|
||||||
|
 | |
| |
| |
| 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 MVB12B |
 Gene summary |
| Gene information | Gene symbol | MVB12B | Gene ID | 89853 |
| Gene name | multivesicular body subunit 12B | |
| Synonyms | C9orf28|FAM125B | |
| Cytomap | 9q33.3 | |
| Type of gene | protein-coding | |
| Description | multivesicular body subunit 12BESCRT-I complex subunit MVB12Bfamily with sequence similarity 125, member B | |
| Modification date | 20200313 | |
| UniProtAcc | F8W922, Q9H7P6, | |
| 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 MVB12B |
| 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. |
 |
ENSG00000196814
| 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 | ENST00000485886.1 | MVB12B-204:retained_intron:MVB12B | 5.139164e+01 | -2.301397e+00 | 9.994554e-11 | 6.310577e-09 |
| TC | DOWN | ENST00000485886.1 | MVB12B-204:retained_intron:MVB12B | 4.210609e+01 | -1.418093e+00 | 4.672946e-07 | 2.179694e-05 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for MVB12B |
| 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_131726 | chr9 | 126386562:126386658:126392066:126392195:126395575:126395697 | 126392066:126392195 |
| exon_skip_138178 | chr9 | 126481369:126481424:126483973:126484032:126503177:126507040 | 126483973:126484032 |
| exon_skip_138380 | chr9 | 126392068:126392195:126395575:126395697:126421854:126421948 | 126395575:126395697 |
| exon_skip_219543 | chr9 | 126381064:126381171:126386562:126386658:126392066:126392195 | 126386562:126386658 |
| exon_skip_52728 | chr9 | 126392066:126392195:126395575:126395697:126421854:126421948 | 126395575:126395697 |
| exon_skip_99239 | chr9 | 126326862:126327010:126340508:126340630:126381064:126381171 | 126340508:126340630 |
| 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 MVB12B |
| 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 |
| ENST00000361171 | 126386562 | 126386658 | Frame-shift |
| ENST00000361171 | 126395575 | 126395697 | In-frame |
| ENST00000361171 | 126483973 | 126484032 | 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 |
| ENST00000361171 | 126395575 | 126395697 | 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 |
| ENST00000361171 | 126386562 | 126386658 | Frame-shift |
| ENST00000361171 | 126392066 | 126392195 | Frame-shift |
| ENST00000361171 | 126395575 | 126395697 | In-frame |
| ENST00000361171 | 126483973 | 126484032 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for MVB12B |
p-ENSG00000196814_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 |
| ENST00000361171 | 4836 | 319 | 126395575 | 126395697 | 622 | 743 | 180 | 220 |
| ENST00000361171 | 4836 | 319 | 126483973 | 126484032 | 896 | 954 | 271 | 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 |
| ENST00000361171 | 4836 | 319 | 126395575 | 126395697 | 622 | 743 | 180 | 220 |
| 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 |
| ENST00000361171 | 4836 | 319 | 126395575 | 126395697 | 622 | 743 | 180 | 220 |
| ENST00000361171 | 4836 | 319 | 126483973 | 126484032 | 896 | 954 | 271 | 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 |
| Q9H7P6 | 180 | 220 | 176 | 182 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3TOW |
| Q9H7P6 | 180 | 220 | 185 | 192 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3TOW |
| Q9H7P6 | 180 | 220 | 1 | 319 | Chain | ID=PRO_0000249074;Note=Multivesicular body subunit 12B |
| Q9H7P6 | 180 | 220 | 47 | 193 | Domain | Note=MABP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00831 |
| Q9H7P6 | 180 | 220 | 204 | 204 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18005716;Dbxref=PMID:18005716 |
| Q9H7P6 | 180 | 220 | 205 | 205 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18005716;Dbxref=PMID:18005716 |
| Q9H7P6 | 271 | 291 | 222 | 319 | Alternative sequence | ID=VSP_020364;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9H7P6 | 271 | 291 | 1 | 319 | Chain | ID=PRO_0000249074;Note=Multivesicular body subunit 12B |
| Q9H7P6 | 271 | 291 | 254 | 303 | Domain | Note=UMA;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00830 |
| 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 |
| Q9H7P6 | 180 | 220 | 176 | 182 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3TOW |
| Q9H7P6 | 180 | 220 | 185 | 192 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3TOW |
| Q9H7P6 | 180 | 220 | 1 | 319 | Chain | ID=PRO_0000249074;Note=Multivesicular body subunit 12B |
| Q9H7P6 | 180 | 220 | 47 | 193 | Domain | Note=MABP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00831 |
| Q9H7P6 | 180 | 220 | 204 | 204 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18005716;Dbxref=PMID:18005716 |
| Q9H7P6 | 180 | 220 | 205 | 205 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18005716;Dbxref=PMID:18005716 |
| 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 |
| Q9H7P6 | 180 | 220 | 176 | 182 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3TOW |
| Q9H7P6 | 180 | 220 | 185 | 192 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:3TOW |
| Q9H7P6 | 180 | 220 | 1 | 319 | Chain | ID=PRO_0000249074;Note=Multivesicular body subunit 12B |
| Q9H7P6 | 180 | 220 | 47 | 193 | Domain | Note=MABP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00831 |
| Q9H7P6 | 180 | 220 | 204 | 204 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18005716;Dbxref=PMID:18005716 |
| Q9H7P6 | 180 | 220 | 205 | 205 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18005716;Dbxref=PMID:18005716 |
| Q9H7P6 | 271 | 291 | 222 | 319 | Alternative sequence | ID=VSP_020364;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q9H7P6 | 271 | 291 | 1 | 319 | Chain | ID=PRO_0000249074;Note=Multivesicular body subunit 12B |
| Q9H7P6 | 271 | 291 | 254 | 303 | Domain | Note=UMA;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00830 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in MVB12B |
| 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 MVB12B |
| - 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 MVB12B |
| 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 |
| CDR | MSBB | IFG | exon_skip_53097 | 4.167975e-01 | 2.735279e-02 | chr9 | + | 126395640 | 126395697 | 126416917 | 126416986 | 126421854 | 126421948 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MVB12B |
| 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 MVB12B |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for MVB12B |
| 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 MVB12B |
| 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)
|