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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 ARHGEF3 |
Gene summary |
Gene information | Gene symbol | ARHGEF3 | Gene ID | 50650 |
Gene name | Rho guanine nucleotide exchange factor 3 | |
Synonyms | GEF3|STA3|XPLN | |
Cytomap | 3p14.3 | |
Type of gene | protein-coding | |
Description | rho guanine nucleotide exchange factor 359.8 kDA proteinRho guanine nucleotide exchange factor (GEF) 3RhoGEF proteinexchange factor found in platelets and leukemic and neuronal tissues, XPLN | |
Modification date | 20200327 | |
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 |
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Gene structures and expression levels for ARHGEF3 |
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 | UP | ENST00000477833.5 | ARHGEF3-209:nonsense_mediated_decay:ARHGEF3 | 8.772105e-01 | 1.182622e+00 | 3.515268e-03 | 3.569296e-02 |
CB | UP | ENST00000495373.5 | ARHGEF3-212:protein_coding:ARHGEF3 | 5.242238e+01 | 8.992915e-01 | 9.139225e-09 | 2.782166e-07 |
CB | UP | ENST00000465659.5 | ARHGEF3-204:nonsense_mediated_decay:ARHGEF3 | 5.585580e+00 | 2.389487e+00 | 2.029257e-03 | 9.326334e-03 |
TC | UP | ENST00000477833.5 | ARHGEF3-209:nonsense_mediated_decay:ARHGEF3 | 1.103223e+00 | 1.404399e+00 | 8.611103e-04 | 8.802176e-03 |
TC | UP | ENST00000338458.8 | ARHGEF3-202:protein_coding:ARHGEF3 | 1.829568e+02 | 8.628464e-01 | 1.179593e-03 | 1.122441e-02 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for ARHGEF3 |
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_110076 | chr3 | 56755072:56755151:56773709:56773816:56801703:56801949 | 56773709:56773816 |
exon_skip_124456 | chr3 | 56745205:56745462:56751056:56751132:56751300:56751396 | 56751056:56751132 |
exon_skip_175749 | chr3 | 56958823:56958889:57007182:57007336:57035088:57035173 | 57007182:57007336 |
exon_skip_184867 | chr3 | 57007182:57007336:57035088:57035176:57079226:57079265 | 57035088:57035176 |
exon_skip_201867 | chr3 | 56729021:56729622:56732238:56732424:56737185:56737355 | 56732238:56732424 |
exon_skip_209073 | chr3 | 56958823:56958889:57007182:57007336:57035088:57035176 | 57007182:57007336 |
exon_skip_227123 | chr3 | 56745205:56745462:56751300:56751396:56753504:56753566 | 56751300:56751396 |
exon_skip_292243 | chr3 | 56958823:56958889:57035088:57035176:57079226:57079265 | 57035088:57035176 |
exon_skip_47975 | chr3 | 56958823:56958889:57035088:57035176:57076746:57076892 | 57035088:57035176 |
exon_skip_56088 | chr3 | 57035088:57035176:57076746:57076892:57079226:57079265 | 57076746:57076892 |
exon_skip_86690 | chr3 | 56958823:56958889:57035088:57035176:57079226:57079308 | 57035088:57035176 |
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 |
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Open reading frame (ORF) annotation in the exon skipping event for ARHGEF3 |
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 |
ENST00000296315 | 56732238 | 56732424 | Frame-shift |
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 |
ENST00000296315 | 56732238 | 56732424 | Frame-shift |
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 |
ENST00000296315 | 56732238 | 56732424 | Frame-shift |
ENST00000296315 | 56751056 | 56751132 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for ARHGEF3 |
p-ENSG00000163947_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 |
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 |
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 |
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 |
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3'-UTR located exon skipping events that lost miRNA binding sites in ARHGEF3 |
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 |
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SNVs in the skipped exons for ARHGEF3 |
- 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 |
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AD stage-associated exon skippint events for ARHGEF3 |
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 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ARHGEF3 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for ARHGEF3 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for ARHGEF3 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for ARHGEF3 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |