|
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 GBP3 |
Gene summary |
Gene information | Gene symbol | GBP3 | Gene ID | 2635 |
Gene name | guanylate binding protein 3 | |
Synonyms | - | |
Cytomap | 1p22.2 | |
Type of gene | protein-coding | |
Description | guanylate-binding protein 3GTP-binding protein 3guanine nucleotide-binding protein 3guanylate-binding protein 3 delta C | |
Modification date | 20200320 | |
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 GBP3 |
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 |
PG | UP | 9.256148e+01 | 8.307116e-01 | 6.669026e-12 | 1.794818e-09 |
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 | ENST00000370481.9 | GBP3-202:protein_coding:GBP3 | 3.973852e+01 | 1.247869e+00 | 2.062187e-04 | 4.662628e-03 |
PG | UP | ENST00000493594.6 | GBP3-208:nonsense_mediated_decay:GBP3 | 9.640293e+00 | 1.678811e+00 | 3.312635e-04 | 6.583957e-03 |
PG | UP | ENST00000564037.1 | GBP3-209:retained_intron:GBP3 | 1.167891e+00 | 1.471339e+00 | 5.196479e-04 | 9.075662e-03 |
TC | UP | ENST00000235878.5 | GBP3-201:nonsense_mediated_decay:GBP3 | 8.227389e+00 | 1.222444e+00 | 3.396416e-06 | 1.093883e-04 |
TC | UP | ENST00000493594.6 | GBP3-208:nonsense_mediated_decay:GBP3 | 1.643998e+01 | 1.153445e+00 | 1.150892e-04 | 1.808471e-03 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for GBP3 |
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_15281 | chr1 | 89015287:89015414:89020532:89020743:89022684:89022866 | 89020532:89020743 |
exon_skip_18278 | chr1 | 89011828:89012027:89013185:89013427:89014083:89014279 | 89013185:89013427 |
exon_skip_55864 | chr1 | 89011747:89012027:89013185:89013427:89014083:89014279 | 89013185:89013427 |
exon_skip_60099 | chr1 | 89015287:89015414:89020126:89020211:89020532:89020743 | 89020126:89020211 |
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 GBP3 |
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 |
ENST00000370481 | 89020532 | 89020743 | 3UTR-3CDS |
ENST00000370481 | 89013185 | 89013427 | 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 |
ENST00000370481 | 89020532 | 89020743 | 3UTR-3CDS |
ENST00000370481 | 89013185 | 89013427 | 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 |
ENST00000370481 | 89020532 | 89020743 | 3UTR-3CDS |
ENST00000370481 | 89013185 | 89013427 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for GBP3 |
p-ENSG00000117226_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 |
ENST00000370481 | 3084 | 595 | 89013185 | 89013427 | 847 | 1088 | 208 | 289 |
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 |
ENST00000370481 | 3084 | 595 | 89013185 | 89013427 | 847 | 1088 | 208 | 289 |
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 |
ENST00000370481 | 3084 | 595 | 89013185 | 89013427 | 847 | 1088 | 208 | 289 |
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 |
Q9H0R5 | 208 | 289 | 1 | 595 | Chain | ID=PRO_0000261159;Note=Guanylate-binding protein 3 |
Q9H0R5 | 208 | 289 | 35 | 276 | Domain | Note=GB1/RHD3-type G |
Q9H0R5 | 208 | 289 | 221 | 221 | Natural variant | ID=VAR_054136;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15489334;Dbxref=dbSNP:rs4656078,PMID:15489334 |
Q9H0R5 | 208 | 289 | 225 | 225 | Natural variant | ID=VAR_054137;Note=R->W;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:22106366;Dbxref=dbSNP:rs4656077,PMID:15489334,PMID:22106366 |
Q9H0R5 | 208 | 289 | 1 | 309 | Region | Note=GTPase domain (Globular);Ontology_term=ECO:0000250;evidence=ECO:0000250 |
Q9H0R5 | 208 | 289 | 271 | 271 | Sequence conflict | Note=I->T;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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 |
Q9H0R5 | 208 | 289 | 1 | 595 | Chain | ID=PRO_0000261159;Note=Guanylate-binding protein 3 |
Q9H0R5 | 208 | 289 | 35 | 276 | Domain | Note=GB1/RHD3-type G |
Q9H0R5 | 208 | 289 | 221 | 221 | Natural variant | ID=VAR_054136;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15489334;Dbxref=dbSNP:rs4656078,PMID:15489334 |
Q9H0R5 | 208 | 289 | 225 | 225 | Natural variant | ID=VAR_054137;Note=R->W;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:22106366;Dbxref=dbSNP:rs4656077,PMID:15489334,PMID:22106366 |
Q9H0R5 | 208 | 289 | 1 | 309 | Region | Note=GTPase domain (Globular);Ontology_term=ECO:0000250;evidence=ECO:0000250 |
Q9H0R5 | 208 | 289 | 271 | 271 | Sequence conflict | Note=I->T;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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 |
Q9H0R5 | 208 | 289 | 1 | 595 | Chain | ID=PRO_0000261159;Note=Guanylate-binding protein 3 |
Q9H0R5 | 208 | 289 | 35 | 276 | Domain | Note=GB1/RHD3-type G |
Q9H0R5 | 208 | 289 | 221 | 221 | Natural variant | ID=VAR_054136;Note=R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:15489334;Dbxref=dbSNP:rs4656078,PMID:15489334 |
Q9H0R5 | 208 | 289 | 225 | 225 | Natural variant | ID=VAR_054137;Note=R->W;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:22106366;Dbxref=dbSNP:rs4656077,PMID:15489334,PMID:22106366 |
Q9H0R5 | 208 | 289 | 1 | 309 | Region | Note=GTPase domain (Globular);Ontology_term=ECO:0000250;evidence=ECO:0000250 |
Q9H0R5 | 208 | 289 | 271 | 271 | Sequence conflict | Note=I->T;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in GBP3 |
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 GBP3 |
- 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 GBP3 |
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 GBP3 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
HCC | exon_skip_60099 | rs11806868 | chr1:88933720 | 3.373968e-04 | 2.483811e-02 |
Top |
Correlation with RNA binding proteins (RBPs) for GBP3 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for GBP3 |
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 GBP3 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |