|
||||||
|
 | |
| |
| |
| |
| 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 LEFTY2 |
 Gene summary |
| Gene information | Gene symbol | LEFTY2 | Gene ID | 7044 |
| Gene name | left-right determination factor 2 | |
| Synonyms | EBAF|LEFTA|LEFTYA|TGFB4 | |
| Cytomap | 1q42.12 | |
| Type of gene | protein-coding | |
| Description | left-right determination factor 2TGF-beta-4endometrial bleeding-associated factorleft-right determination factor Aprotein lefty-2protein lefty-Atransforming growth factor beta-4 | |
| Modification date | 20180523 | |
| UniProtAcc | O00292 | |
| Context | PubMed: LEFTY2 [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 |
Top |
Exon skipping events across known transcript of Ensembl for LEFTY2 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 LEFTY2 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for LEFTY2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_37607 | 1 | 226124303:226125504:226127060:226127300:226127455:226127571 | 226127060:226127300 | ENSG00000143768.7 | ENST00000420304.2,ENST00000366820.5 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for LEFTY2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_37607 | 1 | 226124303:226125504:226127060:226127300:226127455:226127571 | 226127060:226127300 | ENSG00000143768.7 | ENST00000420304.2,ENST00000366820.5 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for LEFTY2 |
| 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 |
| ENST00000366820 | 226127060 | 226127300 | 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 |
| ENST00000366820 | 226127060 | 226127300 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for LEFTY2 |
| 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 |
| ENST00000366820 | 2304 | 366 | 226127060 | 226127300 | 847 | 1086 | 166 | 245 |
| 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 |
| ENST00000366820 | 2304 | 366 | 226127060 | 226127300 | 847 | 1086 | 166 | 245 |
| 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 |
| O00292 | 166 | 245 | 77 | 366 | Chain | ID=PRO_0000033807;Note=Left-right determination factor 2 |
| O00292 | 166 | 245 | 183 | 183 | Sequence conflict | Note=A->P;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| 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 |
| O00292 | 166 | 245 | 77 | 366 | Chain | ID=PRO_0000033807;Note=Left-right determination factor 2 |
| O00292 | 166 | 245 | 183 | 183 | Sequence conflict | Note=A->P;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Top |
SNVs in the skipped exons for LEFTY2 |
| - 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_37607 | 226127061 | 226127300 | 226127291 | 226127291 | Frame_Shift_Del | G | - | p.S169fs |
| SKCM | TCGA-BF-AAP7-01 | exon_skip_37607 | 226127061 | 226127300 | 226127273 | 226127273 | Nonsense_Mutation | C | T | p.W175* |
| COAD | TCGA-AD-6889-01 | exon_skip_37607 | 226127061 | 226127300 | 226127302 | 226127302 | 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 |
| CGTHW1_THYROID | 226127061 | 226127300 | 226127214 | 226127215 | Frame_Shift_Ins | - | G | p.Q195fs |
| SUDHL8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 226127061 | 226127300 | 226127110 | 226127110 | Missense_Mutation | G | A | p.L230F |
| KATOIII_STOMACH | 226127061 | 226127300 | 226127122 | 226127122 | Missense_Mutation | C | G | p.A226P |
| HEC151_ENDOMETRIUM | 226127061 | 226127300 | 226127155 | 226127155 | Missense_Mutation | C | T | p.A215T |
| MC1010_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 226127061 | 226127300 | 226127198 | 226127198 | Missense_Mutation | C | G | p.Q200H |
| SNU1040_LARGE_INTESTINE | 226127061 | 226127300 | 226127213 | 226127213 | Missense_Mutation | C | A | p.Q195H |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LEFTY2 |
| 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 LEFTY2 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LEFTY2 |
Top |
RelatedDrugs for LEFTY2 |
| 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 LEFTY2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| LEFTY2 | C3178805 | Heterotaxy Syndrome | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|