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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 GAD1 |
Gene summary |
Gene information | Gene symbol | GAD1 | Gene ID | 2571 |
Gene name | glutamate decarboxylase 1 | |
Synonyms | CPSQ1|GAD|SCP | |
Cytomap | 2q31.1 | |
Type of gene | protein-coding | |
Description | glutamate decarboxylase 167 kDa glutamic acid decarboxylaseGAD-67glutamate decarboxylase 1 (brain, 67kDa)glutamate decarboxylase 67 kDa isoform | |
Modification date | 20200315 | |
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 GAD1 |
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 |
TC | DOWN | 2.313449e+03 | -8.227472e-01 | 5.075667e-07 | 1.125740e-05 |
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 | ENST00000358196.8 | GAD1-202:protein_coding:GAD1 | 6.154443e+02 | -8.272767e-01 | 1.385748e-05 | 6.421327e-04 |
PG | DOWN | ENST00000488724.5 | GAD1-214:retained_intron:GAD1 | 1.555776e+01 | -8.415396e-01 | 3.443004e-04 | 6.761376e-03 |
CB | DOWN | ENST00000478562.1 | GAD1-211:retained_intron:GAD1 | 8.212936e+01 | -8.821108e-01 | 1.968720e-05 | 1.866345e-04 |
TC | DOWN | ENST00000478562.1 | GAD1-211:retained_intron:GAD1 | 8.134836e+01 | -1.021417e+00 | 2.475196e-08 | 1.916977e-06 |
TC | DOWN | ENST00000358196.8 | GAD1-202:protein_coding:GAD1 | 2.190868e+03 | -8.449586e-01 | 3.849981e-06 | 1.207181e-04 |
TC | DOWN | ENST00000488724.5 | GAD1-214:retained_intron:GAD1 | 9.914114e+00 | -8.277322e-01 | 3.777958e-04 | 4.614872e-03 |
TC | DOWN | ENST00000455008.5 | GAD1-208:protein_coding:GAD1 | 1.602159e+00 | -9.252073e-01 | 8.428561e-03 | 4.942429e-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 GAD1 |
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_116852 | chr2 | 170846009:170846063:170847676:170847792:170849286:170849350 | 170847676:170847792 |
exon_skip_13813 | chr2 | 170836793:170836883:170842569:170842648:170844045:170844157 | 170842569:170842648 |
exon_skip_152024 | chr2 | 170836816:170836883:170842569:170842648:170844045:170844157 | 170842569:170842648 |
exon_skip_226936 | chr2 | 170853873:170854022:170857018:170857125:170858804:170858893 | 170857018:170857125 |
exon_skip_245042 | chr2 | 170847676:170847792:170848683:170848794:170849286:170849350 | 170848683:170848794 |
exon_skip_294904 | chr2 | 170852714:170852792:170853873:170854022:170857018:170857125 | 170853873:170854022 |
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 GAD1 |
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 |
ENST00000358196 | 170847676 | 170847792 | In-frame |
ENST00000358196 | 170857018 | 170857125 | 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 |
ENST00000358196 | 170847676 | 170847792 | In-frame |
ENST00000358196 | 170857018 | 170857125 | 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 |
ENST00000358196 | 170847676 | 170847792 | In-frame |
ENST00000358196 | 170853873 | 170854022 | In-frame |
ENST00000358196 | 170857018 | 170857125 | In-frame |
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Infer the effects of exon skipping event on protein functional features for GAD1 |
p-ENSG00000128683_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 |
ENST00000358196 | 3621 | 594 | 170847676 | 170847792 | 1554 | 1669 | 334 | 373 |
ENST00000358196 | 3621 | 594 | 170857018 | 170857125 | 1965 | 2071 | 471 | 507 |
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 |
ENST00000358196 | 3621 | 594 | 170847676 | 170847792 | 1554 | 1669 | 334 | 373 |
ENST00000358196 | 3621 | 594 | 170857018 | 170857125 | 1965 | 2071 | 471 | 507 |
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 |
ENST00000358196 | 3621 | 594 | 170847676 | 170847792 | 1554 | 1669 | 334 | 373 |
ENST00000358196 | 3621 | 594 | 170853873 | 170854022 | 1815 | 1963 | 421 | 471 |
ENST00000358196 | 3621 | 594 | 170857018 | 170857125 | 1965 | 2071 | 471 | 507 |
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 |
Q99259 | 334 | 373 | 225 | 594 | Alternative sequence | ID=VSP_009124;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10671565,ECO:0000303|PubMed:15489334;Dbxref=PMID:10671565,PMID:15489334 |
Q99259 | 334 | 373 | 337 | 346 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 334 | 373 | 348 | 350 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 334 | 373 | 369 | 374 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 334 | 373 | 1 | 594 | Chain | ID=PRO_0000146963;Note=Glutamate decarboxylase 1 |
Q99259 | 334 | 373 | 356 | 366 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 471 | 507 | 225 | 594 | Alternative sequence | ID=VSP_009124;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10671565,ECO:0000303|PubMed:15489334;Dbxref=PMID:10671565,PMID:15489334 |
Q99259 | 471 | 507 | 426 | 594 | Alternative sequence | ID=VSP_054474;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q99259 | 471 | 507 | 500 | 506 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 471 | 507 | 1 | 594 | Chain | ID=PRO_0000146963;Note=Glutamate decarboxylase 1 |
Q99259 | 471 | 507 | 461 | 495 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 471 | 507 | 474 | 474 | Natural variant | ID=VAR_011882;Note=V->G;Dbxref=dbSNP:rs769403 |
Q99259 | 471 | 507 | 477 | 477 | Sequence conflict | Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q99259 | 471 | 507 | 492 | 492 | Sequence conflict | Note=A->G;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 |
Q99259 | 334 | 373 | 225 | 594 | Alternative sequence | ID=VSP_009124;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10671565,ECO:0000303|PubMed:15489334;Dbxref=PMID:10671565,PMID:15489334 |
Q99259 | 334 | 373 | 337 | 346 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 334 | 373 | 348 | 350 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 334 | 373 | 369 | 374 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 334 | 373 | 1 | 594 | Chain | ID=PRO_0000146963;Note=Glutamate decarboxylase 1 |
Q99259 | 334 | 373 | 356 | 366 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 471 | 507 | 225 | 594 | Alternative sequence | ID=VSP_009124;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10671565,ECO:0000303|PubMed:15489334;Dbxref=PMID:10671565,PMID:15489334 |
Q99259 | 471 | 507 | 426 | 594 | Alternative sequence | ID=VSP_054474;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q99259 | 471 | 507 | 500 | 506 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 471 | 507 | 1 | 594 | Chain | ID=PRO_0000146963;Note=Glutamate decarboxylase 1 |
Q99259 | 471 | 507 | 461 | 495 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 471 | 507 | 474 | 474 | Natural variant | ID=VAR_011882;Note=V->G;Dbxref=dbSNP:rs769403 |
Q99259 | 471 | 507 | 477 | 477 | Sequence conflict | Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q99259 | 471 | 507 | 492 | 492 | Sequence conflict | Note=A->G;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 |
Q99259 | 334 | 373 | 225 | 594 | Alternative sequence | ID=VSP_009124;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10671565,ECO:0000303|PubMed:15489334;Dbxref=PMID:10671565,PMID:15489334 |
Q99259 | 334 | 373 | 337 | 346 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 334 | 373 | 348 | 350 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 334 | 373 | 369 | 374 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 334 | 373 | 1 | 594 | Chain | ID=PRO_0000146963;Note=Glutamate decarboxylase 1 |
Q99259 | 334 | 373 | 356 | 366 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 421 | 471 | 225 | 594 | Alternative sequence | ID=VSP_009124;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10671565,ECO:0000303|PubMed:15489334;Dbxref=PMID:10671565,PMID:15489334 |
Q99259 | 421 | 471 | 374 | 425 | Alternative sequence | ID=VSP_054473;Note=In isoform 4. AAWGGGLLMSRKHRHKLNGIERANSVTWNPHKMMGVLLQCSAILVKEKGILQ->GFNFSQLANRIICLATELMTNKGCVTWHPNYSVNMHHGCLGRWAAHVQEAPP;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q99259 | 421 | 471 | 426 | 594 | Alternative sequence | ID=VSP_054474;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q99259 | 421 | 471 | 1 | 594 | Chain | ID=PRO_0000146963;Note=Glutamate decarboxylase 1 |
Q99259 | 421 | 471 | 423 | 428 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 421 | 471 | 444 | 446 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 421 | 471 | 449 | 451 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 421 | 471 | 461 | 495 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 421 | 471 | 436 | 436 | Sequence conflict | Note=F->L;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q99259 | 421 | 471 | 433 | 435 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 471 | 507 | 225 | 594 | Alternative sequence | ID=VSP_009124;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10671565,ECO:0000303|PubMed:15489334;Dbxref=PMID:10671565,PMID:15489334 |
Q99259 | 471 | 507 | 426 | 594 | Alternative sequence | ID=VSP_054474;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
Q99259 | 471 | 507 | 500 | 506 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 471 | 507 | 1 | 594 | Chain | ID=PRO_0000146963;Note=Glutamate decarboxylase 1 |
Q99259 | 471 | 507 | 461 | 495 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3VP6 |
Q99259 | 471 | 507 | 474 | 474 | Natural variant | ID=VAR_011882;Note=V->G;Dbxref=dbSNP:rs769403 |
Q99259 | 471 | 507 | 477 | 477 | Sequence conflict | Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Q99259 | 471 | 507 | 492 | 492 | Sequence conflict | Note=A->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in GAD1 |
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 GAD1 |
- 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 GAD1 |
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 GAD1 |
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 GAD1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for GAD1 |
Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Q99259 | approved|investigational|nutraceutical | DB00114 | Pyridoxal phosphate | small molecule | Q99259 |
Q99259 | approved|nutraceutical | DB00142 | Glutamic Acid | small molecule | Q99259 |
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RelatedDiseases for GAD1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |