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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for YIPF1 |
 Gene summary |
| Gene information | Gene symbol | YIPF1 | Gene ID | 54432 |
| Gene name | Yip1 domain family member 1 | |
| Synonyms | DJ167A19.1|FinGER1 | |
| Cytomap | 1p32.3 | |
| Type of gene | protein-coding | |
| Description | protein YIPF1YIP1 family member 1 | |
| Modification date | 20200313 | |
| UniProtAcc | L8ECI1, Q9Y548, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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Gene structures and expression levels for YIPF1 |
| 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. |
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ENSG00000058799
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000469457.5 | YIPF1-205:lncRNA:YIPF1 | 1.750227e+01 | 9.418971e-01 | 4.317850e-06 | 5.182111e-05 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for YIPF1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_123275 | chr1 | 53878642:53878722:53883113:53883276:53889713:53889733 | 53883113:53883276 |
| exon_skip_137379 | chr1 | 53878642:53878722:53882943:53883031:53883113:53883276 | 53882943:53883031 |
| exon_skip_138603 | chr1 | 53883113:53883276:53888907:53888986:53889713:53889733 | 53888907:53888986 |
| exon_skip_163247 | chr1 | 53888907:53888986:53889244:53889463:53889713:53889733 | 53889244:53889463 |
| exon_skip_171965 | chr1 | 53855001:53855051:53860056:53860153:53866200:53866382 | 53860056:53860153 |
| exon_skip_18971 | chr1 | 53866804:53866924:53871372:53871488:53878315:53878402 | 53871372:53871488 |
| exon_skip_197852 | chr1 | 53878642:53878722:53883113:53883276:53888907:53888986 | 53883113:53883276 |
| exon_skip_249462 | chr1 | 53878642:53878722:53882943:53883031:53883113:53883261 | 53882943:53883031 |
| exon_skip_258307 | chr1 | 53866201:53866382:53866758:53866924:53871372:53871488 | 53866758:53866924 |
| exon_skip_263468 | chr1 | 53852249:53852270:53855001:53855051:53860056:53860153 | 53855001:53855051 |
| exon_skip_277051 | chr1 | 53851733:53852270:53855001:53855051:53860056:53860153 | 53855001:53855051 |
| exon_skip_97690 | chr1 | 53851733:53852270:53860056:53860153:53866200:53866382 | 53860056:53860153 |
| exon_skip_98934 | chr1 | 53871372:53871488:53878315:53878402:53878642:53878722 | 53878315:53878402 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_277051 | Mayo_CB | 4.620732e-01 | 5.732468e-01 | -1.111736e-01 | 7.233981e-07 |
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Open reading frame (ORF) annotation in the exon skipping event for YIPF1 |
| 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 |
| ENST00000072644 | 53889244 | 53889463 | 3UTR-3UTR |
| ENST00000072644 | 53866758 | 53866924 | Frame-shift |
| ENST00000072644 | 53878315 | 53878402 | Frame-shift |
| ENST00000072644 | 53883113 | 53883276 | 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 |
| ENST00000072644 | 53889244 | 53889463 | 3UTR-3UTR |
| ENST00000072644 | 53883113 | 53883276 | 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 |
| ENST00000072644 | 53889244 | 53889463 | 3UTR-3UTR |
| ENST00000072644 | 53860056 | 53860153 | 5CDS-5UTR |
| ENST00000072644 | 53866758 | 53866924 | Frame-shift |
| ENST00000072644 | 53878315 | 53878402 | Frame-shift |
| ENST00000072644 | 53883113 | 53883276 | Frame-shift |
| ENST00000072644 | 53871372 | 53871488 | In-frame |
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Infer the effects of exon skipping event on protein functional features for YIPF1 |
p-ENSG00000058799_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 |
| ENST00000072644 | 1875 | 306 | 53871372 | 53871488 | 756 | 871 | 121 | 160 |
| 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 |
| Q9Y548 | 121 | 160 | 1 | 183 | Alternative sequence | ID=VSP_019437;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9Y548 | 121 | 160 | 1 | 306 | Chain | ID=PRO_0000240868;Note=Protein YIPF1 |
| Q9Y548 | 121 | 160 | 141 | 162 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27999994;Dbxref=PMID:27999994 |
| Q9Y548 | 121 | 160 | 120 | 140 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in YIPF1 |
| 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 | ENST00000072644 | 53889244 | 53889463 | hsa-miR-3120-5p | chr1:53889386-53889393 | 8mer-1a | chr1:53889383-53889405 | 166.00 | -20.95 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6739-3p | chr1:53889334-53889341 | 8mer-1a | chr1:53889322-53889341 | 161.00 | -17.48 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-4677-5p | chr1:53889333-53889340 | 8mer-1a | chr1:53889322-53889341 | 161.00 | -17.48 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6072 | chr1:53889286-53889293 | 8mer-1a | chr1:53889286-53889305 | 156.00 | -29.06 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6715b-3p | chr1:53889306-53889313 | 8mer-1a | chr1:53889300-53889325 | 157.00 | -27.63 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-3059-3p | chr1:53889272-53889279 | 8mer-1a | chr1:53889271-53889295 | 151.00 | -20.55 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6760-3p | chr1:53889326-53889333 | 8mer-1a | chr1:53889313-53889333 | 171.00 | -26.77 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-22-5p | chr1:53889332-53889339 | 8mer-1a | chr1:53889322-53889341 | 161.00 | -17.48 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-4750-3p | chr1:53889382-53889389 | 8mer-1a | chr1:53889373-53889393 | 146.00 | -17.17 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6804-3p | chr1:53889263-53889270 | 8mer-1a | chr1:53889259-53889277 | 161.00 | -25.42 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-645 | chr1:53889270-53889277 | 8mer-1a | chr1:53889259-53889277 | 161.00 | -25.42 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6069 | chr1:53889352-53889359 | 8mer-1a | chr1:53889341-53889361 | 155.00 | -24.34 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-3667-3p | chr1:53889290-53889297 | 8mer-1a | chr1:53889286-53889305 | 156.00 | -29.06 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6891-3p | chr1:53889286-53889293 | 8mer-1a | chr1:53889286-53889305 | 156.00 | -29.06 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6837-3p | chr1:53889329-53889336 | 8mer-1a | chr1:53889322-53889341 | 161.00 | -17.48 |
| Mayo | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6089 | chr1:53889446-53889453 | 8mer-1a | chr1:53889440-53889461 | 180.00 | -34.29 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-3120-5p | chr1:53889386-53889393 | 8mer-1a | chr1:53889383-53889405 | 166.00 | -20.95 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6739-3p | chr1:53889334-53889341 | 8mer-1a | chr1:53889322-53889341 | 161.00 | -17.48 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-4677-5p | chr1:53889333-53889340 | 8mer-1a | chr1:53889322-53889341 | 161.00 | -17.48 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6072 | chr1:53889286-53889293 | 8mer-1a | chr1:53889286-53889305 | 156.00 | -29.06 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6715b-3p | chr1:53889306-53889313 | 8mer-1a | chr1:53889300-53889325 | 157.00 | -27.63 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-3059-3p | chr1:53889272-53889279 | 8mer-1a | chr1:53889271-53889295 | 151.00 | -20.55 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6760-3p | chr1:53889326-53889333 | 8mer-1a | chr1:53889313-53889333 | 171.00 | -26.77 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-22-5p | chr1:53889332-53889339 | 8mer-1a | chr1:53889322-53889341 | 161.00 | -17.48 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-4750-3p | chr1:53889382-53889389 | 8mer-1a | chr1:53889373-53889393 | 146.00 | -17.17 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6804-3p | chr1:53889263-53889270 | 8mer-1a | chr1:53889259-53889277 | 161.00 | -25.42 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-645 | chr1:53889270-53889277 | 8mer-1a | chr1:53889259-53889277 | 161.00 | -25.42 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6069 | chr1:53889352-53889359 | 8mer-1a | chr1:53889341-53889361 | 155.00 | -24.34 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-3667-3p | chr1:53889290-53889297 | 8mer-1a | chr1:53889286-53889305 | 156.00 | -29.06 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6891-3p | chr1:53889286-53889293 | 8mer-1a | chr1:53889286-53889305 | 156.00 | -29.06 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6837-3p | chr1:53889329-53889336 | 8mer-1a | chr1:53889322-53889341 | 161.00 | -17.48 |
| MSBB | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6089 | chr1:53889446-53889453 | 8mer-1a | chr1:53889440-53889461 | 180.00 | -34.29 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-3120-5p | chr1:53889386-53889393 | 8mer-1a | chr1:53889383-53889405 | 166.00 | -20.95 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6739-3p | chr1:53889334-53889341 | 8mer-1a | chr1:53889322-53889341 | 161.00 | -17.48 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-4677-5p | chr1:53889333-53889340 | 8mer-1a | chr1:53889322-53889341 | 161.00 | -17.48 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6072 | chr1:53889286-53889293 | 8mer-1a | chr1:53889286-53889305 | 156.00 | -29.06 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6715b-3p | chr1:53889306-53889313 | 8mer-1a | chr1:53889300-53889325 | 157.00 | -27.63 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-3059-3p | chr1:53889272-53889279 | 8mer-1a | chr1:53889271-53889295 | 151.00 | -20.55 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6760-3p | chr1:53889326-53889333 | 8mer-1a | chr1:53889313-53889333 | 171.00 | -26.77 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-22-5p | chr1:53889332-53889339 | 8mer-1a | chr1:53889322-53889341 | 161.00 | -17.48 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-4750-3p | chr1:53889382-53889389 | 8mer-1a | chr1:53889373-53889393 | 146.00 | -17.17 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6804-3p | chr1:53889263-53889270 | 8mer-1a | chr1:53889259-53889277 | 161.00 | -25.42 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-645 | chr1:53889270-53889277 | 8mer-1a | chr1:53889259-53889277 | 161.00 | -25.42 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6069 | chr1:53889352-53889359 | 8mer-1a | chr1:53889341-53889361 | 155.00 | -24.34 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-3667-3p | chr1:53889290-53889297 | 8mer-1a | chr1:53889286-53889305 | 156.00 | -29.06 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6891-3p | chr1:53889286-53889293 | 8mer-1a | chr1:53889286-53889305 | 156.00 | -29.06 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6837-3p | chr1:53889329-53889336 | 8mer-1a | chr1:53889322-53889341 | 161.00 | -17.48 |
| ROSMAP | ENST00000072644 | 53889244 | 53889463 | hsa-miR-6089 | chr1:53889446-53889453 | 8mer-1a | chr1:53889440-53889461 | 180.00 | -34.29 |
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SNVs in the skipped exons for YIPF1 |
| - 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 |
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AD stage-associated exon skippint events for YIPF1 |
| 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 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for YIPF1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for YIPF1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | PTBP1 | exon_skip_277051 | -4.395562e-01 | 6.764717e-09 |
| CB | RBM3 | exon_skip_197852 | 5.198082e-01 | 7.942987e-12 |
| CB | TRA2A | exon_skip_197852 | -4.604386e-01 | 2.706392e-09 |
| IFG | ZNF638 | exon_skip_163247 | 5.388885e-01 | 1.171355e-02 |
| IFG | RBM6 | exon_skip_163247 | 5.740334e-01 | 6.505156e-03 |
| IFG | SRSF11 | exon_skip_163247 | 5.115536e-01 | 1.777146e-02 |
| IFG | IGF2BP3 | exon_skip_163247 | 5.221787e-01 | 1.517263e-02 |
| IFG | RBM47 | exon_skip_163247 | 5.089554e-01 | 1.845846e-02 |
| IFG | PCBP1 | exon_skip_163247 | 4.557300e-01 | 3.787411e-02 |
| IFG | PCBP2 | exon_skip_163247 | 5.603659e-01 | 8.238210e-03 |
| IFG | PABPC1 | exon_skip_163247 | 5.317293e-01 | 1.310715e-02 |
| IFG | ZC3H10 | exon_skip_163247 | 4.583342e-01 | 3.665413e-02 |
| PCC | RBM3 | exon_skip_197852 | 4.494476e-01 | 6.918409e-12 |
| TC | RBM3 | exon_skip_197852 | 6.452978e-01 | 2.184045e-19 |
| TC | HNRNPK | exon_skip_197852 | 4.032726e-01 | 2.359830e-07 |
| TC | HNRNPD | exon_skip_197852 | 5.115426e-01 | 1.405500e-11 |
| TC | NOVA1 | exon_skip_197852 | 4.976965e-01 | 5.942634e-11 |
| TC | KHDRBS2 | exon_skip_163247 | -4.625657e-01 | 1.747697e-09 |
| TC | RALYL | exon_skip_163247 | -4.337282e-01 | 2.136229e-08 |
| TC | NOVA1 | exon_skip_163247 | -4.291595e-01 | 3.110224e-08 |
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RelatedDrugs for YIPF1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for YIPF1 |
| 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)
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