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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 PLXNC1 |
 Gene summary |
| Gene information | Gene symbol | PLXNC1 | Gene ID | 10154 |
| Gene name | plexin C1 | |
| Synonyms | CD232|PLXN-C1|VESPR | |
| Cytomap | 12q22 | |
| Type of gene | protein-coding | |
| Description | plexin-C1plexin (semaphorin receptor)receptor for viral semaphorin proteinreceptor for virally-encoded semaphorinvirus-encoded semaphorin protein receptor | |
| Modification date | 20180523 | |
| UniProtAcc | O60486 | |
| Context | PubMed: PLXNC1 [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 PLXNC1 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 PLXNC1 |
| 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 PLXNC1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_85825 | 12 | 94562928:94563069:94575221:94575356:94580148:94580249 | 94575221:94575356 | ENSG00000136040.4 | ENST00000258526.4,ENST00000551850.1,ENST00000546733.1 |
| exon_skip_85826 | 12 | 94575221:94575356:94580148:94580249:94603365:94603405 | 94580148:94580249 | ENSG00000136040.4 | ENST00000258526.4,ENST00000551850.1 |
| exon_skip_85827 | 12 | 94580148:94580249:94603365:94603480:94613791:94613939 | 94603365:94603480 | ENSG00000136040.4 | ENST00000258526.4 |
| exon_skip_85829 | 12 | 94648968:94649072:94653112:94653151:94653385:94653467 | 94653112:94653151 | ENSG00000136040.4 | ENST00000258526.4,ENST00000547057.1,ENST00000549217.1 |
| exon_skip_85831 | 12 | 94688261:94688316:94690964:94690996:94691091:94691199 | 94690964:94690996 | ENSG00000136040.4 | ENST00000545312.1,ENST00000258526.4,ENST00000547057.1,ENST00000549217.1 |
| exon_skip_85832 | 12 | 94691091:94691199:94692407:94692571:94694685:94694833 | 94692407:94692571 | ENSG00000136040.4 | ENST00000545312.1,ENST00000258526.4,ENST00000547057.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PLXNC1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_85825 | 12 | 94562928:94563069:94575221:94575356:94580148:94580249 | 94575221:94575356 | ENSG00000136040.4 | ENST00000258526.4,ENST00000546733.1,ENST00000551850.1 |
| exon_skip_85826 | 12 | 94575221:94575356:94580148:94580249:94603365:94603405 | 94580148:94580249 | ENSG00000136040.4 | ENST00000258526.4,ENST00000551850.1 |
| exon_skip_85827 | 12 | 94580148:94580249:94603365:94603480:94613791:94613939 | 94603365:94603480 | ENSG00000136040.4 | ENST00000258526.4 |
| exon_skip_85829 | 12 | 94648968:94649072:94653112:94653151:94653385:94653467 | 94653112:94653151 | ENSG00000136040.4 | ENST00000258526.4,ENST00000549217.1,ENST00000547057.1 |
| exon_skip_85831 | 12 | 94688261:94688316:94690964:94690996:94691091:94691199 | 94690964:94690996 | ENSG00000136040.4 | ENST00000258526.4,ENST00000549217.1,ENST00000547057.1,ENST00000545312.1 |
| exon_skip_85832 | 12 | 94691091:94691199:94692407:94692571:94694685:94694833 | 94692407:94692571 | ENSG00000136040.4 | ENST00000258526.4,ENST00000547057.1,ENST00000545312.1 |
| 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 PLXNC1 |
| 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 |
| ENST00000258526 | 94580148 | 94580249 | Frame-shift |
| ENST00000258526 | 94603365 | 94603480 | Frame-shift |
| ENST00000258526 | 94690964 | 94690996 | Frame-shift |
| ENST00000258526 | 94692407 | 94692571 | Frame-shift |
| ENST00000258526 | 94575221 | 94575356 | In-frame |
| ENST00000258526 | 94653112 | 94653151 | 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 |
| ENST00000258526 | 94580148 | 94580249 | Frame-shift |
| ENST00000258526 | 94603365 | 94603480 | Frame-shift |
| ENST00000258526 | 94690964 | 94690996 | Frame-shift |
| ENST00000258526 | 94692407 | 94692571 | Frame-shift |
| ENST00000258526 | 94575221 | 94575356 | In-frame |
| ENST00000258526 | 94653112 | 94653151 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PLXNC1 |
| 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 |
| ENST00000258526 | 7363 | 1568 | 94575221 | 94575356 | 1453 | 1587 | 401 | 446 |
| ENST00000258526 | 7363 | 1568 | 94653112 | 94653151 | 3337 | 3375 | 1029 | 1042 |
| 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 |
| ENST00000258526 | 7363 | 1568 | 94575221 | 94575356 | 1453 | 1587 | 401 | 446 |
| ENST00000258526 | 7363 | 1568 | 94653112 | 94653151 | 3337 | 3375 | 1029 | 1042 |
| 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 |
| O60486 | 401 | 446 | 397 | 403 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NVN |
| O60486 | 401 | 446 | 414 | 418 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NVN |
| O60486 | 401 | 446 | 438 | 443 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NVN |
| O60486 | 401 | 446 | 446 | 452 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NVN |
| O60486 | 401 | 446 | 35 | 1568 | Chain | ID=PRO_0000232749;Note=Plexin-C1 |
| O60486 | 401 | 446 | 35 | 452 | Domain | Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00352 |
| O60486 | 401 | 446 | 407 | 407 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20727575;Dbxref=PMID:20727575 |
| O60486 | 401 | 446 | 35 | 944 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O60486 | 1029 | 1042 | 35 | 1568 | Chain | ID=PRO_0000232749;Note=Plexin-C1 |
| O60486 | 1029 | 1042 | 966 | 1568 | 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 |
| O60486 | 401 | 446 | 397 | 403 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NVN |
| O60486 | 401 | 446 | 414 | 418 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NVN |
| O60486 | 401 | 446 | 438 | 443 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NVN |
| O60486 | 401 | 446 | 446 | 452 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3NVN |
| O60486 | 401 | 446 | 35 | 1568 | Chain | ID=PRO_0000232749;Note=Plexin-C1 |
| O60486 | 401 | 446 | 35 | 452 | Domain | Note=Sema;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00352 |
| O60486 | 401 | 446 | 407 | 407 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20727575;Dbxref=PMID:20727575 |
| O60486 | 401 | 446 | 35 | 944 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O60486 | 1029 | 1042 | 35 | 1568 | Chain | ID=PRO_0000232749;Note=Plexin-C1 |
| O60486 | 1029 | 1042 | 966 | 1568 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for PLXNC1 |
| - 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. |
PLXNC1_SKCM_exon_skip_85832_psi_boxplot.png |
| - 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-A39Y-01 | exon_skip_85825 | 94575222 | 94575356 | 94575262 | 94575262 | Frame_Shift_Del | T | - | p.V415fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_85832 | 94692408 | 94692571 | 94692430 | 94692430 | Frame_Shift_Del | A | - | p.E1366fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_85832 | 94692408 | 94692571 | 94692430 | 94692430 | Frame_Shift_Del | A | - | p.E1366fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_85832 | 94692408 | 94692571 | 94692436 | 94692436 | Frame_Shift_Del | T | - | p.L1368fs |
| LUSC | TCGA-60-2698-01 | exon_skip_85825 | 94575222 | 94575356 | 94575247 | 94575247 | Nonsense_Mutation | C | G | p.S410* |
| STAD | TCGA-BR-4361-01 | exon_skip_85826 | 94580149 | 94580249 | 94580155 | 94580155 | Nonsense_Mutation | A | T | p.R449* |
| STAD | TCGA-BR-8683-01 | exon_skip_85827 | 94603366 | 94603480 | 94603463 | 94603463 | Nonsense_Mutation | C | T | p.R513* |
| UCEC | TCGA-A5-A0GP-01 | exon_skip_85827 | 94603366 | 94603480 | 94603463 | 94603463 | Nonsense_Mutation | C | T | p.R513* |
| SKCM | TCGA-GN-A4U4-06 | exon_skip_85832 | 94692408 | 94692571 | 94692559 | 94692559 | Nonsense_Mutation | G | A | p.W1409* |
| COAD | TCGA-D5-6536-01 | exon_skip_85825 | 94575222 | 94575356 | 94575221 | 94575221 | Splice_Site | G | T | . |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-GN-A4U4-06 |
| Cancer type: SKCM | |
| ESID: exon_skip_85832 | |
| Skipped exon start: 94692408 | |
| Skipped exon end: 94692571 | |
| Mutation start: 94692559 | |
| Mutation end: 94692559 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: A | |
| AAchange: p.W1409* | |
exon_skip_85832_SKCM_TCGA-GN-A4U4-06.png | |
| - 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 |
| DOV13_OVARY | 94692408 | 94692571 | 94692525 | 94692525 | Frame_Shift_Del | A | - | p.K1399fs |
| SW1573_LUNG | 94575222 | 94575356 | 94575242 | 94575242 | Missense_Mutation | G | C | p.L408F |
| HCC1143_MATCHED_NORMAL_TISSUE | 94575222 | 94575356 | 94575296 | 94575296 | Missense_Mutation | C | G | p.F426L |
| KASUMI1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 94575222 | 94575356 | 94575324 | 94575324 | Missense_Mutation | A | G | p.N436D |
| HEC251_ENDOMETRIUM | 94580149 | 94580249 | 94580161 | 94580161 | Missense_Mutation | C | T | p.R451C |
| DU4475_BREAST | 94580149 | 94580249 | 94580171 | 94580171 | Missense_Mutation | A | C | p.N454T |
| H4_CENTRAL_NERVOUS_SYSTEM | 94580149 | 94580249 | 94580236 | 94580236 | Missense_Mutation | C | T | p.H476Y |
| BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 94603366 | 94603480 | 94603376 | 94603376 | Missense_Mutation | C | A | p.Q484K |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PLXNC1 |
| 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 PLXNC1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PLXNC1 |
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RelatedDrugs for PLXNC1 |
| 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 PLXNC1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PLXNC1 | C0014175 | Endometriosis | 1 | CTD_human |
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