XYLB |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_372892 | 3 | 38390040:38390123:38401829:38401899:38404427:38404508 | 38401829:38401899 | ENSG00000093217.5 | ENST00000207870.3 |
| exon_skip_372895 | 3 | 38401829:38401899:38404427:38404508:38406689:38406776 | 38404427:38404508 | ENSG00000093217.5 | ENST00000207870.3 |
| exon_skip_372896 | 3 | 38407098:38407227:38408298:38408364:38409675:38409748 | 38408298:38408364 | ENSG00000093217.5 | ENST00000207870.3,ENST00000542835.1,ENST00000424034.1 |
| exon_skip_372899 | 3 | 38414145:38414227:38415952:38415993:38416634:38416750 | 38415952:38415993 | ENSG00000093217.5 | ENST00000207870.3,ENST00000542835.1,ENST00000424034.1 |
| exon_skip_372900 | 3 | 38416634:38416750:38417607:38417723:38418408:38418482 | 38417607:38417723 | ENSG00000093217.5 | ENST00000207870.3,ENST00000542835.1,ENST00000424034.1 |
| exon_skip_372905 | 3 | 38418411:38418482:38420736:38420833:38436995:38437054 | 38420736:38420833 | ENSG00000093217.5 | ENST00000207870.3,ENST00000472721.1,ENST00000542835.1,ENST00000424034.1 |
| exon_skip_372907 | 3 | 38436995:38437054:38438562:38438650:38442381:38442476 | 38438562:38438650 | ENSG00000093217.5 | ENST00000207870.3,ENST00000472721.1,ENST00000542835.1,ENST00000424034.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for XYLB |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_372895 | 3 | 38401829:38401899:38404427:38404508:38406689:38406776 | 38404427:38404508 | ENSG00000093217.5 | ENST00000207870.3 |
| exon_skip_372896 | 3 | 38407098:38407227:38408298:38408364:38409675:38409748 | 38408298:38408364 | ENSG00000093217.5 | ENST00000207870.3,ENST00000424034.1,ENST00000542835.1 |
| exon_skip_372899 | 3 | 38414145:38414227:38415952:38415993:38416634:38416750 | 38415952:38415993 | ENSG00000093217.5 | ENST00000207870.3,ENST00000424034.1,ENST00000542835.1 |
| exon_skip_372900 | 3 | 38416634:38416750:38417607:38417723:38418408:38418482 | 38417607:38417723 | ENSG00000093217.5 | ENST00000207870.3,ENST00000424034.1,ENST00000542835.1 |
| exon_skip_372905 | 3 | 38418411:38418482:38420736:38420833:38436995:38437054 | 38420736:38420833 | ENSG00000093217.5 | ENST00000207870.3,ENST00000424034.1,ENST00000542835.1,ENST00000472721.1 |
| exon_skip_372907 | 3 | 38436995:38437054:38438562:38438650:38442381:38442476 | 38438562:38438650 | ENSG00000093217.5 | ENST00000207870.3,ENST00000424034.1,ENST00000542835.1,ENST00000472721.1 |
| 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 XYLB |
| 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 |
| ENST00000207870 | 38401829 | 38401899 | Frame-shift |
| ENST00000207870 | 38415952 | 38415993 | Frame-shift |
| ENST00000207870 | 38417607 | 38417723 | Frame-shift |
| ENST00000207870 | 38420736 | 38420833 | Frame-shift |
| ENST00000207870 | 38438562 | 38438650 | Frame-shift |
| ENST00000207870 | 38404427 | 38404508 | In-frame |
| ENST00000207870 | 38408298 | 38408364 | 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 |
| ENST00000207870 | 38415952 | 38415993 | Frame-shift |
| ENST00000207870 | 38417607 | 38417723 | Frame-shift |
| ENST00000207870 | 38420736 | 38420833 | Frame-shift |
| ENST00000207870 | 38438562 | 38438650 | Frame-shift |
| ENST00000207870 | 38404427 | 38404508 | In-frame |
| ENST00000207870 | 38408298 | 38408364 | In-frame |
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Infer the effects of exon skipping event on protein functional features for XYLB |
| 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 |
| ENST00000207870 | 3681 | 536 | 38404427 | 38404508 | 301 | 381 | 70 | 97 |
| ENST00000207870 | 3681 | 536 | 38408298 | 38408364 | 598 | 663 | 169 | 191 |
| 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 |
| ENST00000207870 | 3681 | 536 | 38404427 | 38404508 | 301 | 381 | 70 | 97 |
| ENST00000207870 | 3681 | 536 | 38408298 | 38408364 | 598 | 663 | 169 | 191 |
| 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 |
| O75191 | 70 | 97 | 1 | 137 | Alternative sequence | ID=VSP_055522;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| O75191 | 70 | 97 | 89 | 96 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BC3 |
| O75191 | 70 | 97 | 1 | 536 | Chain | ID=PRO_0000230985;Note=Xylulose kinase |
| O75191 | 70 | 97 | 65 | 81 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BC3 |
| O75191 | 70 | 97 | 86 | 88 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BC3 |
| O75191 | 70 | 97 | 85 | 85 | Natural variant | ID=VAR_055151;Note=D->E;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:14702039,ECO:0000269|PubMed:9763671,ECO:0000269|Ref.3;Dbxref=dbSNP:rs17118,PMID:14702039,PMID:9763671 |
| O75191 | 169 | 191 | 190 | 195 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BC3 |
| O75191 | 169 | 191 | 170 | 170 | Binding site | Note=Substrate |
| O75191 | 169 | 191 | 1 | 536 | Chain | ID=PRO_0000230985;Note=Xylulose kinase |
| O75191 | 169 | 191 | 172 | 182 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BC3 |
| O75191 | 169 | 191 | 184 | 188 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BC3 |
| 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 |
| O75191 | 70 | 97 | 1 | 137 | Alternative sequence | ID=VSP_055522;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| O75191 | 70 | 97 | 89 | 96 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BC3 |
| O75191 | 70 | 97 | 1 | 536 | Chain | ID=PRO_0000230985;Note=Xylulose kinase |
| O75191 | 70 | 97 | 65 | 81 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BC3 |
| O75191 | 70 | 97 | 86 | 88 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BC3 |
| O75191 | 70 | 97 | 85 | 85 | Natural variant | ID=VAR_055151;Note=D->E;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:14702039,ECO:0000269|PubMed:9763671,ECO:0000269|Ref.3;Dbxref=dbSNP:rs17118,PMID:14702039,PMID:9763671 |
| O75191 | 169 | 191 | 190 | 195 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BC3 |
| O75191 | 169 | 191 | 170 | 170 | Binding site | Note=Substrate |
| O75191 | 169 | 191 | 1 | 536 | Chain | ID=PRO_0000230985;Note=Xylulose kinase |
| O75191 | 169 | 191 | 172 | 182 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BC3 |
| O75191 | 169 | 191 | 184 | 188 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4BC3 |
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SNVs in the skipped exons for XYLB |
| - 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. |
| - 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 |
| BLCA | TCGA-ZF-A9R7-01 | exon_skip_372896 | 38408299 | 38408364 | 38408354 | 38408354 | Nonsense_Mutation | C | G | p.S188* |
| THYM | TCGA-4X-A9F9-01 | exon_skip_372905 | 38420737 | 38420833 | 38420761 | 38420761 | Nonsense_Mutation | G | T | p.E407X |
| LUAD | TCGA-55-8506-01 | exon_skip_372905 | 38420737 | 38420833 | 38420767 | 38420767 | Nonsense_Mutation | C | T | p.R409* |
| THCA | TCGA-E3-A3E5-01 | exon_skip_372905 | 38420737 | 38420833 | 38420767 | 38420767 | Nonsense_Mutation | C | T | p.R409* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| NCIH1915_LUNG | 38401830 | 38401899 | 38401893 | 38401893 | Missense_Mutation | G | T | p.W68C |
| ZR7530_BREAST | 38404428 | 38404508 | 38404458 | 38404458 | Missense_Mutation | G | A | p.A81T |
| CW2_LARGE_INTESTINE | 38404428 | 38404508 | 38404485 | 38404485 | Missense_Mutation | C | A | p.L90I |
| HS633T_SOFT_TISSUE | 38404428 | 38404508 | 38404485 | 38404485 | Missense_Mutation | C | A | p.L90I |
| MCC13_SKIN | 38417608 | 38417723 | 38417660 | 38417660 | Missense_Mutation | C | T | p.R353C |
| SEKI_SKIN | 38417608 | 38417723 | 38417720 | 38417720 | Missense_Mutation | C | G | p.L373V |
| LOVO_LARGE_INTESTINE | 38420737 | 38420833 | 38420822 | 38420822 | Missense_Mutation | G | A | p.G427D |
| KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 38438563 | 38438650 | 38438588 | 38438588 | Missense_Mutation | C | T | p.P459L |
| SNU175_LARGE_INTESTINE | 38438563 | 38438650 | 38438609 | 38438609 | Missense_Mutation | C | T | p.A466V |
| NCIH1048_LUNG | 38438563 | 38438650 | 38438613 | 38438613 | Missense_Mutation | C | G | p.N467K |
| MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 38408299 | 38408364 | 38408364 | 38408364 | Splice_Site | G | A | p.E191E |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for XYLB |
| 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 XYLB |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for XYLB |
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RelatedDrugs for XYLB |
| 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 XYLB |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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