|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for APAF1 |
 Gene summary |
| Gene information | Gene symbol | APAF1 | Gene ID | 317 |
| Gene name | apoptotic peptidase activating factor 1 | |
| Synonyms | APAF-1|CED4 | |
| Cytomap | 12q23.1 | |
| Type of gene | protein-coding | |
| Description | apoptotic protease-activating factor 1 | |
| Modification date | 20180527 | |
| UniProtAcc | O14727 | |
| Context | PubMed: APAF1 [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 |
| APAF1 | GO:0006919 | activation of cysteine-type endopeptidase activity involved in apoptotic process | 21827945 |
| APAF1 | GO:0008635 | activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c | 9267021 |
Top |
Exon skipping events across known transcript of Ensembl for APAF1 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. |
 |
Top |
Gene isoform structures and expression levels for APAF1 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for APAF1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_86068 | 12 | 99043264:99043462:99052937:99053121:99056233:99056346 | 99052937:99053121 | ENSG00000120868.9 | ENST00000552268.1,ENST00000339433.3,ENST00000547045.1,ENST00000550527.1,ENST00000359972.2,ENST00000549007.1,ENST00000333991.1,ENST00000551964.1,ENST00000357310.1 |
| exon_skip_86070 | 12 | 99056452:99056584:99059330:99059569:99059967:99060135 | 99059330:99059569 | ENSG00000120868.9 | ENST00000339433.3,ENST00000547045.1,ENST00000550527.1,ENST00000359972.2,ENST00000549007.1,ENST00000551964.1,ENST00000357310.1 |
| exon_skip_86072 | 12 | 99065312:99065497:99071202:99071329:99074054:99074180 | 99071202:99071329 | ENSG00000120868.9 | ENST00000339433.3,ENST00000547045.1,ENST00000550527.1,ENST00000359972.2,ENST00000549007.1,ENST00000551964.1,ENST00000357310.1 |
| exon_skip_86074 | 12 | 99076920:99077052:99080525:99080651:99093185:99093347 | 99080525:99080651 | ENSG00000120868.9 | ENST00000339433.3,ENST00000547045.1,ENST00000550527.1,ENST00000359972.2,ENST00000549007.1,ENST00000551964.1,ENST00000357310.1 |
| exon_skip_86075 | 12 | 99093273:99093347:99097148:99097277:99100262:99100388 | 99097148:99097277 | ENSG00000120868.9 | ENST00000546491.1,ENST00000550527.1,ENST00000551964.1 |
| exon_skip_86077 | 12 | 99106096:99106213:99109204:99109330:99116970:99117090 | 99109204:99109330 | ENSG00000120868.9 | ENST00000339433.3,ENST00000547045.1,ENST00000550527.1,ENST00000359972.2,ENST00000549007.1,ENST00000551964.1,ENST00000357310.1 |
| exon_skip_86080 | 12 | 99117467:99117542:99119192:99119318:99120950:99121094 | 99119192:99119318 | ENSG00000120868.9 | ENST00000547045.1,ENST00000550527.1,ENST00000359972.2,ENST00000552929.1,ENST00000551964.1,ENST00000357310.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for APAF1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_86068 | 12 | 99043264:99043462:99052937:99053121:99056233:99056346 | 99052937:99053121 | ENSG00000120868.9 | ENST00000551964.1,ENST00000359972.2,ENST00000357310.1,ENST00000339433.3,ENST00000333991.1,ENST00000552268.1,ENST00000550527.1,ENST00000547045.1,ENST00000549007.1 |
| exon_skip_86070 | 12 | 99056452:99056584:99059330:99059569:99059967:99060135 | 99059330:99059569 | ENSG00000120868.9 | ENST00000551964.1,ENST00000359972.2,ENST00000357310.1,ENST00000339433.3,ENST00000550527.1,ENST00000547045.1,ENST00000549007.1 |
| exon_skip_86072 | 12 | 99065312:99065497:99071202:99071329:99074054:99074180 | 99071202:99071329 | ENSG00000120868.9 | ENST00000551964.1,ENST00000359972.2,ENST00000357310.1,ENST00000339433.3,ENST00000550527.1,ENST00000547045.1,ENST00000549007.1 |
| exon_skip_86074 | 12 | 99076920:99077052:99080525:99080651:99093185:99093347 | 99080525:99080651 | ENSG00000120868.9 | ENST00000551964.1,ENST00000359972.2,ENST00000357310.1,ENST00000339433.3,ENST00000550527.1,ENST00000547045.1,ENST00000549007.1 |
| exon_skip_86075 | 12 | 99093273:99093347:99097148:99097277:99100262:99100388 | 99097148:99097277 | ENSG00000120868.9 | ENST00000551964.1,ENST00000550527.1,ENST00000546491.1 |
| exon_skip_86077 | 12 | 99106096:99106213:99109204:99109330:99116970:99117090 | 99109204:99109330 | ENSG00000120868.9 | ENST00000551964.1,ENST00000359972.2,ENST00000357310.1,ENST00000339433.3,ENST00000550527.1,ENST00000547045.1,ENST00000549007.1 |
| exon_skip_86080 | 12 | 99117467:99117542:99119192:99119318:99120950:99121094 | 99119192:99119318 | ENSG00000120868.9 | ENST00000551964.1,ENST00000359972.2,ENST00000357310.1,ENST00000550527.1,ENST00000547045.1,ENST00000552929.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for APAF1 |
| 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 |
| ENST00000551964 | 99052937 | 99053121 | Frame-shift |
| ENST00000551964 | 99059330 | 99059569 | Frame-shift |
| ENST00000551964 | 99071202 | 99071329 | Frame-shift |
| ENST00000551964 | 99080525 | 99080651 | In-frame |
| ENST00000551964 | 99097148 | 99097277 | In-frame |
| ENST00000551964 | 99109204 | 99109330 | In-frame |
| ENST00000551964 | 99119192 | 99119318 | 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 |
| ENST00000551964 | 99052937 | 99053121 | Frame-shift |
| ENST00000551964 | 99059330 | 99059569 | Frame-shift |
| ENST00000551964 | 99071202 | 99071329 | Frame-shift |
| ENST00000551964 | 99080525 | 99080651 | In-frame |
| ENST00000551964 | 99097148 | 99097277 | In-frame |
| ENST00000551964 | 99109204 | 99109330 | In-frame |
| ENST00000551964 | 99119192 | 99119318 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for APAF1 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| 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 |
| ENST00000551964 | 5461 | 1248 | 99080525 | 99080651 | 2915 | 3040 | 726 | 768 |
| ENST00000551964 | 5461 | 1248 | 99097148 | 99097277 | 3203 | 3331 | 822 | 865 |
| ENST00000551964 | 5461 | 1248 | 99109204 | 99109330 | 3695 | 3820 | 986 | 1028 |
| ENST00000551964 | 5461 | 1248 | 99119192 | 99119318 | 4067 | 4192 | 1110 | 1152 |
| 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 |
| ENST00000551964 | 5461 | 1248 | 99080525 | 99080651 | 2915 | 3040 | 726 | 768 |
| ENST00000551964 | 5461 | 1248 | 99097148 | 99097277 | 3203 | 3331 | 822 | 865 |
| ENST00000551964 | 5461 | 1248 | 99109204 | 99109330 | 3695 | 3820 | 986 | 1028 |
| ENST00000551964 | 5461 | 1248 | 99119192 | 99119318 | 4067 | 4192 | 1110 | 1152 |
| 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 |
| 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 |
Top |
SNVs in the skipped exons for APAF1 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - 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-A3A0-01 | exon_skip_86068 | 99052938 | 99053121 | 99052949 | 99052949 | Frame_Shift_Del | G | - | p.G181fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_86068 | 99052938 | 99053121 | 99052965 | 99052965 | Frame_Shift_Del | T | - | p.V185fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_86068 | 99052938 | 99053121 | 99053070 | 99053070 | Frame_Shift_Del | T | - | p.I220fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_86070 | 99059331 | 99059569 | 99059566 | 99059566 | Frame_Shift_Del | A | - | p.T397fs |
| COAD | TCGA-AA-3516-01 | exon_skip_86072 | 99071203 | 99071329 | 99071207 | 99071208 | Frame_Shift_Del | AA | - | p.589_589del |
| STAD | TCGA-HU-A4GQ-01 | exon_skip_86072 | 99071203 | 99071329 | 99071207 | 99071207 | Frame_Shift_Del | A | - | p.N599fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_86075 | 99097149 | 99097277 | 99097261 | 99097261 | Frame_Shift_Del | C | - | p.S849fs |
| KIRP | TCGA-SX-A71S-01 | exon_skip_86077 | 99109205 | 99109330 | 99109218 | 99109218 | Frame_Shift_Del | T | - | p.V991X |
| BLCA | TCGA-YF-AA3L-01 | exon_skip_86077 | 99109205 | 99109330 | 99109219 | 99109219 | Frame_Shift_Del | A | - | p.V948fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_86080 | 99119193 | 99119318 | 99119233 | 99119233 | Frame_Shift_Del | G | - | p.R1081fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_86080 | 99119193 | 99119318 | 99119233 | 99119233 | Frame_Shift_Del | G | - | p.R1124fs |
| STAD | TCGA-BR-4292-01 | exon_skip_86072 | 99071203 | 99071329 | 99071207 | 99071208 | Frame_Shift_Ins | - | A | p.N599fs |
| STAD | TCGA-CD-A4MG-01 | exon_skip_86072 | 99071203 | 99071329 | 99071207 | 99071208 | Frame_Shift_Ins | - | A | p.N599fs |
| BLCA | TCGA-K4-A54R-01 | exon_skip_86068 | 99052938 | 99053121 | 99053033 | 99053033 | Nonsense_Mutation | C | T | p.Q208* |
| SKCM | TCGA-EE-A185-06 | exon_skip_86068 | 99052938 | 99053121 | 99053033 | 99053033 | Nonsense_Mutation | C | T | p.Q208* |
| SKCM | TCGA-YG-AA3O-06 | exon_skip_86074 | 99080526 | 99080651 | 99080553 | 99080553 | Nonsense_Mutation | C | T | p.R736* |
| UCEC | TCGA-AP-A054-01 | exon_skip_86074 | 99080526 | 99080651 | 99080653 | 99080653 | Splice_Site | T | C | e15+2 |
| - 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 |
| HEC108_ENDOMETRIUM | 99071203 | 99071329 | 99071207 | 99071207 | Frame_Shift_Del | A | - | p.K601fs |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99071203 | 99071329 | 99071207 | 99071207 | Frame_Shift_Del | A | - | p.K601fs |
| MN60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99071203 | 99071329 | 99071207 | 99071207 | Frame_Shift_Del | A | - | p.K601fs |
| SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99071203 | 99071329 | 99071207 | 99071207 | Frame_Shift_Del | A | - | p.K601fs |
| LNCAPCLONEFGC_PROSTATE | 99071203 | 99071329 | 99071206 | 99071207 | Frame_Shift_Ins | - | A | p.K600fs |
| MFE319_ENDOMETRIUM | 99071203 | 99071329 | 99071206 | 99071207 | Frame_Shift_Ins | - | A | p.K600fs |
| DKMG_CENTRAL_NERVOUS_SYSTEM | 99071203 | 99071329 | 99071206 | 99071207 | Frame_Shift_Ins | - | A | p.K600fs |
| HUH6_LIVER | 99071203 | 99071329 | 99071206 | 99071207 | Frame_Shift_Ins | - | A | p.K600fs |
| KNS60_CENTRAL_NERVOUS_SYSTEM | 99071203 | 99071329 | 99071206 | 99071207 | Frame_Shift_Ins | - | A | p.K600fs |
| KPNYN_AUTONOMIC_GANGLIA | 99071203 | 99071329 | 99071206 | 99071207 | Frame_Shift_Ins | - | A | p.K600fs |
| PC9_LUNG | 99071203 | 99071329 | 99071206 | 99071207 | Frame_Shift_Ins | - | A | p.K600fs |
| SNU685_ENDOMETRIUM | 99071203 | 99071329 | 99071206 | 99071207 | Frame_Shift_Ins | - | A | p.K600fs |
| SARC9371_BONE | 99052938 | 99053121 | 99052946 | 99052946 | Missense_Mutation | C | T | p.P179S |
| CW2_LARGE_INTESTINE | 99052938 | 99053121 | 99053025 | 99053025 | Missense_Mutation | G | A | p.R205Q |
| MCC13_SKIN | 99052938 | 99053121 | 99053049 | 99053049 | Missense_Mutation | C | T | p.S213F |
| LS411N_LARGE_INTESTINE | 99052938 | 99053121 | 99053087 | 99053087 | Missense_Mutation | C | A | p.R226S |
| CA922_UPPER_AERODIGESTIVE_TRACT | 99052938 | 99053121 | 99053108 | 99053108 | Missense_Mutation | C | T | p.R233C |
| CL34_LARGE_INTESTINE | 99052938 | 99053121 | 99053108 | 99053108 | Missense_Mutation | C | T | p.R233C |
| HRT18_LARGE_INTESTINE | 99059331 | 99059569 | 99059339 | 99059339 | Missense_Mutation | C | A | p.L322I |
| LIM1215_LARGE_INTESTINE | 99059331 | 99059569 | 99059519 | 99059519 | Missense_Mutation | T | C | p.Y382H |
| IM95_STOMACH | 99071203 | 99071329 | 99071232 | 99071232 | Missense_Mutation | G | A | p.R608H |
| NCIH1339_LUNG | 99080526 | 99080651 | 99080554 | 99080554 | Missense_Mutation | G | A | p.R736Q |
| ETK1_BILIARY_TRACT | 99080526 | 99080651 | 99080581 | 99080581 | Missense_Mutation | C | T | p.S745L |
| L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99109205 | 99109330 | 99109247 | 99109247 | Missense_Mutation | C | G | p.Q1001E |
| NCIH2810_PLEURA | 99109205 | 99109330 | 99109253 | 99109253 | Missense_Mutation | A | G | p.K1003E |
| NCIH1385_LUNG | 99119193 | 99119318 | 99119250 | 99119250 | Missense_Mutation | G | T | p.V1130L |
| EN_ENDOMETRIUM | 99119193 | 99119318 | 99119253 | 99119253 | Missense_Mutation | C | T | p.R1131C |
| CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99119193 | 99119318 | 99119274 | 99119274 | Missense_Mutation | G | A | p.D1138N |
| KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 99119193 | 99119318 | 99119277 | 99119277 | Missense_Mutation | A | G | p.S1139G |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for APAF1 |
| 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 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for APAF1 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for APAF1 |
Top |
RelatedDrugs for APAF1 |
| 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 |
Top |
RelatedDiseases for APAF1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| APAF1 | C0041696 | Unipolar Depression | 2 | PSYGENET |
| APAF1 | C0376634 | Craniofacial Abnormalities | 2 | CTD_human |
| APAF1 | C1269683 | Major Depressive Disorder | 2 | PSYGENET |
| APAF1 | C0007134 | Renal Cell Carcinoma | 1 | CTD_human |
| APAF1 | C0007138 | Carcinoma, Transitional Cell | 1 | CTD_human |
| APAF1 | C0015393 | Eye Abnormalities | 1 | CTD_human |
| APAF1 | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| APAF1 | C0035305 | Retinal Detachment | 1 | CTD_human |
| APAF1 | C0037268 | Skin Abnormalities | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|