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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for RAPGEF2 |
 Gene summary |
| Gene information | Gene symbol | RAPGEF2 | Gene ID | 9693 |
| Gene name | Rap guanine nucleotide exchange factor 2 | |
| Synonyms | CNrasGEF|NRAPGEP|PDZ-GEF1|PDZGEF1|RA-GEF|RA-GEF-1|RAGEF|Rap-GEP|nRap GEP | |
| Cytomap | 4q32.1 | |
| Type of gene | protein-coding | |
| Description | rap guanine nucleotide exchange factor 2PDZ domain containing guanine nucleotide exchange factor (GEF) 1PDZ domain-containing guanine nucleotide exchange factor 1RA(Ras/Rap1A-associating)-GEFRap guanine nucleotide exchange factor (GEF) 2cyclic nucleo | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context | - 27878761(Genome-Wide Association Analysis of the Sense of Smell in U.S. Older Adults: Identification of Novel Risk Loci in African-Americans and European-Americans) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| RAPGEF2 | GO:0007186 | G protein-coupled receptor signaling pathway | 23800469 |
| RAPGEF2 | GO:0007218 | neuropeptide signaling pathway | 23800469 |
| RAPGEF2 | GO:0008285 | negative regulation of cell proliferation | 16272156 |
| RAPGEF2 | GO:0019933 | cAMP-mediated signaling | 23800469 |
| RAPGEF2 | GO:0031175 | neuron projection development | 23800469 |
| RAPGEF2 | GO:0043547 | positive regulation of GTPase activity | 10548487|10608844|10801446|11359771|16272156|17724123|23800469 |
| RAPGEF2 | GO:0043950 | positive regulation of cAMP-mediated signaling | 12391161 |
| RAPGEF2 | GO:0045860 | positive regulation of protein kinase activity | 11359771|23800469 |
| RAPGEF2 | GO:0050774 | negative regulation of dendrite morphogenesis | 16272156 |
| RAPGEF2 | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 16272156|23800469 |
| RAPGEF2 | GO:0071320 | cellular response to cAMP | 10801446|16272156|21840392|23800469 |
| RAPGEF2 | GO:0071321 | cellular response to cGMP | 10801446 |
| RAPGEF2 | GO:0071880 | adenylate cyclase-activating adrenergic receptor signaling pathway | 12391161 |
| RAPGEF2 | GO:2000481 | positive regulation of cAMP-dependent protein kinase activity | 16272156 |
| RAPGEF2 | GO:2000670 | positive regulation of dendritic cell apoptotic process | 16272156 |
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Gene structures and expression levels for RAPGEF2 |
| 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. |
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ENSG00000109756
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000504604.5 | RAPGEF2-204:lncRNA:RAPGEF2 | 4.580195e+00 | 8.115113e-01 | 1.009631e-02 | 3.503911e-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 RAPGEF2 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_119390 | chr4 | 159186642:159186712:159193200:159193256:159210500:159210583 | 159193200:159193256 |
| exon_skip_141492 | chr4 | 159267737:159268215:159304342:159304473:159314591:159314768 | 159304342:159304473 |
| exon_skip_176682 | chr4 | 159350228:159350289:159351059:159351181:159352685:159352719 | 159351059:159351181 |
| exon_skip_189892 | chr4 | 159343294:159343404:159344036:159344059:159345106:159345329 | 159344036:159344059 |
| exon_skip_198053 | chr4 | 159210500:159210583:159238809:159238884:159241201:159241363 | 159238809:159238884 |
| exon_skip_228307 | chr4 | 159241201:159241368:159243774:159243791:159304342:159304473 | 159243774:159243791 |
| exon_skip_262272 | chr4 | 159350228:159350289:159351059:159351181:159352685:159352910 | 159351059:159351181 |
| exon_skip_277506 | chr4 | 159350228:159350289:159351059:159351133:159352685:159352719 | 159351059:159351133 |
| exon_skip_71132 | chr4 | 159350228:159350289:159351059:159351133:159352685:159352910 | 159351059:159351133 |
| exon_skip_92797 | chr4 | 159353487:159354046:159355853:159356158:159358114:159360169 | 159355853:159356158 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_228307 | Mayo_TC | 6.250000e-01 | 7.576190e-01 | -1.326190e-01 | 1.077743e-07 |
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Open reading frame (ORF) annotation in the exon skipping event for RAPGEF2 |
| 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 |
| ENST00000264431 | 159344036 | 159344059 | 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 |
| ENST00000264431 | 159344036 | 159344059 | In-frame |
| 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 |
| ENST00000264431 | 159304342 | 159304473 | In-frame |
| ENST00000264431 | 159344036 | 159344059 | In-frame |
| ENST00000264431 | 159355853 | 159356158 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RAPGEF2 |
p-ENSG00000109756_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 |
| ENST00000264431 | 6966 | 1499 | 159304342 | 159304473 | 481 | 611 | 20 | 64 |
| ENST00000264431 | 6966 | 1499 | 159355853 | 159356158 | 4589 | 4893 | 1390 | 1491 |
| 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 |
| Q9Y4G8 | 20 | 64 | 1 | 1499 | Chain | ID=PRO_0000068865;Note=Rap guanine nucleotide exchange factor 2 |
| Q9Y4G8 | 1390 | 1491 | 1 | 1499 | Chain | ID=PRO_0000068865;Note=Rap guanine nucleotide exchange factor 2 |
| Q9Y4G8 | 1390 | 1491 | 1406 | 1406 | Mutagenesis | Note=Abolishes interaction with NEDD4 and NEDD4-induced ubiquitination and degradation%3B when associated with A-1428. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11598133;Dbxref=PMID:11598133 |
| Q9Y4G8 | 1390 | 1491 | 1428 | 1428 | Mutagenesis | Note=Abolishes interaction with NEDD4 and NEDD4-induced ubiquitination and degradation%3B when associated with A-1406. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11598133;Dbxref=PMID:11598133 |
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3'-UTR located exon skipping events that lost miRNA binding sites in RAPGEF2 |
| 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 RAPGEF2 |
| - 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 RAPGEF2 |
| 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 |
| ADstage | MSBB | IFG | exon_skip_228307 | -4.048481e-01 | 3.259454e-02 | chr4 | + | 159241201 | 159241368 | 159243774 | 159243791 | 159304342 | 159304473 |
| CDR | MSBB | IFG | exon_skip_228307 | -5.561012e-01 | 2.120875e-03 | chr4 | + | 159241201 | 159241368 | 159243774 | 159243791 | 159304342 | 159304473 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAPGEF2 |
| 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 RAPGEF2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| IFG | A1CF | exon_skip_71132 | 4.697308e-01 | 1.166734e-02 |
| IFG | CNOT4 | exon_skip_262272 | 4.565164e-01 | 1.460937e-02 |
| IFG | IGF2BP3 | exon_skip_262272 | 4.627009e-01 | 1.316393e-02 |
| IFG | TRA2A | exon_skip_262272 | 5.545055e-01 | 2.197922e-03 |
| IFG | SF1 | exon_skip_262272 | 5.558767e-01 | 2.131572e-03 |
| IFG | HNRNPD | exon_skip_262272 | 4.351352e-01 | 2.065629e-02 |
| PG | KHDRBS2 | exon_skip_228307 | 4.696227e-01 | 9.297206e-12 |
| TC | KHDRBS2 | exon_skip_228307 | 6.899330e-01 | 8.188513e-22 |
| TC | RALYL | exon_skip_262272 | -4.293382e-01 | 2.014224e-08 |
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RelatedDrugs for RAPGEF2 |
| 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 RAPGEF2 |
| 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)
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