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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 PLXND1 |
 Gene summary |
| Gene information | Gene symbol | PLXND1 | Gene ID | 23129 |
| Gene name | plexin D1 | |
| Synonyms | PLEXD1 | |
| Cytomap | 3q22.1 | |
| Type of gene | protein-coding | |
| Description | plexin-D1 | |
| Modification date | 20180523 | |
| UniProtAcc | Q9Y4D7 | |
| Context | PubMed: PLXND1 [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 PLXND1 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 PLXND1 |
| 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 PLXND1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_388108 | 3 | 129277378:129277418:129278455:129278626:129279172:129279257 | 129278455:129278626 | ENSG00000004399.8 | ENST00000393239.1,ENST00000512744.1 |
| exon_skip_388110 | 3 | 129277378:129277418:129278462:129278626:129279172:129279257 | 129278462:129278626 | ENSG00000004399.8 | ENST00000324093.4,ENST00000506979.1,ENST00000508630.1 |
| exon_skip_388112 | 3 | 129279531:129279566:129280488:129280552:129280642:129280746 | 129280488:129280552 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1,ENST00000512744.1 |
| exon_skip_388115 | 3 | 129284729:129284860:129285369:129285474:129286334:129286447 | 129285369:129285474 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1 |
| exon_skip_388124 | 3 | 129285369:129285474:129286334:129286447:129286540:129286648 | 129286334:129286447 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1 |
| exon_skip_388125 | 3 | 129286540:129286648:129288685:129288800:129289628:129289778 | 129288685:129288800 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1 |
| exon_skip_388128 | 3 | 129290519:129290687:129291451:129291591:129291684:129291784 | 129291451:129291591 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1 |
| exon_skip_388135 | 3 | 129292436:129292588:129293178:129293333:129294311:129294405 | 129293178:129293333 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1 |
| exon_skip_388136 | 3 | 129293178:129293333:129294311:129294405:129294608:129294698 | 129294311:129294405 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1,ENST00000505505.1 |
| exon_skip_388137 | 3 | 129294311:129294405:129294608:129294698:129297171:129297276 | 129294608:129294698 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1,ENST00000505505.1 |
| exon_skip_388142 | 3 | 129302967:129303076:129303227:129303405:129304794:129304891 | 129303227:129303405 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1 |
| exon_skip_388143 | 3 | 129304794:129304924:129305014:129305115:129305430:129305528 | 129305014:129305115 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1,ENST00000505665.1 |
| exon_skip_388144 | 3 | 129305014:129305115:129305430:129305562:129308193:129308370 | 129305430:129305562 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1,ENST00000505237.2 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PLXND1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_388108 | 3 | 129277378:129277418:129278455:129278626:129279172:129279257 | 129278455:129278626 | ENSG00000004399.8 | ENST00000393239.1,ENST00000512744.1 |
| exon_skip_388110 | 3 | 129277378:129277418:129278462:129278626:129279172:129279257 | 129278462:129278626 | ENSG00000004399.8 | ENST00000324093.4,ENST00000506979.1,ENST00000508630.1 |
| exon_skip_388112 | 3 | 129279531:129279566:129280488:129280552:129280642:129280746 | 129280488:129280552 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1,ENST00000512744.1 |
| exon_skip_388115 | 3 | 129284729:129284860:129285369:129285474:129286334:129286447 | 129285369:129285474 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1 |
| exon_skip_388124 | 3 | 129285369:129285474:129286334:129286447:129286540:129286648 | 129286334:129286447 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1 |
| exon_skip_388125 | 3 | 129286540:129286648:129288685:129288800:129289628:129289778 | 129288685:129288800 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1 |
| exon_skip_388128 | 3 | 129290519:129290687:129291451:129291591:129291684:129291784 | 129291451:129291591 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1 |
| exon_skip_388135 | 3 | 129292436:129292588:129293178:129293333:129294311:129294405 | 129293178:129293333 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1 |
| exon_skip_388136 | 3 | 129293178:129293333:129294311:129294405:129294608:129294698 | 129294311:129294405 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1,ENST00000505505.1 |
| exon_skip_388137 | 3 | 129294311:129294405:129294608:129294698:129297171:129297276 | 129294608:129294698 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1,ENST00000505505.1 |
| exon_skip_388142 | 3 | 129302967:129303076:129303227:129303405:129304794:129304891 | 129303227:129303405 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1 |
| exon_skip_388143 | 3 | 129304794:129304924:129305014:129305115:129305430:129305528 | 129305014:129305115 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1,ENST00000505665.1 |
| exon_skip_388144 | 3 | 129305014:129305115:129305430:129305562:129308193:129308370 | 129305430:129305562 | ENSG00000004399.8 | ENST00000324093.4,ENST00000393239.1,ENST00000505237.2 |
| 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 PLXND1 |
| 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 |
| ENST00000324093 | 129278462 | 129278626 | Frame-shift |
| ENST00000324093 | 129280488 | 129280552 | Frame-shift |
| ENST00000324093 | 129286334 | 129286447 | Frame-shift |
| ENST00000324093 | 129288685 | 129288800 | Frame-shift |
| ENST00000324093 | 129291451 | 129291591 | Frame-shift |
| ENST00000324093 | 129293178 | 129293333 | Frame-shift |
| ENST00000324093 | 129294311 | 129294405 | Frame-shift |
| ENST00000324093 | 129303227 | 129303405 | Frame-shift |
| ENST00000324093 | 129305014 | 129305115 | Frame-shift |
| ENST00000324093 | 129285369 | 129285474 | In-frame |
| ENST00000324093 | 129294608 | 129294698 | In-frame |
| ENST00000324093 | 129305430 | 129305562 | 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 |
| ENST00000324093 | 129278462 | 129278626 | Frame-shift |
| ENST00000324093 | 129280488 | 129280552 | Frame-shift |
| ENST00000324093 | 129286334 | 129286447 | Frame-shift |
| ENST00000324093 | 129288685 | 129288800 | Frame-shift |
| ENST00000324093 | 129291451 | 129291591 | Frame-shift |
| ENST00000324093 | 129293178 | 129293333 | Frame-shift |
| ENST00000324093 | 129294311 | 129294405 | Frame-shift |
| ENST00000324093 | 129303227 | 129303405 | Frame-shift |
| ENST00000324093 | 129305014 | 129305115 | Frame-shift |
| ENST00000324093 | 129285369 | 129285474 | In-frame |
| ENST00000324093 | 129294608 | 129294698 | In-frame |
| ENST00000324093 | 129305430 | 129305562 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PLXND1 |
| 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 |
| ENST00000324093 | 7111 | 1925 | 129305430 | 129305562 | 1668 | 1799 | 496 | 540 |
| ENST00000324093 | 7111 | 1925 | 129294608 | 129294698 | 2526 | 2615 | 782 | 812 |
| ENST00000324093 | 7111 | 1925 | 129285369 | 129285474 | 4266 | 4370 | 1362 | 1397 |
| 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 |
| ENST00000324093 | 7111 | 1925 | 129305430 | 129305562 | 1668 | 1799 | 496 | 540 |
| ENST00000324093 | 7111 | 1925 | 129294608 | 129294698 | 2526 | 2615 | 782 | 812 |
| ENST00000324093 | 7111 | 1925 | 129285369 | 129285474 | 4266 | 4370 | 1362 | 1397 |
| 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 |
| Q9Y4D7 | 496 | 540 | 47 | 1925 | Chain | ID=PRO_0000024676;Note=Plexin-D1 |
| Q9Y4D7 | 496 | 540 | 47 | 546 | Domain | Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00352 |
| Q9Y4D7 | 496 | 540 | 500 | 500 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:16335952,ECO:0000269|PubMed:19159218;Dbxref=PMID:16335952,PMID:19159218 |
| Q9Y4D7 | 496 | 540 | 531 | 531 | Sequence conflict | Note=G->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9Y4D7 | 496 | 540 | 531 | 531 | Sequence conflict | Note=G->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9Y4D7 | 496 | 540 | 47 | 1271 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9Y4D7 | 782 | 812 | 47 | 1925 | Chain | ID=PRO_0000024676;Note=Plexin-D1 |
| Q9Y4D7 | 782 | 812 | 802 | 802 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9Y4D7 | 782 | 812 | 47 | 1271 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9Y4D7 | 1362 | 1397 | 47 | 1925 | Chain | ID=PRO_0000024676;Note=Plexin-D1 |
| Q9Y4D7 | 1362 | 1397 | 1293 | 1925 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q9Y4D7 | 496 | 540 | 47 | 1925 | Chain | ID=PRO_0000024676;Note=Plexin-D1 |
| Q9Y4D7 | 496 | 540 | 47 | 546 | Domain | Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00352 |
| Q9Y4D7 | 496 | 540 | 500 | 500 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:16335952,ECO:0000269|PubMed:19159218;Dbxref=PMID:16335952,PMID:19159218 |
| Q9Y4D7 | 496 | 540 | 531 | 531 | Sequence conflict | Note=G->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9Y4D7 | 496 | 540 | 531 | 531 | Sequence conflict | Note=G->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9Y4D7 | 496 | 540 | 47 | 1271 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9Y4D7 | 782 | 812 | 47 | 1925 | Chain | ID=PRO_0000024676;Note=Plexin-D1 |
| Q9Y4D7 | 782 | 812 | 802 | 802 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9Y4D7 | 782 | 812 | 47 | 1271 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9Y4D7 | 1362 | 1397 | 47 | 1925 | Chain | ID=PRO_0000024676;Note=Plexin-D1 |
| Q9Y4D7 | 1362 | 1397 | 1293 | 1925 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for PLXND1 |
| - 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-A3A0-01 | exon_skip_388108 exon_skip_388110 | 129278456 | 129278626 | 129278510 | 129278510 | Frame_Shift_Del | C | - | p.K1750fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_388108 exon_skip_388110 | 129278463 | 129278626 | 129278510 | 129278510 | Frame_Shift_Del | C | - | p.K1750fs |
| UCEC | TCGA-AP-A0LT-01 | exon_skip_388124 | 129286335 | 129286447 | 129286424 | 129286427 | Frame_Shift_Del | TGTC | - | p.D1332fs |
| HNSC | TCGA-BA-4076-01 | exon_skip_388135 | 129293179 | 129293333 | 129293227 | 129293227 | Frame_Shift_Del | C | - | p.G879fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_388135 | 129293179 | 129293333 | 129293227 | 129293227 | Frame_Shift_Del | C | - | p.G879fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_388135 | 129293179 | 129293333 | 129293235 | 129293235 | Frame_Shift_Del | G | - | p.L877fs |
| COAD | TCGA-CK-5916-01 | exon_skip_388125 | 129288686 | 129288800 | 129288750 | 129288751 | Frame_Shift_Ins | - | C | p.G1267fs |
| STAD | TCGA-BR-8591-01 | exon_skip_388142 | 129303228 | 129303405 | 129303235 | 129303236 | Frame_Shift_Ins | - | G | p.P674fs |
| UCEC | TCGA-D1-A103-01 | exon_skip_388112 | 129280489 | 129280552 | 129280492 | 129280492 | Nonsense_Mutation | G | A | p.R1664* |
| BLCA | TCGA-KQ-A41Q-01 | exon_skip_388115 | 129285370 | 129285474 | 129285420 | 129285420 | Nonsense_Mutation | G | A | p.Q1381* |
| LUAD | TCGA-17-Z030-01 | exon_skip_388115 | 129285370 | 129285474 | 129285420 | 129285420 | Nonsense_Mutation | G | A | p.Q1381* |
| - 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 |
| SW1573_LUNG | 129278456 | 129278626 | 129278491 | 129278491 | Missense_Mutation | C | T | p.D1757N |
| SW1573_LUNG | 129278463 | 129278626 | 129278491 | 129278491 | Missense_Mutation | C | T | p.D1757N |
| SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 129278456 | 129278626 | 129278536 | 129278536 | Missense_Mutation | C | T | p.D1742N |
| SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 129278463 | 129278626 | 129278536 | 129278536 | Missense_Mutation | C | T | p.D1742N |
| WIL2NS_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 129280489 | 129280552 | 129280526 | 129280526 | Missense_Mutation | C | T | p.M1652I |
| MCC142_SKIN | 129280489 | 129280552 | 129280535 | 129280536 | Missense_Mutation | GG | AA | p.S1649F |
| CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 129285370 | 129285474 | 129285405 | 129285405 | Missense_Mutation | C | T | p.A1386T |
| KGN_OVARY | 129286335 | 129286447 | 129286364 | 129286364 | Missense_Mutation | G | A | p.H1353Y |
| HUPT3_PANCREAS | 129286335 | 129286447 | 129286364 | 129286364 | Missense_Mutation | G | A | p.H1353Y |
| NCIH1155_LUNG | 129286335 | 129286447 | 129286437 | 129286437 | Missense_Mutation | C | A | p.E1328D |
| NCIH2882_LUNG | 129291452 | 129291591 | 129291535 | 129291535 | Missense_Mutation | C | G | p.R998S |
| KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 129291452 | 129291591 | 129291548 | 129291548 | Missense_Mutation | G | A | p.A994V |
| NCIH1299_LUNG | 129293179 | 129293333 | 129293282 | 129293282 | Missense_Mutation | C | T | p.G861D |
| SBC5_LUNG | 129294312 | 129294405 | 129294341 | 129294341 | Missense_Mutation | C | T | p.R834Q |
| GI1_CENTRAL_NERVOUS_SYSTEM | 129294312 | 129294405 | 129294341 | 129294341 | Missense_Mutation | C | T | p.R834Q |
| LK2_LUNG | 129294312 | 129294405 | 129294341 | 129294341 | Missense_Mutation | C | T | p.R834Q |
| HEC1A_ENDOMETRIUM | 129294312 | 129294405 | 129294374 | 129294374 | Missense_Mutation | G | A | p.P823L |
| HEC1_ENDOMETRIUM | 129294312 | 129294405 | 129294374 | 129294374 | Missense_Mutation | G | A | p.P823L |
| GSS_STOMACH | 129294312 | 129294405 | 129294374 | 129294374 | Missense_Mutation | G | A | p.P823L |
| HEC1B_ENDOMETRIUM | 129294312 | 129294405 | 129294374 | 129294374 | Missense_Mutation | G | A | p.P823L |
| CAL51_BREAST | 129294312 | 129294405 | 129294398 | 129294398 | Missense_Mutation | G | A | p.T815M |
| SNU1040_LARGE_INTESTINE | 129303228 | 129303405 | 129303264 | 129303264 | Missense_Mutation | G | A | p.P665S |
| HEC151_ENDOMETRIUM | 129303228 | 129303405 | 129303270 | 129303270 | Missense_Mutation | G | T | p.L663I |
| OCILY12_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 129303228 | 129303405 | 129303339 | 129303339 | Missense_Mutation | C | T | p.G640R |
| 8305C_THYROID | 129303228 | 129303405 | 129303391 | 129303391 | Missense_Mutation | C | A | p.Q622H |
| NCIH510_LUNG | 129305015 | 129305115 | 129305021 | 129305021 | Missense_Mutation | T | A | p.E572V |
| JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 129305015 | 129305115 | 129305054 | 129305054 | Missense_Mutation | G | A | p.A561V |
| NCIH650_LUNG | 129305015 | 129305115 | 129305100 | 129305100 | Missense_Mutation | C | A | p.V546F |
| SNU324_PANCREAS | 129305431 | 129305562 | 129305439 | 129305439 | Missense_Mutation | A | G | p.S538P |
| NCIH630_LARGE_INTESTINE | 129303228 | 129303405 | 129303404 | 129303404 | Splice_Site | C | T | p.G618D |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PLXND1 |
| 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 PLXND1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PLXND1 |
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RelatedDrugs for PLXND1 |
| 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 PLXND1 |
| 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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