|
Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for NGEF |
Gene summary |
Gene information | Gene symbol | NGEF | Gene ID | 25791 |
Gene name | neuronal guanine nucleotide exchange factor | |
Synonyms | ARHGEF27|EPHEXIN | |
Cytomap | 2q37.1 | |
Type of gene | protein-coding | |
Description | ephexin-1eph-interacting exchange proteinephexin1 | |
Modification date | 20200313 | |
UniProtAcc | ||
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
Top |
Gene structures and expression levels for NGEF |
Skipped exons in the ROSMAP, MSBB, and Mayo 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. |
Differentially expressed gene analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
PG | DOWN | ENST00000424488.5 | NGEF-207:protein_coding:NGEF | 4.300950e+01 | -1.239643e+00 | 4.362283e-06 | 2.712475e-04 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for NGEF |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_123712 | chr2 | 232892898:232893050:232894756:232894916:232920284:232920585 | 232894756:232894916 |
exon_skip_168894 | chr2 | 232888033:232888107:232891358:232891487:232892898:232893050 | 232891358:232891487 |
exon_skip_170704 | chr2 | 232883981:232884144:232885280:232885369:232888033:232888107 | 232885280:232885369 |
exon_skip_252597 | chr2 | 232885323:232885369:232888033:232888107:232891358:232891487 | 232888033:232888107 |
Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
Top |
Open reading frame (ORF) annotation in the exon skipping event for NGEF |
Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000264051 | 232891358 | 232891487 | Frame-shift |
ENST00000264051 | 232885280 | 232885369 | In-frame |
ENST00000264051 | 232888033 | 232888107 | In-frame |
Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
ENST | Start of skipped exon | End of skipped exon | ORF |
ENST00000264051 | 232891358 | 232891487 | Frame-shift |
ENST00000264051 | 232894756 | 232894916 | Frame-shift |
ENST00000264051 | 232885280 | 232885369 | In-frame |
ENST00000264051 | 232888033 | 232888107 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for NGEF |
p-ENSG00000066248_img4.png |
Loci of skipped exons in ROSMAP 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 |
ENST00000264051 | 3232 | 710 | 232888033 | 232888107 | 1552 | 1625 | 424 | 448 |
ENST00000264051 | 3232 | 710 | 232885280 | 232885369 | 1627 | 1715 | 449 | 478 |
Loci of skipped exons in MSBB 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 Mayo 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 |
ENST00000264051 | 3232 | 710 | 232888033 | 232888107 | 1552 | 1625 | 424 | 448 |
ENST00000264051 | 3232 | 710 | 232885280 | 232885369 | 1627 | 1715 | 449 | 478 |
Lost protein functional features of individual exon skipping events in ROSMAP. |
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 |
Q8N5V2 | 424 | 448 | 331 | 710 | Alternative sequence | ID=VSP_020261;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q8N5V2 | 424 | 448 | 1 | 710 | Chain | ID=PRO_0000248388;Note=Ephexin-1 |
Q8N5V2 | 424 | 448 | 273 | 457 | Domain | Note=DH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00062 |
Q8N5V2 | 449 | 478 | 331 | 710 | Alternative sequence | ID=VSP_020261;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q8N5V2 | 449 | 478 | 1 | 710 | Chain | ID=PRO_0000248388;Note=Ephexin-1 |
Q8N5V2 | 449 | 478 | 273 | 457 | Domain | Note=DH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00062 |
Lost protein functional features of individual exon skipping events in MSBB. |
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 Mayo. |
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 |
Q8N5V2 | 424 | 448 | 331 | 710 | Alternative sequence | ID=VSP_020261;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q8N5V2 | 424 | 448 | 1 | 710 | Chain | ID=PRO_0000248388;Note=Ephexin-1 |
Q8N5V2 | 424 | 448 | 273 | 457 | Domain | Note=DH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00062 |
Q8N5V2 | 449 | 478 | 331 | 710 | Alternative sequence | ID=VSP_020261;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q8N5V2 | 449 | 478 | 1 | 710 | Chain | ID=PRO_0000248388;Note=Ephexin-1 |
Q8N5V2 | 449 | 478 | 273 | 457 | Domain | Note=DH;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00062 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in NGEF |
3'-UTR exon skipping evnets lost miRNA binding. |
Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
Top |
SNVs in the skipped exons for NGEF |
- Differential PSIs between mutated versus non-mutated samples. |
- Depth of Coverage in the skipped exon of the mutated samples. |
- Sashimi plot in the skipped exon of the mutated samples. |
- Non-synonymous mutations located in the skipped exons. |
Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
- 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 |
Top |
AD stage-associated exon skippint events for NGEF |
Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NGEF |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for NGEF |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for NGEF |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for NGEF |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |