|
||||||
|
 | |
| |
| |
| 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 GPBP1L1 |
 Gene summary |
| Gene information | Gene symbol | GPBP1L1 | Gene ID | 60313 |
| Gene name | GC-rich promoter binding protein 1 like 1 | |
| Synonyms | SP192 | |
| Cytomap | 1p34.1 | |
| Type of gene | protein-coding | |
| Description | vasculin-like protein 1 | |
| Modification date | 20200313 | |
| UniProtAcc | D3DQ09, Q9HC44, | |
| 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 GPBP1L1 |
| 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. |
 |
ENSG00000159592
| 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 | ENST00000493083.5 | GPBP1L1-211:lncRNA:GPBP1L1 | 3.005411e+00 | 1.745473e+00 | 3.827742e-03 | 3.792418e-02 |
| CB | UP | ENST00000480941.1 | GPBP1L1-208:lncRNA:GPBP1L1 | 5.710025e+01 | 8.726276e-01 | 1.482315e-06 | 2.095070e-05 |
| CB | UP | ENST00000488278.5 | GPBP1L1-210:lncRNA:GPBP1L1 | 4.013089e+01 | 8.180195e-01 | 1.232771e-05 | 1.256853e-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 GPBP1L1 |
| 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_100154 | chr1 | 45654543:45654829:45655190:45655319:45659028:45659142 | 45655190:45655319 |
| exon_skip_128424 | chr1 | 45660798:45661225:45685576:45685620:45686993:45687133 | 45685576:45685620 |
| exon_skip_33481 | chr1 | 45659028:45659142:45660184:45661225:45686412:45686533 | 45660184:45661225 |
| exon_skip_41995 | chr1 | 45660798:45661225:45685576:45685620:45687983:45688113 | 45685576:45685620 |
| exon_skip_58656 | chr1 | 45660798:45661225:45685576:45685620:45686412:45686533 | 45685576:45685620 |
| exon_skip_71208 | chr1 | 45630482:45630606:45633489:45633647:45634096:45634236 | 45633489:45633647 |
| 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 |
| exon_skip_128424 | MSBB_IFG | 5.921429e-01 | 4.240000e-01 | 1.681429e-01 | 4.190352e-02 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for GPBP1L1 |
| 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 |
| ENST00000355105 | 45685576 | 45685620 | 3UTR-3UTR |
| ENST00000290795 | 45655190 | 45655319 | Frame-shift |
| ENST00000355105 | 45655190 | 45655319 | 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 |
| ENST00000355105 | 45685576 | 45685620 | 3UTR-3UTR |
| 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 |
| ENST00000290795 | 45660184 | 45661225 | 3UTR-3UTR |
| ENST00000355105 | 45685576 | 45685620 | 3UTR-3UTR |
| ENST00000290795 | 45655190 | 45655319 | Frame-shift |
| ENST00000355105 | 45655190 | 45655319 | Frame-shift |
| ENST00000290795 | 45633489 | 45633647 | In-frame |
| ENST00000355105 | 45633489 | 45633647 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for GPBP1L1 |
p-ENSG00000159592_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 |
| ENST00000290795 | 3616 | 474 | 45633489 | 45633647 | 2108 | 2265 | 295 | 347 |
| ENST00000355105 | 3753 | 474 | 45633489 | 45633647 | 2247 | 2404 | 295 | 347 |
| 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 |
| Q9HC44 | 295 | 347 | 1 | 474 | Chain | ID=PRO_0000324115;Note=Vasculin-like protein 1 |
| Q9HC44 | 295 | 347 | 1 | 474 | Chain | ID=PRO_0000324115;Note=Vasculin-like protein 1 |
| Q9HC44 | 295 | 347 | 301 | 301 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q9HC44 | 295 | 347 | 301 | 301 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q9HC44 | 295 | 347 | 306 | 306 | Sequence conflict | Note=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9HC44 | 295 | 347 | 306 | 306 | Sequence conflict | Note=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in GPBP1L1 |
| 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 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-4684-5p | chr1:45661149-45661156 | 8mer-1a | chr1:45661144-45661162 | 159.00 | -22.06 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-6734-5p | chr1:45660345-45660352 | 8mer-1a | chr1:45660329-45660352 | 155.00 | -27.16 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-4421 | chr1:45660853-45660860 | 8mer-1a | chr1:45660839-45660860 | 157.00 | -16.46 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-7856-5p | chr1:45660713-45660720 | 8mer-1a | chr1:45660700-45660720 | 154.00 | -14.27 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-5699-3p | chr1:45660853-45660860 | 8mer-1a | chr1:45660839-45660860 | 157.00 | -16.46 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-3611 | chr1:45661188-45661195 | 8mer-1a | chr1:45661173-45661195 | 143.00 | -12.36 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-7151-5p | chr1:45661002-45661009 | 8mer-1a | chr1:45660988-45661009 | 159.00 | -22.36 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-607 | chr1:45661198-45661205 | 8mer-1a | chr1:45661197-45661214 | 159.00 | -17.24 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-3158-3p | chr1:45660660-45660667 | 8mer-1a | chr1:45660652-45660678 | 152.00 | -16.96 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-4680-3p | chr1:45660964-45660971 | 8mer-1a | chr1:45660952-45660971 | 157.00 | -13.21 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-5691 | chr1:45660968-45660975 | 8mer-1a | chr1:45660954-45660975 | 152.00 | -17.69 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-6756-3p | chr1:45660464-45660471 | 8mer-1a | chr1:45660452-45660471 | 162.00 | -30.65 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-200c-5p | chr1:45660540-45660547 | 8mer-1a | chr1:45660536-45660561 | 159.00 | -18.10 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-6505-3p | chr1:45661153-45661160 | 8mer-1a | chr1:45661144-45661162 | 159.00 | -22.06 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-7703 | chr1:45660562-45660569 | 8mer-1a | chr1:45660548-45660571 | 148.00 | -20.16 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-889-3p | chr1:45661006-45661013 | 8mer-1a | chr1:45660991-45661013 | 150.00 | -17.01 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-369-5p | chr1:45660327-45660334 | 8mer-1a | chr1:45660322-45660344 | 156.00 | -25.10 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-1233-5p | chr1:45660238-45660245 | 8mer-1a | chr1:45660222-45660245 | 156.00 | -32.62 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-6768-3p | chr1:45660947-45660954 | 8mer-1a | chr1:45660940-45660961 | 144.00 | -20.49 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-7854-3p | chr1:45660489-45660496 | 8mer-1a | chr1:45660476-45660496 | 161.00 | -21.98 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-5093 | chr1:45661177-45661184 | 8mer-1a | chr1:45661171-45661193 | 164.00 | -15.46 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-6778-5p | chr1:45660238-45660245 | 8mer-1a | chr1:45660222-45660245 | 156.00 | -32.62 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-7850-5p | chr1:45661037-45661044 | 8mer-1a | chr1:45661025-45661044 | 153.00 | -13.74 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-4747-5p | chr1:45661090-45661097 | 8mer-1a | chr1:45661073-45661098 | 151.00 | -26.41 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-5196-5p | chr1:45661090-45661097 | 8mer-1a | chr1:45661073-45661098 | 151.00 | -26.41 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-6797-5p | chr1:45660875-45660882 | 8mer-1a | chr1:45660860-45660882 | 164.00 | -25.41 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-498-3p | chr1:45660264-45660271 | 8mer-1a | chr1:45660249-45660271 | 141.00 | -14.23 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-8061 | chr1:45661099-45661106 | 8mer-1a | chr1:45661099-45661118 | 151.00 | -18.05 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-6805-3p | chr1:45660968-45660975 | 8mer-1a | chr1:45660954-45660975 | 152.00 | -17.69 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-3127-3p | chr1:45660464-45660471 | 8mer-1a | chr1:45660452-45660471 | 162.00 | -30.65 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-4760-5p | chr1:45661099-45661106 | 8mer-1a | chr1:45661099-45661118 | 151.00 | -18.05 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-6815-3p | chr1:45660311-45660318 | 8mer-1a | chr1:45660297-45660318 | 148.00 | -16.43 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-33a-3p | chr1:45660981-45660988 | 8mer-1a | chr1:45660968-45660988 | 154.00 | -10.42 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-1249-5p | chr1:45660875-45660882 | 8mer-1a | chr1:45660860-45660882 | 164.00 | -25.41 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-4535 | chr1:45661035-45661042 | 8mer-1a | chr1:45661025-45661044 | 153.00 | -13.74 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-8064 | chr1:45660762-45660769 | 8mer-1a | chr1:45660750-45660769 | 141.00 | -17.40 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-4795-5p | chr1:45661185-45661192 | 8mer-1a | chr1:45661171-45661193 | 164.00 | -15.46 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-10397-5p | chr1:45661020-45661027 | 8mer-1a | chr1:45661008-45661027 | 148.00 | -14.30 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-6830-3p | chr1:45660597-45660604 | 8mer-1a | chr1:45660580-45660604 | 158.00 | -20.70 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-3691-5p | chr1:45660696-45660703 | 8mer-1a | chr1:45660681-45660703 | 149.00 | -19.19 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-6834-3p | chr1:45660807-45660814 | 8mer-1a | chr1:45660795-45660814 | 140.00 | -13.62 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-550a-3p | chr1:45660540-45660547 | 8mer-1a | chr1:45660536-45660561 | 159.00 | -18.10 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-873-5p | chr1:45660374-45660381 | 8mer-1a | chr1:45660361-45660381 | 150.00 | -15.47 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-374b-3p | chr1:45660750-45660757 | 8mer-1a | chr1:45660737-45660757 | 159.00 | -13.26 |
| Mayo | ENST00000290795 | 45660184 | 45661225 | hsa-miR-450a-1-3p | chr1:45661092-45661099 | 8mer-1a | chr1:45661088-45661109 | 153.00 | -9.90 |
Top |
SNVs in the skipped exons for GPBP1L1 |
| - 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 GPBP1L1 |
| 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 GPBP1L1 |
| 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 GPBP1L1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | TARDBP | exon_skip_58656 | -4.240833e-01 | 6.375661e-08 |
| CB | ZNF638 | exon_skip_58656 | -5.367745e-01 | 1.436124e-12 |
| IFG | MSI1 | exon_skip_128424 | 4.223483e-01 | 3.978668e-02 |
| IFG | ZNF638 | exon_skip_128424 | 4.476382e-01 | 2.827570e-02 |
| IFG | IGF2BP3 | exon_skip_128424 | 4.685729e-01 | 2.091569e-02 |
| IFG | HNRNPL | exon_skip_128424 | -4.750713e-01 | 1.897720e-02 |
Top |
RelatedDrugs for GPBP1L1 |
| 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 GPBP1L1 |
| 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)
|