|
||||||
|
 | |
| |
| |
| 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 TBC1D1 |
 Gene summary |
| Gene information | Gene symbol | TBC1D1 | Gene ID | 23216 |
| Gene name | TBC1 domain family member 1 | |
| Synonyms | TBC|TBC1 | |
| Cytomap | 4p14 | |
| Type of gene | protein-coding | |
| Description | TBC1 domain family member 1TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1 | |
| 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 TBC1D1 |
| 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. |
 |
ENSG00000065882
| 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 | ENST00000406664.5 | TBC1D1-205:lncRNA:TBC1D1 | 1.078238e+02 | -1.183071e+00 | 3.247085e-05 | 2.850448e-04 |
| CB | DOWN | ENST00000407365.5 | TBC1D1-206:lncRNA:TBC1D1 | 3.073369e+02 | -1.080409e+00 | 3.896109e-05 | 3.329250e-04 |
| CB | UP | ENST00000443855.5 | TBC1D1-208:protein_coding:TBC1D1 | 6.284617e+00 | 8.240295e-01 | 4.108070e-03 | 1.673493e-02 |
| TC | UP | ENST00000446803.6 | TBC1D1-209:protein_coding:TBC1D1 | 4.395997e+01 | 1.088368e+00 | 1.887204e-09 | 2.224475e-07 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for TBC1D1 |
| 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_107160 | chr4 | 38014883:38014973:38018354:38018443:38020591:38020695 | 38018354:38018443 |
| exon_skip_117703 | chr4 | 38021586:38021718:38027788:38027879:38035588:38035698 | 38027788:38027879 |
| exon_skip_12096 | chr4 | 38044474:38044490:38045817:38045903:38049618:38049804 | 38045817:38045903 |
| exon_skip_135983 | chr4 | 38049757:38049898:38053106:38053225:38054199:38054244 | 38053106:38053225 |
| exon_skip_138649 | chr4 | 38054199:38054338:38060620:38060658:38089932:38089999 | 38060620:38060658 |
| exon_skip_183435 | chr4 | 38115900:38115954:38118033:38118192:38124962:38125131 | 38118033:38118192 |
| exon_skip_192816 | chr4 | 38103048:38103157:38115710:38115954:38118033:38118192 | 38115710:38115954 |
| exon_skip_193489 | chr4 | 38049757:38049898:38051899:38052060:38054199:38054244 | 38051899:38052060 |
| exon_skip_231293 | chr4 | 38049757:38049898:38051899:38052060:38053106:38053225 | 38051899:38052060 |
| exon_skip_249997 | chr4 | 38118033:38118192:38124962:38125131:38133084:38133257 | 38124962:38125131 |
| exon_skip_290447 | chr4 | 38051899:38052060:38053106:38053225:38054199:38054244 | 38053106:38053225 |
| exon_skip_35155 | chr4 | 38054231:38054338:38060620:38060658:38089932:38089999 | 38060620:38060658 |
| exon_skip_80860 | chr4 | 38035588:38035698:38049618:38049898:38054199:38054244 | 38049618:38049898 |
| exon_skip_95273 | chr4 | 38027788:38027879:38035588:38035698:38044362:38044490 | 38035588:38035698 |
| 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 TBC1D1 |
| 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 |
| ENST00000261439 | 38027788 | 38027879 | Frame-shift |
| ENST00000261439 | 38115710 | 38115954 | Frame-shift |
| ENST00000261439 | 38118033 | 38118192 | Frame-shift |
| ENST00000261439 | 38124962 | 38125131 | Frame-shift |
| ENST00000261439 | 38035588 | 38035698 | 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 |
| ENST00000261439 | 38115710 | 38115954 | Frame-shift |
| ENST00000261439 | 38118033 | 38118192 | Frame-shift |
| 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 |
| ENST00000261439 | 38027788 | 38027879 | Frame-shift |
| ENST00000261439 | 38115710 | 38115954 | Frame-shift |
| ENST00000261439 | 38118033 | 38118192 | Frame-shift |
| ENST00000261439 | 38124962 | 38125131 | Frame-shift |
| ENST00000261439 | 38018354 | 38018443 | In-frame |
| ENST00000261439 | 38035588 | 38035698 | In-frame |
| ENST00000261439 | 38045817 | 38045903 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for TBC1D1 |
p-ENSG00000065882_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 |
| ENST00000261439 | 5717 | 1168 | 38035588 | 38035698 | 1659 | 1768 | 434 | 471 |
| 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 |
| ENST00000261439 | 5717 | 1168 | 38018354 | 38018443 | 1239 | 1327 | 294 | 324 |
| ENST00000261439 | 5717 | 1168 | 38035588 | 38035698 | 1659 | 1768 | 434 | 471 |
| ENST00000261439 | 5717 | 1168 | 38045817 | 38045903 | 1899 | 1984 | 514 | 543 |
| 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 |
| Q86TI0 | 434 | 471 | 1 | 1168 | Chain | ID=PRO_0000208022;Note=TBC1 domain family member 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 |
| 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 |
| Q86TI0 | 294 | 324 | 1 | 1168 | Chain | ID=PRO_0000208022;Note=TBC1 domain family member 1 |
| Q86TI0 | 294 | 324 | 246 | 404 | Domain | Note=PID;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00148 |
| Q86TI0 | 434 | 471 | 1 | 1168 | Chain | ID=PRO_0000208022;Note=TBC1 domain family member 1 |
| Q86TI0 | 514 | 543 | 1 | 1168 | Chain | ID=PRO_0000208022;Note=TBC1 domain family member 1 |
| Q86TI0 | 514 | 543 | 525 | 525 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q60949 |
| Q86TI0 | 514 | 543 | 527 | 527 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q60949 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in TBC1D1 |
| 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 TBC1D1 |
| - 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 TBC1D1 |
| 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 TBC1D1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| CB | exon_skip_290447 | rs16994140 | chr4:38009944 | 5.942993e-05 | 1.143268e-02 |
| HCC | exon_skip_135983 | rs1544867 | chr4:37995409 | 7.135892e-06 | 9.378965e-04 |
| HCC | exon_skip_135983 | rs4832748 | chr4:38054424 | 9.700790e-06 | 1.217803e-03 |
| HCC | exon_skip_290447 | rs959694 | chr4:38050574 | 2.201814e-05 | 2.509464e-03 |
| HCC | exon_skip_135983 | rs2052693 | chr4:38068985 | 4.184618e-05 | 4.323435e-03 |
| HCC | exon_skip_135983 | rs13142228 | chr4:38016560 | 4.265151e-05 | 4.393212e-03 |
| HCC | exon_skip_135983 | rs6845120 | chr4:38045924 | 4.902767e-05 | 4.963354e-03 |
| HCC | exon_skip_135983 | rs4832984 | chr4:38069318 | 4.902767e-05 | 4.963354e-03 |
| HCC | exon_skip_135983 | rs7671645 | chr4:38017681 | 5.331265e-05 | 5.332594e-03 |
| HCC | exon_skip_135983 | rs6833071 | chr4:38018192 | 8.153459e-05 | 7.698766e-03 |
| HCC | exon_skip_135983 | rs1863326 | chr4:38085174 | 3.417668e-04 | 2.509523e-02 |
| HCC | exon_skip_135983 | rs17579610 | chr4:38076950 | 4.303908e-04 | 3.005937e-02 |
| HCC | exon_skip_135983 | rs933818 | chr4:38077673 | 4.303908e-04 | 3.005937e-02 |
| HCC | exon_skip_135983 | rs2303422 | chr4:38090179 | 4.303908e-04 | 3.005937e-02 |
| HCC | exon_skip_135983 | rs6841167 | chr4:37988960 | 7.054246e-04 | 4.448098e-02 |
Top |
Correlation with RNA binding proteins (RBPs) for TBC1D1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| HCC | PTBP1 | exon_skip_135983 | -4.183094e-01 | 8.077687e-13 |
| IFG | SRSF1 | exon_skip_192816 | -4.225185e-01 | 2.509751e-02 |
| IFG | EIF4B | exon_skip_192816 | -4.400598e-01 | 1.910784e-02 |
| PCC | PTBP1 | exon_skip_193489 | -4.964682e-01 | 2.416251e-14 |
Top |
RelatedDrugs for TBC1D1 |
| 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 TBC1D1 |
| 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)
|