|
||||||
|
 | |
| |
| |
| 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 GTDC1 |
 Gene summary |
| Gene information | Gene symbol | GTDC1 | Gene ID | 79712 |
| Gene name | glycosyltransferase like domain containing 1 | |
| Synonyms | Hmat-Xa|mat-Xa | |
| Cytomap | 2q22.3 | |
| Type of gene | protein-coding | |
| Description | glycosyltransferase-like domain-containing protein 1glycosyltransferase-like 1mannosyltransferase candidatemannosyltransferase-like protein Xa | |
| 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 GTDC1 |
| 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. |
 |
ENSG00000121964
| 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 |
| CB | DOWN | ENST00000409298.5 | GTDC1-207:protein_coding:GTDC1 | 9.763603e+01 | -8.151666e-01 | 1.036312e-07 | 2.189254e-06 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for GTDC1 |
| 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_105456 | chr2 | 144141882:144142055:144145572:144145739:144208603:144208804 | 144145572:144145739 |
| exon_skip_105799 | chr2 | 143951982:143952073:143952773:143952843:143970653:143970762 | 143952773:143952843 |
| exon_skip_132322 | chr2 | 143951982:143952073:143952773:143952843:144007182:144007535 | 143952773:143952843 |
| exon_skip_1598 | chr2 | 143951982:143952073:143952773:143952843:143957195:143957339 | 143952773:143952843 |
| exon_skip_193521 | chr2 | 143952773:143952843:144007182:144007535:144141882:144141976 | 144007182:144007535 |
| exon_skip_196844 | chr2 | 143970729:143970762:144007182:144007535:144141882:144142055 | 144007182:144007535 |
| exon_skip_202319 | chr2 | 144211515:144211579:144235676:144235737:144332439:144332516 | 144235676:144235737 |
| exon_skip_210522 | chr2 | 143957195:143957339:143970653:143970762:144141882:144141976 | 143970653:143970762 |
| exon_skip_210606 | chr2 | 143957195:143957339:143970653:143970762:144007182:144007535 | 143970653:143970762 |
| exon_skip_213970 | chr2 | 143952773:143952843:144007182:144007535:144141882:144142055 | 144007182:144007535 |
| exon_skip_217830 | chr2 | 143970653:143970762:144007182:144007535:144141882:144142055 | 144007182:144007535 |
| exon_skip_228093 | chr2 | 143970653:143970762:144007182:144007535:144141882:144141976 | 144007182:144007535 |
| exon_skip_239368 | chr2 | 144208603:144208804:144211515:144211579:144235676:144235737 | 144211515:144211579 |
| exon_skip_253223 | chr2 | 144211515:144211579:144230241:144230322:144235676:144235737 | 144230241:144230322 |
| exon_skip_261899 | chr2 | 143952773:143952843:143970653:143970762:144007182:144007535 | 143970653:143970762 |
| exon_skip_268345 | chr2 | 143957195:143957339:143970653:143970762:144141882:144142055 | 143970653:143970762 |
| exon_skip_274893 | chr2 | 143952773:143952843:143957195:143957339:143970653:143970762 | 143957195:143957339 |
| exon_skip_54993 | chr2 | 144235676:144235737:144317479:144317588:144319719:144319868 | 144317479:144317588 |
| exon_skip_66026 | chr2 | 144127924:144128044:144128246:144128322:144141882:144142055 | 144128246:144128322 |
| 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 GTDC1 |
| 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 |
| ENST00000344850 | 144211515 | 144211579 | 3UTR-3UTR |
| ENST00000409214 | 144211515 | 144211579 | 3UTR-3UTR |
| ENST00000344850 | 143952773 | 143952843 | Frame-shift |
| ENST00000392869 | 143952773 | 143952843 | Frame-shift |
| ENST00000409214 | 143952773 | 143952843 | Frame-shift |
| ENST00000542155 | 143952773 | 143952843 | Frame-shift |
| ENST00000344850 | 143957195 | 143957339 | Frame-shift |
| ENST00000392869 | 143957195 | 143957339 | Frame-shift |
| ENST00000409214 | 143957195 | 143957339 | Frame-shift |
| ENST00000542155 | 143957195 | 143957339 | Frame-shift |
| ENST00000344850 | 143970653 | 143970762 | Frame-shift |
| ENST00000392869 | 143970653 | 143970762 | Frame-shift |
| ENST00000409214 | 143970653 | 143970762 | Frame-shift |
| ENST00000542155 | 143970653 | 143970762 | Frame-shift |
| ENST00000344850 | 144007182 | 144007535 | In-frame |
| ENST00000392869 | 144007182 | 144007535 | In-frame |
| ENST00000409214 | 144007182 | 144007535 | In-frame |
| ENST00000542155 | 144007182 | 144007535 | In-frame |
| ENST00000344850 | 144145572 | 144145739 | In-frame |
| ENST00000392869 | 144145572 | 144145739 | In-frame |
| ENST00000409214 | 144145572 | 144145739 | In-frame |
| ENST00000542155 | 144145572 | 144145739 | 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 |
| ENST00000344850 | 143952773 | 143952843 | Frame-shift |
| ENST00000392869 | 143952773 | 143952843 | Frame-shift |
| ENST00000409214 | 143952773 | 143952843 | Frame-shift |
| ENST00000542155 | 143952773 | 143952843 | Frame-shift |
| ENST00000344850 | 143957195 | 143957339 | Frame-shift |
| ENST00000392869 | 143957195 | 143957339 | Frame-shift |
| ENST00000409214 | 143957195 | 143957339 | Frame-shift |
| ENST00000542155 | 143957195 | 143957339 | Frame-shift |
| ENST00000344850 | 143970653 | 143970762 | Frame-shift |
| ENST00000392869 | 143970653 | 143970762 | Frame-shift |
| ENST00000409214 | 143970653 | 143970762 | Frame-shift |
| ENST00000542155 | 143970653 | 143970762 | Frame-shift |
| ENST00000344850 | 144007182 | 144007535 | In-frame |
| ENST00000392869 | 144007182 | 144007535 | In-frame |
| ENST00000409214 | 144007182 | 144007535 | In-frame |
| ENST00000542155 | 144007182 | 144007535 | 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 |
| ENST00000344850 | 144211515 | 144211579 | 3UTR-3UTR |
| ENST00000409214 | 144211515 | 144211579 | 3UTR-3UTR |
| ENST00000344850 | 143952773 | 143952843 | Frame-shift |
| ENST00000392869 | 143952773 | 143952843 | Frame-shift |
| ENST00000409214 | 143952773 | 143952843 | Frame-shift |
| ENST00000542155 | 143952773 | 143952843 | Frame-shift |
| ENST00000344850 | 143957195 | 143957339 | Frame-shift |
| ENST00000392869 | 143957195 | 143957339 | Frame-shift |
| ENST00000409214 | 143957195 | 143957339 | Frame-shift |
| ENST00000542155 | 143957195 | 143957339 | Frame-shift |
| ENST00000344850 | 143970653 | 143970762 | Frame-shift |
| ENST00000392869 | 143970653 | 143970762 | Frame-shift |
| ENST00000409214 | 143970653 | 143970762 | Frame-shift |
| ENST00000542155 | 143970653 | 143970762 | Frame-shift |
| ENST00000344850 | 144007182 | 144007535 | In-frame |
| ENST00000392869 | 144007182 | 144007535 | In-frame |
| ENST00000409214 | 144007182 | 144007535 | In-frame |
| ENST00000542155 | 144007182 | 144007535 | In-frame |
| ENST00000344850 | 144145572 | 144145739 | In-frame |
| ENST00000392869 | 144145572 | 144145739 | In-frame |
| ENST00000409214 | 144145572 | 144145739 | In-frame |
| ENST00000542155 | 144145572 | 144145739 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for GTDC1 |
p-ENSG00000121964_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 |
| ENST00000344850 | 2624 | 458 | 144145572 | 144145739 | 374 | 540 | 60 | 115 |
| ENST00000392869 | 10531 | 458 | 144145572 | 144145739 | 333 | 499 | 60 | 115 |
| ENST00000409214 | 2971 | 458 | 144145572 | 144145739 | 459 | 625 | 60 | 115 |
| ENST00000542155 | 2694 | 458 | 144145572 | 144145739 | 444 | 610 | 60 | 115 |
| ENST00000344850 | 2624 | 458 | 144007182 | 144007535 | 716 | 1068 | 174 | 291 |
| ENST00000392869 | 10531 | 458 | 144007182 | 144007535 | 675 | 1027 | 174 | 291 |
| ENST00000409214 | 2971 | 458 | 144007182 | 144007535 | 801 | 1153 | 174 | 291 |
| ENST00000542155 | 2694 | 458 | 144007182 | 144007535 | 786 | 1138 | 174 | 291 |
| 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 |
| ENST00000344850 | 2624 | 458 | 144007182 | 144007535 | 716 | 1068 | 174 | 291 |
| ENST00000392869 | 10531 | 458 | 144007182 | 144007535 | 675 | 1027 | 174 | 291 |
| ENST00000409214 | 2971 | 458 | 144007182 | 144007535 | 801 | 1153 | 174 | 291 |
| ENST00000542155 | 2694 | 458 | 144007182 | 144007535 | 786 | 1138 | 174 | 291 |
| 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 |
| ENST00000344850 | 2624 | 458 | 144145572 | 144145739 | 374 | 540 | 60 | 115 |
| ENST00000392869 | 10531 | 458 | 144145572 | 144145739 | 333 | 499 | 60 | 115 |
| ENST00000409214 | 2971 | 458 | 144145572 | 144145739 | 459 | 625 | 60 | 115 |
| ENST00000542155 | 2694 | 458 | 144145572 | 144145739 | 444 | 610 | 60 | 115 |
| ENST00000344850 | 2624 | 458 | 144007182 | 144007535 | 716 | 1068 | 174 | 291 |
| ENST00000392869 | 10531 | 458 | 144007182 | 144007535 | 675 | 1027 | 174 | 291 |
| ENST00000409214 | 2971 | 458 | 144007182 | 144007535 | 801 | 1153 | 174 | 291 |
| ENST00000542155 | 2694 | 458 | 144007182 | 144007535 | 786 | 1138 | 174 | 291 |
| 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 |
| Q4AE62 | 60 | 115 | 1 | 129 | Alternative sequence | ID=VSP_057596;Note=In isoform 6. Missing |
| Q4AE62 | 60 | 115 | 1 | 129 | Alternative sequence | ID=VSP_057596;Note=In isoform 6. Missing |
| Q4AE62 | 60 | 115 | 1 | 129 | Alternative sequence | ID=VSP_057596;Note=In isoform 6. Missing |
| Q4AE62 | 60 | 115 | 1 | 129 | Alternative sequence | ID=VSP_057596;Note=In isoform 6. Missing |
| Q4AE62 | 60 | 115 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 60 | 115 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 60 | 115 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 60 | 115 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 174 | 291 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 174 | 291 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 174 | 291 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 174 | 291 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| 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 |
| Q4AE62 | 174 | 291 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 174 | 291 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 174 | 291 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 174 | 291 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| 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 |
| Q4AE62 | 60 | 115 | 1 | 129 | Alternative sequence | ID=VSP_057596;Note=In isoform 6. Missing |
| Q4AE62 | 60 | 115 | 1 | 129 | Alternative sequence | ID=VSP_057596;Note=In isoform 6. Missing |
| Q4AE62 | 60 | 115 | 1 | 129 | Alternative sequence | ID=VSP_057596;Note=In isoform 6. Missing |
| Q4AE62 | 60 | 115 | 1 | 129 | Alternative sequence | ID=VSP_057596;Note=In isoform 6. Missing |
| Q4AE62 | 60 | 115 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 60 | 115 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 60 | 115 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 60 | 115 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 174 | 291 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 174 | 291 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 174 | 291 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
| Q4AE62 | 174 | 291 | 1 | 458 | Chain | ID=PRO_0000311088;Note=Glycosyltransferase-like domain-containing protein 1 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in GTDC1 |
| 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 | ENST00000409214 | 144211515 | 144211579 | hsa-miR-9500 | chr2:144211552-144211559 | 8mer-1a | chr2:144211541-144211561 | 146.00 | -18.45 |
| Mayo | ENST00000409214 | 144211515 | 144211579 | hsa-miR-218-5p | chr2:144211571-144211578 | 8mer-1a | chr2:144211557-144211578 | 154.00 | -17.49 |
| ROSMAP | ENST00000409214 | 144211515 | 144211579 | hsa-miR-9500 | chr2:144211552-144211559 | 8mer-1a | chr2:144211541-144211561 | 146.00 | -18.45 |
| ROSMAP | ENST00000409214 | 144211515 | 144211579 | hsa-miR-218-5p | chr2:144211571-144211578 | 8mer-1a | chr2:144211557-144211578 | 154.00 | -17.49 |
Top |
SNVs in the skipped exons for GTDC1 |
| - 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 GTDC1 |
| 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 GTDC1 |
| 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 GTDC1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | TIA1 | exon_skip_274893 | -4.539200e-01 | 5.414198e-09 |
| CB | FUBP3 | exon_skip_274893 | -4.740781e-01 | 8.900995e-10 |
| CB | HNRNPD | exon_skip_274893 | -4.189118e-01 | 9.547291e-08 |
| CB | CNOT4 | exon_skip_217830 | 4.622144e-01 | 3.783187e-09 |
| HCC | PTBP1 | exon_skip_274893 | 4.071870e-01 | 3.632367e-12 |
| HCC | RBM3 | exon_skip_217830 | -4.207515e-01 | 5.218967e-13 |
| IFG | CPEB4 | exon_skip_274893 | -4.227160e-01 | 2.502242e-02 |
| IFG | HNRNPDL | exon_skip_217830 | 4.571561e-01 | 1.651280e-02 |
| PCC | RBM3 | exon_skip_196844 | -4.909033e-01 | 3.900127e-14 |
Top |
RelatedDrugs for GTDC1 |
| 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 GTDC1 |
| 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)
|