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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 PYGB |
 Gene summary |
| Gene information | Gene symbol | PYGB | Gene ID | 5834 |
| Gene name | glycogen phosphorylase B | |
| Synonyms | GPBB | |
| Cytomap | 20p11.21 | |
| Type of gene | protein-coding | |
| Description | glycogen phosphorylase, brain formphosphorylase, glycogen; brain | |
| Modification date | 20180523 | |
| UniProtAcc | P11216 | |
| Context | PubMed: PYGB [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 PYGB 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 PYGB |
| 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 PYGB |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_349712 | 20 | 25255227:25255359:25257281:25257393:25257879:25257962 | 25257281:25257393 | ENSG00000100994.7 | ENST00000216962.4 |
| exon_skip_349716 | 20 | 25257879:25257962:25258954:25259098:25259692:25259785 | 25258954:25259098 | ENSG00000100994.7 | ENST00000216962.4 |
| exon_skip_349725 | 20 | 25264739:25264887:25269060:25269119:25271116:25271258 | 25269060:25269119 | ENSG00000100994.7 | ENST00000216962.4 |
| exon_skip_349731 | 20 | 25271116:25271258:25273041:25273249:25274793:25274928 | 25273041:25273249 | ENSG00000100994.7 | ENST00000216962.4,ENST00000428458.1 |
| exon_skip_349735 | 20 | 25274793:25274928:25276239:25276306:25277005:25277104 | 25276239:25276306 | ENSG00000100994.7 | ENST00000216962.4,ENST00000471359.1,ENST00000428458.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PYGB |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_349712 | 20 | 25255227:25255359:25257281:25257393:25257879:25257962 | 25257281:25257393 | ENSG00000100994.7 | ENST00000216962.4 |
| exon_skip_349716 | 20 | 25257879:25257962:25258954:25259098:25259692:25259785 | 25258954:25259098 | ENSG00000100994.7 | ENST00000216962.4 |
| exon_skip_349725 | 20 | 25264739:25264887:25269060:25269119:25271116:25271258 | 25269060:25269119 | ENSG00000100994.7 | ENST00000216962.4 |
| exon_skip_349731 | 20 | 25271116:25271258:25273041:25273249:25274793:25274928 | 25273041:25273249 | ENSG00000100994.7 | ENST00000216962.4,ENST00000428458.1 |
| exon_skip_349735 | 20 | 25274793:25274928:25276239:25276306:25277005:25277104 | 25276239:25276306 | ENSG00000100994.7 | ENST00000216962.4,ENST00000428458.1,ENST00000471359.1 |
| 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 PYGB |
| 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 |
| ENST00000216962 | 25257281 | 25257393 | Frame-shift |
| ENST00000216962 | 25269060 | 25269119 | Frame-shift |
| ENST00000216962 | 25273041 | 25273249 | Frame-shift |
| ENST00000216962 | 25276239 | 25276306 | Frame-shift |
| ENST00000216962 | 25258954 | 25259098 | 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 |
| ENST00000216962 | 25257281 | 25257393 | Frame-shift |
| ENST00000216962 | 25269060 | 25269119 | Frame-shift |
| ENST00000216962 | 25273041 | 25273249 | Frame-shift |
| ENST00000216962 | 25276239 | 25276306 | Frame-shift |
| ENST00000216962 | 25258954 | 25259098 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PYGB |
| 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 |
| ENST00000216962 | 4151 | 843 | 25258954 | 25259098 | 966 | 1109 | 285 | 333 |
| 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 |
| ENST00000216962 | 4151 | 843 | 25258954 | 25259098 | 966 | 1109 | 285 | 333 |
| 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 |
| P11216 | 285 | 333 | 310 | 310 | Binding site | Note=AMP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27402852;Dbxref=PMID:27402852 |
| P11216 | 285 | 333 | 2 | 843 | Chain | ID=PRO_0000188535;Note=Glycogen phosphorylase%2C brain form |
| P11216 | 285 | 333 | 290 | 313 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IKO |
| P11216 | 285 | 333 | 326 | 329 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IKO |
| P11216 | 285 | 333 | 330 | 333 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IKO |
| P11216 | 285 | 333 | 303 | 303 | Natural variant | ID=VAR_034428;Note=A->S;Dbxref=dbSNP:rs2228976 |
| P11216 | 285 | 333 | 302 | 302 | Sequence conflict | Note=A->G;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 |
| P11216 | 285 | 333 | 310 | 310 | Binding site | Note=AMP;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27402852;Dbxref=PMID:27402852 |
| P11216 | 285 | 333 | 2 | 843 | Chain | ID=PRO_0000188535;Note=Glycogen phosphorylase%2C brain form |
| P11216 | 285 | 333 | 290 | 313 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IKO |
| P11216 | 285 | 333 | 326 | 329 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IKO |
| P11216 | 285 | 333 | 330 | 333 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:5IKO |
| P11216 | 285 | 333 | 303 | 303 | Natural variant | ID=VAR_034428;Note=A->S;Dbxref=dbSNP:rs2228976 |
| P11216 | 285 | 333 | 302 | 302 | Sequence conflict | Note=A->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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SNVs in the skipped exons for PYGB |
| - 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 |
| BRCA | TCGA-A2-A0YH-01 | exon_skip_349712 | 25257282 | 25257393 | 25257355 | 25257355 | Frame_Shift_Del | G | - | p.W245fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_349716 | 25258955 | 25259098 | 25258963 | 25258963 | Frame_Shift_Del | G | - | p.E288fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_349716 | 25258955 | 25259098 | 25259029 | 25259029 | Frame_Shift_Del | C | - | p.R311fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_349725 | 25269061 | 25269119 | 25269074 | 25269074 | Frame_Shift_Del | C | - | p.D594fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_349725 | 25269061 | 25269119 | 25269111 | 25269111 | Frame_Shift_Del | G | - | p.G608fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_349725 | 25269061 | 25269119 | 25269111 | 25269111 | Frame_Shift_Del | G | - | p.G608fs |
| COAD | TCGA-CM-5861-01 | exon_skip_349731 | 25273042 | 25273249 | 25273102 | 25273102 | Frame_Shift_Del | C | - | p.T677fs |
| HNSC | TCGA-QK-A8ZA-01 | exon_skip_349735 | 25276240 | 25276306 | 25276271 | 25276272 | Frame_Shift_Ins | - | T | p.A782fs |
| LUAD | TCGA-55-6970-01 | exon_skip_349712 | 25257282 | 25257393 | 25257281 | 25257281 | Splice_Site | G | A | p.V221_splice |
| COAD | TCGA-AZ-6600-01 | exon_skip_349725 | 25269061 | 25269119 | 25269059 | 25269059 | Splice_Site | A | T | . |
| - 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 |
| SNU175_LARGE_INTESTINE | 25257282 | 25257393 | 25257348 | 25257348 | Missense_Mutation | C | T | p.R243W |
| REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 25258955 | 25259098 | 25259030 | 25259030 | Missense_Mutation | C | T | p.R311C |
| RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 25258955 | 25259098 | 25259031 | 25259031 | Missense_Mutation | G | A | p.R311H |
| LU99_LUNG | 25258955 | 25259098 | 25259079 | 25259079 | Missense_Mutation | T | C | p.F327S |
| 201T_LUNG | 25258955 | 25259098 | 25259089 | 25259089 | Missense_Mutation | C | G | p.F330L |
| T98G_CENTRAL_NERVOUS_SYSTEM | 25273042 | 25273249 | 25273086 | 25273086 | Missense_Mutation | A | G | p.T672A |
| CP67MEL_SKIN | 25273042 | 25273249 | 25273228 | 25273228 | Missense_Mutation | T | C | p.V719A |
| ATN1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 25273042 | 25273249 | 25273243 | 25273243 | Missense_Mutation | G | A | p.R724Q |
| NCIH513_PLEURA | 25276240 | 25276306 | 25276287 | 25276287 | Missense_Mutation | A | T | p.Q787L |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PYGB |
| 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 PYGB |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PYGB |
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RelatedDrugs for PYGB |
| 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 |
| P11216 | DB00114 | Pyridoxal phosphate | Glycogen phosphorylase, brain form {ECO:0000303|PubMed:3346228} | small molecule | approved|investigational|nutraceutical |
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RelatedDiseases for PYGB |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PYGB | C0010606 | Adenoid Cystic Carcinoma | 1 | CTD_human |
| PYGB | C0036095 | Salivary Gland Neoplasms | 1 | CTD_human |
| PYGB | C0151744 | Myocardial Ischemia | 1 | CTD_human |
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