|
||||||
|
 | |
| |
| |
| |
| 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 SEMA4D |
 Gene summary |
| Gene information | Gene symbol | SEMA4D | Gene ID | 10507 |
| Gene name | semaphorin 4D | |
| Synonyms | C9orf164|CD100|COLL4|M-sema-G|SEMAJ|coll-4 | |
| Cytomap | 9q22.2 | |
| Type of gene | protein-coding | |
| Description | semaphorin-4DA8BB18GR3sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Dsema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, 4D | |
| Modification date | 20180527 | |
| UniProtAcc | Q92854 | |
| Context | PubMed: SEMA4D [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 |
| SEMA4D | GO:0001934 | positive regulation of protein phosphorylation | 16055703 |
| SEMA4D | GO:0007162 | negative regulation of cell adhesion | 15218527 |
| SEMA4D | GO:0030335 | positive regulation of cell migration | 16055703 |
| SEMA4D | GO:0071526 | semaphorin-plexin signaling pathway | 15218527 |
Top |
Exon skipping events across known transcript of Ensembl for SEMA4D 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 SEMA4D |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for SEMA4D |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_504854 | 9 | 91978655:91978865:91991747:91991966:91995969:91996013 | 91991747:91991966 | ENSG00000187764.7 | ENST00000420987.1,ENST00000455551.2,ENST00000339861.4,ENST00000343780.4 |
| exon_skip_504859 | 9 | 91991747:91991966:91995969:91996013:91996088:91996261 | 91995969:91996013 | ENSG00000187764.7 | ENST00000420987.1,ENST00000455551.2,ENST00000339861.4,ENST00000343780.4 |
| exon_skip_504864 | 9 | 91995970:91996013:91996088:91996261:92001281:92001397 | 91996088:91996261 | ENSG00000187764.7 | ENST00000420987.1,ENST00000450295.1,ENST00000455551.2,ENST00000356444.2,ENST00000438547.2,ENST00000339861.4,ENST00000422704.2,ENST00000544513.1,ENST00000343780.4 |
| exon_skip_504866 | 9 | 92002300:92002523:92003550:92003707:92003786:92003962 | 92003550:92003707 | ENSG00000187764.7 | ENST00000420987.1,ENST00000450295.1,ENST00000455551.2,ENST00000356444.2,ENST00000429836.1,ENST00000438547.2,ENST00000339861.4,ENST00000422704.2,ENST00000343780.4,ENST00000537934.1 |
| exon_skip_504867 | 9 | 92014190:92014253:92017785:92017931:92020265:92020614 | 92017785:92017931 | ENSG00000187764.7 | ENST00000420987.1,ENST00000450295.1,ENST00000455551.2,ENST00000356444.2,ENST00000429836.1,ENST00000438547.2,ENST00000339861.4,ENST00000420681.2,ENST00000422704.2,ENST00000343780.4,ENST00000537934.1 |
| exon_skip_504868 | 9 | 92020516:92020614:92032970:92033033:92051236:92051378 | 92032970:92033033 | ENSG00000187764.7 | ENST00000420681.2 |
| exon_skip_504870 | 9 | 92020516:92020614:92032970:92033033:92070802:92070868 | 92032970:92033033 | ENSG00000187764.7 | ENST00000455551.2,ENST00000429836.1,ENST00000420670.1 |
| exon_skip_504872 | 9 | 92032970:92033033:92033277:92033352:92051236:92051378 | 92033277:92033352 | ENSG00000187764.7 | ENST00000482128.1 |
| exon_skip_504875 | 9 | 92032970:92033033:92033277:92033352:92070802:92070868 | 92033277:92033352 | ENSG00000187764.7 | ENST00000420987.1,ENST00000356444.2,ENST00000438547.2,ENST00000343780.4,ENST00000537934.1 |
| exon_skip_504877 | 9 | 92032970:92033033:92070802:92070868:92112833:92112953 | 92070802:92070868 | ENSG00000187764.7 | ENST00000455551.2 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for SEMA4D |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_504854 | 9 | 91978655:91978865:91991747:91991966:91995969:91996013 | 91991747:91991966 | ENSG00000187764.7 | ENST00000339861.4,ENST00000420987.1,ENST00000455551.2,ENST00000343780.4 |
| exon_skip_504859 | 9 | 91991747:91991966:91995969:91996013:91996088:91996261 | 91995969:91996013 | ENSG00000187764.7 | ENST00000339861.4,ENST00000420987.1,ENST00000455551.2,ENST00000343780.4 |
| exon_skip_504864 | 9 | 91995970:91996013:91996088:91996261:92001281:92001397 | 91996088:91996261 | ENSG00000187764.7 | ENST00000339861.4,ENST00000420987.1,ENST00000455551.2,ENST00000343780.4,ENST00000450295.1,ENST00000438547.2,ENST00000356444.2,ENST00000422704.2,ENST00000544513.1 |
| exon_skip_504866 | 9 | 92002300:92002523:92003550:92003707:92003786:92003962 | 92003550:92003707 | ENSG00000187764.7 | ENST00000339861.4,ENST00000420987.1,ENST00000455551.2,ENST00000429836.1,ENST00000537934.1,ENST00000343780.4,ENST00000450295.1,ENST00000438547.2,ENST00000356444.2,ENST00000422704.2 |
| exon_skip_504867 | 9 | 92014190:92014253:92017785:92017931:92020265:92020614 | 92017785:92017931 | ENSG00000187764.7 | ENST00000339861.4,ENST00000420987.1,ENST00000455551.2,ENST00000429836.1,ENST00000537934.1,ENST00000343780.4,ENST00000450295.1,ENST00000438547.2,ENST00000356444.2,ENST00000422704.2,ENST00000420681.2 |
| exon_skip_504868 | 9 | 92020516:92020614:92032970:92033033:92051236:92051378 | 92032970:92033033 | ENSG00000187764.7 | ENST00000420681.2 |
| exon_skip_504870 | 9 | 92020516:92020614:92032970:92033033:92070802:92070868 | 92032970:92033033 | ENSG00000187764.7 | ENST00000455551.2,ENST00000429836.1,ENST00000420670.1 |
| exon_skip_504872 | 9 | 92032970:92033033:92033277:92033352:92051236:92051378 | 92033277:92033352 | ENSG00000187764.7 | ENST00000482128.1 |
| exon_skip_504875 | 9 | 92032970:92033033:92033277:92033352:92070802:92070868 | 92033277:92033352 | ENSG00000187764.7 | ENST00000420987.1,ENST00000537934.1,ENST00000343780.4,ENST00000438547.2,ENST00000356444.2 |
| exon_skip_504877 | 9 | 92032970:92033033:92070802:92070868:92112833:92112953 | 92070802:92070868 | ENSG00000187764.7 | ENST00000455551.2 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for SEMA4D |
| 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 |
| ENST00000356444 | 92033277 | 92033352 | 3UTR-3UTR |
| ENST00000438547 | 92033277 | 92033352 | 3UTR-3UTR |
| ENST00000356444 | 91996088 | 91996261 | Frame-shift |
| ENST00000422704 | 91996088 | 91996261 | Frame-shift |
| ENST00000438547 | 91996088 | 91996261 | Frame-shift |
| ENST00000450295 | 91996088 | 91996261 | Frame-shift |
| ENST00000356444 | 92003550 | 92003707 | Frame-shift |
| ENST00000422704 | 92003550 | 92003707 | Frame-shift |
| ENST00000438547 | 92003550 | 92003707 | Frame-shift |
| ENST00000450295 | 92003550 | 92003707 | Frame-shift |
| ENST00000356444 | 92017785 | 92017931 | Frame-shift |
| ENST00000422704 | 92017785 | 92017931 | Frame-shift |
| ENST00000438547 | 92017785 | 92017931 | Frame-shift |
| ENST00000450295 | 92017785 | 92017931 | Frame-shift |
| 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 |
| ENST00000356444 | 92033277 | 92033352 | 3UTR-3UTR |
| ENST00000438547 | 92033277 | 92033352 | 3UTR-3UTR |
| ENST00000356444 | 91996088 | 91996261 | Frame-shift |
| ENST00000422704 | 91996088 | 91996261 | Frame-shift |
| ENST00000438547 | 91996088 | 91996261 | Frame-shift |
| ENST00000450295 | 91996088 | 91996261 | Frame-shift |
| ENST00000356444 | 92003550 | 92003707 | Frame-shift |
| ENST00000422704 | 92003550 | 92003707 | Frame-shift |
| ENST00000438547 | 92003550 | 92003707 | Frame-shift |
| ENST00000450295 | 92003550 | 92003707 | Frame-shift |
| ENST00000356444 | 92017785 | 92017931 | Frame-shift |
| ENST00000422704 | 92017785 | 92017931 | Frame-shift |
| ENST00000438547 | 92017785 | 92017931 | Frame-shift |
| ENST00000450295 | 92017785 | 92017931 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for SEMA4D |
| 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 |
| 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 |
| 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 SEMA4D |
| - 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-G3-A3CJ-01 | exon_skip_504867 | 92017786 | 92017931 | 92017839 | 92017839 | Frame_Shift_Del | G | - | p.R67fs |
| BRCA | TCGA-A2-A04P-01 | exon_skip_504867 | 92017786 | 92017931 | 92017794 | 92017794 | Nonsense_Mutation | G | A | p.Q82* |
| - 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 |
| MM415_SKIN | 91995970 | 91996013 | 91995991 | 91995991 | Missense_Mutation | C | T | p.G548S |
| SU8686_PANCREAS | 91996089 | 91996261 | 91996095 | 91996095 | Missense_Mutation | G | C | p.P538R |
| OVK18_OVARY | 91996089 | 91996261 | 91996117 | 91996117 | Missense_Mutation | C | A | p.A531S |
| OVK18_OVARY | 91996089 | 91996261 | 91996117 | 91996118 | Missense_Mutation | CC | AA | p.A531S |
| JHH7_LIVER | 91996089 | 91996261 | 91996126 | 91996126 | Missense_Mutation | T | C | p.T528A |
| 647V_URINARY_TRACT | 91996089 | 91996261 | 91996153 | 91996153 | Missense_Mutation | A | T | p.Y519N |
| IALM_LUNG | 92003551 | 92003707 | 92003588 | 92003588 | Missense_Mutation | C | T | p.R357H |
| LS411N_LARGE_INTESTINE | 92003551 | 92003707 | 92003658 | 92003658 | Missense_Mutation | C | T | p.E334K |
| SNU886_LIVER | 92003551 | 92003707 | 92003690 | 92003690 | Missense_Mutation | G | A | p.S323L |
| DU145_PROSTATE | 92017786 | 92017931 | 92017845 | 92017845 | Missense_Mutation | C | A | p.G65C |
| NCIH716_LARGE_INTESTINE | 92017786 | 92017931 | 92017874 | 92017874 | Missense_Mutation | A | G | p.L55P |
| EN_ENDOMETRIUM | 92017786 | 92017931 | 92017913 | 92017913 | Missense_Mutation | A | G | p.F42S |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SEMA4D |
| 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 SEMA4D |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SEMA4D |
Top |
RelatedDrugs for SEMA4D |
| 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 SEMA4D |
| 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)
|