|
||||||
|
 | |
| |
| |
| |
| 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 SLIT2 |
 Gene summary |
| Gene information | Gene symbol | SLIT2 | Gene ID | 9353 |
| Gene name | slit guidance ligand 2 | |
| Synonyms | SLIL3|Slit-2 | |
| Cytomap | 4p15.31 | |
| Type of gene | protein-coding | |
| Description | slit homolog 2 protein | |
| Modification date | 20180523 | |
| UniProtAcc | O94813 | |
| Context | PubMed: SLIT2 [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 |
| SLIT2 | GO:0001933 | negative regulation of protein phosphorylation | 18345009 |
| SLIT2 | GO:0002689 | negative regulation of leukocyte chemotaxis | 11309622 |
| SLIT2 | GO:0007411 | axon guidance | 11748139 |
| SLIT2 | GO:0008045 | motor neuron axon guidance | 10102268 |
| SLIT2 | GO:0010593 | negative regulation of lamellipodium assembly | 16439689 |
| SLIT2 | GO:0010596 | negative regulation of endothelial cell migration | 18345009 |
| SLIT2 | GO:0014912 | negative regulation of smooth muscle cell migration | 16439689 |
| SLIT2 | GO:0021834 | chemorepulsion involved in embryonic olfactory bulb interneuron precursor migration | 11748139 |
| SLIT2 | GO:0021836 | chemorepulsion involved in postnatal olfactory bulb interneuron migration | 15207848 |
| SLIT2 | GO:0030336 | negative regulation of cell migration | 19005219 |
| SLIT2 | GO:0030837 | negative regulation of actin filament polymerization | 19759280 |
| SLIT2 | GO:0031290 | retinal ganglion cell axon guidance | 10864954|19498462 |
| SLIT2 | GO:0043116 | negative regulation of vascular permeability | 18345009 |
| SLIT2 | GO:0048754 | branching morphogenesis of an epithelial tube | 18345009 |
| SLIT2 | GO:0048846 | axon extension involved in axon guidance | 16840550 |
| SLIT2 | GO:0050919 | negative chemotaxis | 11748139 |
| SLIT2 | GO:0050929 | induction of negative chemotaxis | 10197527 |
| SLIT2 | GO:0051058 | negative regulation of small GTPase mediated signal transduction | 16439689 |
| SLIT2 | GO:0071504 | cellular response to heparin | 17062560 |
| SLIT2 | GO:0071672 | negative regulation of smooth muscle cell chemotaxis | 16439689 |
| SLIT2 | GO:0071676 | negative regulation of mononuclear cell migration | 16439689 |
| SLIT2 | GO:0090024 | negative regulation of neutrophil chemotaxis | 19759280 |
| SLIT2 | GO:0090260 | negative regulation of retinal ganglion cell axon guidance | 17062560 |
| SLIT2 | GO:0090288 | negative regulation of cellular response to growth factor stimulus | 16439689 |
Top |
Exon skipping events across known transcript of Ensembl for SLIT2 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 SLIT2 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for SLIT2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_422728 | 4 | 20270432:20270504:20469374:20469446:20482338:20482410 | 20469374:20469446 | ENSG00000145147.15 | ENST00000273739.5,ENST00000508824.1,ENST00000503837.1,ENST00000504154.1,ENST00000503823.1 |
| exon_skip_422729 | 4 | 20490441:20490605:20492425:20492437:20493383:20493522 | 20492425:20492437 | ENSG00000145147.15 | ENST00000273739.5,ENST00000503837.1 |
| exon_skip_422730 | 4 | 20512688:20512760:20521004:20521076:20525382:20525526 | 20521004:20521076 | ENSG00000145147.15 | ENST00000273739.5,ENST00000503837.1,ENST00000504154.1,ENST00000503823.1 |
| exon_skip_422731 | 4 | 20525636:20525800:20526771:20526795:20530571:20530722 | 20526771:20526795 | ENSG00000145147.15 | ENST00000273739.5,ENST00000504154.1 |
| exon_skip_422732 | 4 | 20547653:20547722:20550110:20550182:20550679:20550751 | 20550110:20550182 | ENSG00000145147.15 | ENST00000511508.1,ENST00000273739.5,ENST00000509394.2,ENST00000503837.1,ENST00000504154.1,ENST00000503823.1 |
| exon_skip_422733 | 4 | 20555427:20555591:20555930:20555963:20568884:20569009 | 20555930:20555963 | ENSG00000145147.15 | ENST00000511508.1 |
| exon_skip_422734 | 4 | 20570487:20570627:20574856:20574883:20591266:20591360 | 20574856:20574883 | ENSG00000145147.15 | ENST00000273739.5 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for SLIT2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_422728 | 4 | 20270432:20270504:20469374:20469446:20482338:20482410 | 20469374:20469446 | ENSG00000145147.15 | ENST00000503823.1,ENST00000504154.1,ENST00000273739.5,ENST00000503837.1,ENST00000508824.1 |
| exon_skip_422729 | 4 | 20490441:20490605:20492425:20492437:20493383:20493522 | 20492425:20492437 | ENSG00000145147.15 | ENST00000273739.5,ENST00000503837.1 |
| exon_skip_422730 | 4 | 20512688:20512760:20521004:20521076:20525382:20525526 | 20521004:20521076 | ENSG00000145147.15 | ENST00000503823.1,ENST00000504154.1,ENST00000273739.5,ENST00000503837.1 |
| exon_skip_422731 | 4 | 20525636:20525800:20526771:20526795:20530571:20530722 | 20526771:20526795 | ENSG00000145147.15 | ENST00000504154.1,ENST00000273739.5 |
| exon_skip_422732 | 4 | 20547653:20547722:20550110:20550182:20550679:20550751 | 20550110:20550182 | ENSG00000145147.15 | ENST00000503823.1,ENST00000504154.1,ENST00000273739.5,ENST00000503837.1,ENST00000509394.2,ENST00000511508.1 |
| exon_skip_422733 | 4 | 20555427:20555591:20555930:20555963:20568884:20569009 | 20555930:20555963 | ENSG00000145147.15 | ENST00000511508.1 |
| exon_skip_422734 | 4 | 20570487:20570627:20574856:20574883:20591266:20591360 | 20574856:20574883 | ENSG00000145147.15 | ENST00000273739.5 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for SLIT2 |
| 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 |
| ENST00000504154 | 20469374 | 20469446 | In-frame |
| ENST00000504154 | 20521004 | 20521076 | In-frame |
| ENST00000504154 | 20526771 | 20526795 | In-frame |
| ENST00000504154 | 20550110 | 20550182 | 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 |
| ENST00000504154 | 20469374 | 20469446 | In-frame |
| ENST00000504154 | 20521004 | 20521076 | In-frame |
| ENST00000504154 | 20526771 | 20526795 | In-frame |
| ENST00000504154 | 20550110 | 20550182 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for SLIT2 |
| 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 |
| ENST00000504154 | 6407 | 1529 | 20469374 | 20469446 | 648 | 719 | 132 | 155 |
| ENST00000504154 | 6407 | 1529 | 20521004 | 20521076 | 1311 | 1382 | 353 | 376 |
| ENST00000504154 | 6407 | 1529 | 20550110 | 20550182 | 2598 | 2669 | 782 | 805 |
| 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 |
| ENST00000504154 | 6407 | 1529 | 20469374 | 20469446 | 648 | 719 | 132 | 155 |
| ENST00000504154 | 6407 | 1529 | 20521004 | 20521076 | 1311 | 1382 | 353 | 376 |
| ENST00000504154 | 6407 | 1529 | 20550110 | 20550182 | 2598 | 2669 | 782 | 805 |
| 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 |
| O94813 | 132 | 155 | 31 | 1529 | Chain | ID=PRO_0000007725;Note=Slit homolog 2 protein |
| O94813 | 132 | 155 | 31 | 1121 | Chain | ID=PRO_0000007726;Note=Slit homolog 2 protein N-product |
| O94813 | 132 | 155 | 128 | 149 | Repeat | Note=LRR 4 |
| O94813 | 132 | 155 | 152 | 173 | Repeat | Note=LRR 5 |
| O94813 | 353 | 376 | 352 | 354 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2V9T |
| O94813 | 353 | 376 | 376 | 378 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2V9T |
| O94813 | 353 | 376 | 31 | 1529 | Chain | ID=PRO_0000007725;Note=Slit homolog 2 protein |
| O94813 | 353 | 376 | 31 | 1121 | Chain | ID=PRO_0000007726;Note=Slit homolog 2 protein N-product |
| O94813 | 353 | 376 | 349 | 370 | Repeat | Note=LRR 9 |
| O94813 | 353 | 376 | 373 | 394 | Repeat | Note=LRR 10 |
| O94813 | 353 | 376 | 365 | 370 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2V9T |
| O94813 | 782 | 805 | 781 | 783 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2WFH |
| O94813 | 782 | 805 | 805 | 807 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2WFH |
| O94813 | 782 | 805 | 31 | 1529 | Chain | ID=PRO_0000007725;Note=Slit homolog 2 protein |
| O94813 | 782 | 805 | 31 | 1121 | Chain | ID=PRO_0000007726;Note=Slit homolog 2 protein N-product |
| O94813 | 782 | 805 | 794 | 794 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O94813 | 782 | 805 | 799 | 799 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O94813 | 782 | 805 | 778 | 799 | Repeat | Note=LRR 18 |
| O94813 | 782 | 805 | 802 | 823 | Repeat | Note=LRR 19 |
| O94813 | 782 | 805 | 794 | 799 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2WFH |
| 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 |
| O94813 | 132 | 155 | 31 | 1529 | Chain | ID=PRO_0000007725;Note=Slit homolog 2 protein |
| O94813 | 132 | 155 | 31 | 1121 | Chain | ID=PRO_0000007726;Note=Slit homolog 2 protein N-product |
| O94813 | 132 | 155 | 128 | 149 | Repeat | Note=LRR 4 |
| O94813 | 132 | 155 | 152 | 173 | Repeat | Note=LRR 5 |
| O94813 | 353 | 376 | 352 | 354 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2V9T |
| O94813 | 353 | 376 | 376 | 378 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2V9T |
| O94813 | 353 | 376 | 31 | 1529 | Chain | ID=PRO_0000007725;Note=Slit homolog 2 protein |
| O94813 | 353 | 376 | 31 | 1121 | Chain | ID=PRO_0000007726;Note=Slit homolog 2 protein N-product |
| O94813 | 353 | 376 | 349 | 370 | Repeat | Note=LRR 9 |
| O94813 | 353 | 376 | 373 | 394 | Repeat | Note=LRR 10 |
| O94813 | 353 | 376 | 365 | 370 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2V9T |
| O94813 | 782 | 805 | 781 | 783 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2WFH |
| O94813 | 782 | 805 | 805 | 807 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2WFH |
| O94813 | 782 | 805 | 31 | 1529 | Chain | ID=PRO_0000007725;Note=Slit homolog 2 protein |
| O94813 | 782 | 805 | 31 | 1121 | Chain | ID=PRO_0000007726;Note=Slit homolog 2 protein N-product |
| O94813 | 782 | 805 | 794 | 794 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O94813 | 782 | 805 | 799 | 799 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O94813 | 782 | 805 | 778 | 799 | Repeat | Note=LRR 18 |
| O94813 | 782 | 805 | 802 | 823 | Repeat | Note=LRR 19 |
| O94813 | 782 | 805 | 794 | 799 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2WFH |
Top |
SNVs in the skipped exons for SLIT2 |
| - 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-A39Y-01 | exon_skip_422728 | 20469375 | 20469446 | 20469392 | 20469392 | Frame_Shift_Del | A | - | p.Q138fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_422728 | 20469375 | 20469446 | 20469405 | 20469405 | Frame_Shift_Del | C | - | p.I142fs |
| STAD | TCGA-BR-4361-01 | exon_skip_422728 | 20469375 | 20469446 | 20469438 | 20469438 | Frame_Shift_Del | A | - | p.I153fs |
| LUAD | TCGA-64-5778-01 | exon_skip_422732 | 20550111 | 20550182 | 20550132 | 20550132 | Frame_Shift_Del | A | - | p.I789fs |
| COAD | TCGA-G4-6586-01 | exon_skip_422728 | 20469375 | 20469446 | 20469448 | 20469448 | Splice_Site | T | C | . |
| - 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 |
| HCC2450_LUNG | 20469375 | 20469446 | 20469414 | 20469414 | Missense_Mutation | A | T | p.K145N |
| CORL23_LUNG | 20521005 | 20521076 | 20521060 | 20521060 | Missense_Mutation | T | C | p.F372L |
| SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 20526772 | 20526795 | 20526781 | 20526781 | Missense_Mutation | A | G | p.Q483R |
| SNUC5_LARGE_INTESTINE | 20550111 | 20550182 | 20550158 | 20550158 | Missense_Mutation | G | A | p.S798N |
| CAL51_BREAST | 20521005 | 20521076 | 20521030 | 20521030 | Nonsense_Mutation | G | T | p.E362* |
| MM386_SKIN | 20550111 | 20550182 | 20550112 | 20550112 | Splice_Site | G | A | p.D783N |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLIT2 |
| 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 SLIT2 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SLIT2 |
Top |
RelatedDrugs for SLIT2 |
| 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 SLIT2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| SLIT2 | C0014556 | Epilepsy, Temporal Lobe | 1 | CTD_human |
| SLIT2 | C0149925 | Small cell carcinoma of lung | 1 | CTD_human |
| SLIT2 | C2239176 | Liver carcinoma | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|