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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 PDE6B |
 Gene summary |
| Gene information | Gene symbol | PDE6B | Gene ID | 5158 |
| Gene name | phosphodiesterase 6B | |
| Synonyms | CSNB3|CSNBAD2|GMP-PDEbeta|PDEB|RP40|rd1 | |
| Cytomap | 4p16.3 | |
| Type of gene | protein-coding | |
| Description | rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit betaGMP-PDE betaphosphodiesterase 6B, cGMP-specific, rod, betarod cGMP-phosphodiesterase beta-subunit | |
| Modification date | 20180522 | |
| UniProtAcc | P35913 | |
| Context | PubMed: PDE6B [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 PDE6B 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 PDE6B |
| 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 PDE6B |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_421047 | 4 | 646965:647108:647225:647496:647640:647781 | 647225:647496 | ENSG00000133256.8 | ENST00000488061.1 |
| exon_skip_421048 | 4 | 648612:648677:649728:649795:650033:650081 | 649728:649795 | ENSG00000133256.8 | ENST00000429163.2,ENST00000496514.1,ENST00000255622.6 |
| exon_skip_421049 | 4 | 649728:649795:650033:650081:650662:650732 | 650033:650081 | ENSG00000133256.8 | ENST00000429163.2,ENST00000496514.1,ENST00000255622.6 |
| exon_skip_421050 | 4 | 652740:652806:654255:654402:655922:656030 | 654255:654402 | ENSG00000133256.8 | ENST00000429163.2,ENST00000496514.1,ENST00000255622.6 |
| exon_skip_421051 | 4 | 658698:658733:659043:659118:660319:660403 | 659043:659118 | ENSG00000133256.8 | ENST00000461490.1,ENST00000471824.2,ENST00000429163.2,ENST00000496514.1,ENST00000255622.6 |
| exon_skip_421052 | 4 | 660319:660403:661644:661730:663834:663982 | 661644:661730 | ENSG00000133256.8 | ENST00000461490.1 |
| exon_skip_421054 | 4 | 660319:660403:661644:661795:663834:663982 | 661644:661795 | ENSG00000133256.8 | ENST00000429163.2,ENST00000496514.1 |
| exon_skip_421055 | 4 | 660319:660403:661644:661795:663837:664571 | 661644:661795 | ENSG00000133256.8 | ENST00000255622.6 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PDE6B |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_421046 | 4 | 645773:645877:646284:646342:647640:647781 | 646284:646342 | ENSG00000133256.8 | ENST00000474251.1 |
| exon_skip_421047 | 4 | 646965:647108:647225:647496:647640:647781 | 647225:647496 | ENSG00000133256.8 | ENST00000488061.1 |
| exon_skip_421048 | 4 | 648612:648677:649728:649795:650033:650081 | 649728:649795 | ENSG00000133256.8 | ENST00000255622.6,ENST00000496514.1,ENST00000429163.2 |
| exon_skip_421049 | 4 | 649728:649795:650033:650081:650662:650732 | 650033:650081 | ENSG00000133256.8 | ENST00000255622.6,ENST00000496514.1,ENST00000429163.2 |
| exon_skip_421050 | 4 | 652740:652806:654255:654402:655922:656030 | 654255:654402 | ENSG00000133256.8 | ENST00000255622.6,ENST00000496514.1,ENST00000429163.2 |
| exon_skip_421051 | 4 | 658698:658733:659043:659118:660319:660403 | 659043:659118 | ENSG00000133256.8 | ENST00000255622.6,ENST00000496514.1,ENST00000429163.2,ENST00000471824.2,ENST00000461490.1 |
| exon_skip_421052 | 4 | 660319:660403:661644:661730:663834:663982 | 661644:661730 | ENSG00000133256.8 | ENST00000461490.1 |
| exon_skip_421054 | 4 | 660319:660403:661644:661795:663834:663982 | 661644:661795 | ENSG00000133256.8 | ENST00000496514.1,ENST00000429163.2 |
| exon_skip_421055 | 4 | 660319:660403:661644:661795:663837:664571 | 661644:661795 | ENSG00000133256.8 | ENST00000255622.6 |
| 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 PDE6B |
| 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 |
| ENST00000496514 | 649728 | 649795 | Frame-shift |
| ENST00000496514 | 661644 | 661795 | Frame-shift |
| ENST00000496514 | 650033 | 650081 | In-frame |
| ENST00000496514 | 654255 | 654402 | In-frame |
| ENST00000496514 | 659043 | 659118 | 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 |
| ENST00000496514 | 649728 | 649795 | Frame-shift |
| ENST00000496514 | 661644 | 661795 | Frame-shift |
| ENST00000496514 | 650033 | 650081 | In-frame |
| ENST00000496514 | 654255 | 654402 | In-frame |
| ENST00000496514 | 659043 | 659118 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PDE6B |
| 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 |
| ENST00000496514 | 3249 | 854 | 650033 | 650081 | 1081 | 1128 | 353 | 369 |
| ENST00000496514 | 3249 | 854 | 654255 | 654402 | 1489 | 1635 | 489 | 538 |
| ENST00000496514 | 3249 | 854 | 659043 | 659118 | 2215 | 2289 | 731 | 756 |
| 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 |
| ENST00000496514 | 3249 | 854 | 650033 | 650081 | 1081 | 1128 | 353 | 369 |
| ENST00000496514 | 3249 | 854 | 654255 | 654402 | 1489 | 1635 | 489 | 538 |
| ENST00000496514 | 3249 | 854 | 659043 | 659118 | 2215 | 2289 | 731 | 756 |
| 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 |
| P35913 | 353 | 369 | 2 | 851 | Chain | ID=PRO_0000023348;Note=Rod cGMP-specific 3'%2C5'-cyclic phosphodiesterase subunit beta |
| P35913 | 353 | 369 | 252 | 429 | Domain | Note=GAF 2 |
| P35913 | 353 | 369 | 360 | 360 | Sequence conflict | Note=A->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P35913 | 489 | 538 | 2 | 851 | Chain | ID=PRO_0000023348;Note=Rod cGMP-specific 3'%2C5'-cyclic phosphodiesterase subunit beta |
| P35913 | 489 | 538 | 481 | 814 | Domain | Note=PDEase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01192 |
| P35913 | 489 | 538 | 527 | 527 | Natural variant | ID=VAR_009290;Note=In RP40%3B autosomal recessive. L->P;Dbxref=dbSNP:rs760766981 |
| P35913 | 489 | 538 | 535 | 535 | Natural variant | ID=VAR_009291;Note=In RP40%3B autosomal recessive. I->N;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9543643;Dbxref=dbSNP:rs527236088,PMID:9543643 |
| P35913 | 731 | 756 | 2 | 851 | Chain | ID=PRO_0000023348;Note=Rod cGMP-specific 3'%2C5'-cyclic phosphodiesterase subunit beta |
| P35913 | 731 | 756 | 481 | 814 | Domain | Note=PDEase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01192 |
| 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 |
| P35913 | 353 | 369 | 2 | 851 | Chain | ID=PRO_0000023348;Note=Rod cGMP-specific 3'%2C5'-cyclic phosphodiesterase subunit beta |
| P35913 | 353 | 369 | 252 | 429 | Domain | Note=GAF 2 |
| P35913 | 353 | 369 | 360 | 360 | Sequence conflict | Note=A->R;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P35913 | 489 | 538 | 2 | 851 | Chain | ID=PRO_0000023348;Note=Rod cGMP-specific 3'%2C5'-cyclic phosphodiesterase subunit beta |
| P35913 | 489 | 538 | 481 | 814 | Domain | Note=PDEase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01192 |
| P35913 | 489 | 538 | 527 | 527 | Natural variant | ID=VAR_009290;Note=In RP40%3B autosomal recessive. L->P;Dbxref=dbSNP:rs760766981 |
| P35913 | 489 | 538 | 535 | 535 | Natural variant | ID=VAR_009291;Note=In RP40%3B autosomal recessive. I->N;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:9543643;Dbxref=dbSNP:rs527236088,PMID:9543643 |
| P35913 | 731 | 756 | 2 | 851 | Chain | ID=PRO_0000023348;Note=Rod cGMP-specific 3'%2C5'-cyclic phosphodiesterase subunit beta |
| P35913 | 731 | 756 | 481 | 814 | Domain | Note=PDEase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU01192 |
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SNVs in the skipped exons for PDE6B |
| - 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 |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_421050 | 654256 | 654402 | 654393 | 654393 | Frame_Shift_Del | C | - | p.I535fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_421050 | 654256 | 654402 | 654393 | 654393 | Frame_Shift_Del | C | - | p.I535fs |
| SKCM | TCGA-ER-A19N-06 | exon_skip_421049 | 650034 | 650081 | 650079 | 650079 | Nonsense_Mutation | C | T | p.Q369* |
| CESC | TCGA-MU-A51Y-01 | exon_skip_421052 | 661645 | 661730 | 661666 | 661666 | Nonsense_Mutation | G | T | p.E792* |
| CESC | TCGA-MU-A51Y-01 | exon_skip_421054 exon_skip_421055 | 661645 | 661795 | 661666 | 661666 | Nonsense_Mutation | G | T | p.E792* |
| - 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 |
| OVMIU_OVARY | 654256 | 654402 | 654327 | 654329 | In_Frame_Del | ACT | - | p.L514del |
| NCIH513_PLEURA | 649729 | 649795 | 649766 | 649766 | Missense_Mutation | C | G | p.L344V |
| RO82W1_THYROID | 650034 | 650081 | 650058 | 650058 | Missense_Mutation | G | A | p.A362T |
| SW1116_LARGE_INTESTINE | 654256 | 654402 | 654380 | 654380 | Missense_Mutation | G | A | p.R531Q |
| PC9_LUNG | 659044 | 659118 | 659090 | 659090 | Missense_Mutation | A | T | p.E747V |
| HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 661645 | 661795 | 661684 | 661684 | Missense_Mutation | G | A | p.D798N |
| HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 661645 | 661730 | 661684 | 661684 | Missense_Mutation | G | A | p.D798N |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PDE6B |
| 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 PDE6B |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PDE6B |
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RelatedDrugs for PDE6B |
| 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 PDE6B |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PDE6B | C3151107 | RETINITIS PIGMENTOSA 40 (disorder) | 7 | UNIPROT |
| PDE6B | C0035304 | Retinal Degeneration | 4 | CTD_human |
| PDE6B | C0035334 | Retinitis Pigmentosa | 1 | CTD_human;HPO;ORPHANET |
| PDE6B | C0339535 | Night blindness, congenital stationary | 1 | CTD_human;HPO;ORPHANET |
| PDE6B | C1876182 | NIGHT BLINDNESS, CONGENITAL STATIONARY, AUTOSOMAL DOMINANT 2 | 1 | CTD_human;UNIPROT |
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