|
||||||
|
 | |
| |
| |
| 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 YIF1B |
 Gene summary |
| Gene information | Gene symbol | YIF1B | Gene ID | 90522 |
| Gene name | Yip1 interacting factor homolog B, membrane trafficking protein | |
| Synonyms | FinGER8 | |
| Cytomap | 19q13.2 | |
| Type of gene | protein-coding | |
| Description | protein YIF1BYIP1-interacting factor homolog B | |
| Modification date | 20200327 | |
| 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 YIF1B |
| 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. |
 |
ENSG00000167645
| 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 | ENST00000337679.12 | YIF1B-202:protein_coding:YIF1B | 3.704155e+01 | -8.009688e-01 | 2.245884e-06 | 2.982543e-05 |
| CB | DOWN | ENST00000589151.1 | YIF1B-210:retained_intron:YIF1B | 1.362520e+00 | -1.241036e+00 | 4.507747e-03 | 1.807135e-02 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for YIF1B |
| 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_174366 | chr19 | 38307428:38307521:38307597:38307752:38308792:38308849 | 38307597:38307752 |
| exon_skip_258442 | chr19 | 38305362:38305507:38306914:38306990:38307428:38307521 | 38306914:38306990 |
| exon_skip_286184 | chr19 | 38308979:38309057:38309224:38309328:38309405:38309643 | 38309224:38309328 |
| exon_skip_32667 | chr19 | 38305498:38305507:38306914:38306990:38307428:38307521 | 38306914:38306990 |
| exon_skip_3744 | chr19 | 38305362:38305507:38307428:38307521:38307597:38307752 | 38307428:38307521 |
| exon_skip_40405 | chr19 | 38305495:38305507:38306914:38306990:38307428:38307521 | 38306914:38306990 |
| 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 YIF1B |
| 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 |
| ENST00000339413 | 38307428 | 38307521 | Frame-shift |
| ENST00000339413 | 38307597 | 38307752 | In-frame |
| ENST00000339413 | 38309224 | 38309328 | 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 |
| 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 |
| ENST00000339413 | 38307428 | 38307521 | Frame-shift |
| ENST00000339413 | 38307597 | 38307752 | In-frame |
| ENST00000339413 | 38309224 | 38309328 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for YIF1B |
p-ENSG00000167645_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 |
| ENST00000339413 | 1242 | 314 | 38309224 | 38309328 | 344 | 447 | 99 | 133 |
| ENST00000339413 | 1242 | 314 | 38307597 | 38307752 | 586 | 740 | 180 | 231 |
| 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 |
| ENST00000339413 | 1242 | 314 | 38309224 | 38309328 | 344 | 447 | 99 | 133 |
| ENST00000339413 | 1242 | 314 | 38307597 | 38307752 | 586 | 740 | 180 | 231 |
| 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 |
| Q5BJH7 | 99 | 133 | 1 | 314 | Chain | ID=PRO_0000307258;Note=Protein YIF1B |
| Q5BJH7 | 99 | 133 | 1 | 156 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q5BJH7 | 180 | 231 | 1 | 314 | Chain | ID=PRO_0000307258;Note=Protein YIF1B |
| Q5BJH7 | 180 | 231 | 178 | 192 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q5BJH7 | 180 | 231 | 214 | 219 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q5BJH7 | 180 | 231 | 193 | 213 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q5BJH7 | 180 | 231 | 220 | 240 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q5BJH7 | 99 | 133 | 1 | 314 | Chain | ID=PRO_0000307258;Note=Protein YIF1B |
| Q5BJH7 | 99 | 133 | 1 | 156 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q5BJH7 | 180 | 231 | 1 | 314 | Chain | ID=PRO_0000307258;Note=Protein YIF1B |
| Q5BJH7 | 180 | 231 | 178 | 192 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q5BJH7 | 180 | 231 | 214 | 219 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q5BJH7 | 180 | 231 | 193 | 213 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q5BJH7 | 180 | 231 | 220 | 240 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in YIF1B |
| 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 YIF1B |
| - 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 YIF1B |
| 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_289223 | -4.476773e-01 | 1.690156e-02 | chr19 | - | 38305362 | 38305507 | 38306882 | 38306990 | 38307428 | 38307521 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for YIF1B |
| 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 YIF1B |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for YIF1B |
| 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 YIF1B |
| 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)
|