|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for YIPF4 |
 Gene summary |
| Gene information | Gene symbol | YIPF4 | Gene ID | 84272 |
| Gene name | Yip1 domain family member 4 | |
| Synonyms | FinGER4|Nbla11189 | |
| Cytomap | 2p22.3 | |
| Type of gene | protein-coding | |
| Description | protein YIPF4YIP1 family member 4putative protein product of Nbla11189 | |
| Modification date | 20180519 | |
| UniProtAcc | Q9BSR8 | |
| Context | PubMed: YIPF4 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
Top |
Exon skipping events across known transcript of Ensembl for YIPF4 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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. |
 |
Top |
Gene isoform structures and expression levels for YIPF4 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for YIPF4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_324648 | 2 | 32503299:32503303:32515551:32515705:32523302:32523380 | 32515551:32515705 | ENSG00000119820.6 | ENST00000437765.1 |
| exon_skip_324653 | 2 | 32515558:32515705:32517245:32517417:32523302:32523380 | 32517245:32517417 | ENSG00000119820.6 | ENST00000238831.4 |
| exon_skip_324655 | 2 | 32515551:32515705:32523302:32523380:32526450:32526564 | 32523302:32523380 | ENSG00000119820.6 | ENST00000437765.1 |
| exon_skip_324656 | 2 | 32517245:32517417:32523302:32523380:32526450:32526564 | 32523302:32523380 | ENSG00000119820.6 | ENST00000238831.4 |
| exon_skip_324659 | 2 | 32523302:32523380:32526450:32526564:32530557:32530935 | 32526450:32526564 | ENSG00000119820.6 | ENST00000238831.4,ENST00000437765.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for YIPF4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_324648 | 2 | 32503299:32503303:32515551:32515705:32523302:32523380 | 32515551:32515705 | ENSG00000119820.6 | ENST00000437765.1 |
| exon_skip_324653 | 2 | 32515558:32515705:32517245:32517417:32523302:32523380 | 32517245:32517417 | ENSG00000119820.6 | ENST00000238831.4 |
| exon_skip_324655 | 2 | 32515551:32515705:32523302:32523380:32526450:32526564 | 32523302:32523380 | ENSG00000119820.6 | ENST00000437765.1 |
| exon_skip_324656 | 2 | 32517245:32517417:32523302:32523380:32526450:32526564 | 32523302:32523380 | ENSG00000119820.6 | ENST00000238831.4 |
| exon_skip_324659 | 2 | 32523302:32523380:32526450:32526564:32530557:32530935 | 32526450:32526564 | ENSG00000119820.6 | ENST00000238831.4,ENST00000437765.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for YIPF4 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000238831 | 32517245 | 32517417 | Frame-shift |
| ENST00000238831 | 32523302 | 32523380 | In-frame |
| ENST00000238831 | 32526450 | 32526564 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000238831 | 32517245 | 32517417 | Frame-shift |
| ENST00000238831 | 32523302 | 32523380 | In-frame |
| ENST00000238831 | 32526450 | 32526564 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for YIPF4 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| Loci of skipped exons in TCGA 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 |
| ENST00000238831 | 11966 | 244 | 32523302 | 32523380 | 652 | 729 | 135 | 161 |
| ENST00000238831 | 11966 | 244 | 32526450 | 32526564 | 730 | 843 | 161 | 199 |
| Loci of skipped exons in GTEx 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 |
| ENST00000238831 | 11966 | 244 | 32523302 | 32523380 | 652 | 729 | 135 | 161 |
| ENST00000238831 | 11966 | 244 | 32526450 | 32526564 | 730 | 843 | 161 | 199 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| 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 |
| Q9BSR8 | 135 | 161 | 1 | 244 | Chain | ID=PRO_0000242632;Note=Protein YIPF4 |
| Q9BSR8 | 135 | 161 | 135 | 138 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9BSR8 | 135 | 161 | 160 | 166 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9BSR8 | 135 | 161 | 139 | 159 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BSR8 | 161 | 199 | 1 | 244 | Chain | ID=PRO_0000242632;Note=Protein YIPF4 |
| Q9BSR8 | 161 | 199 | 160 | 166 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9BSR8 | 161 | 199 | 188 | 195 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9BSR8 | 161 | 199 | 167 | 187 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BSR8 | 161 | 199 | 196 | 216 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Lost protein functional features of individual exon skipping events in GTEx. |
| 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 |
| Q9BSR8 | 135 | 161 | 1 | 244 | Chain | ID=PRO_0000242632;Note=Protein YIPF4 |
| Q9BSR8 | 135 | 161 | 135 | 138 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9BSR8 | 135 | 161 | 160 | 166 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9BSR8 | 135 | 161 | 139 | 159 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BSR8 | 161 | 199 | 1 | 244 | Chain | ID=PRO_0000242632;Note=Protein YIPF4 |
| Q9BSR8 | 161 | 199 | 160 | 166 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9BSR8 | 161 | 199 | 188 | 195 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9BSR8 | 161 | 199 | 167 | 187 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BSR8 | 161 | 199 | 196 | 216 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
SNVs in the skipped exons for YIPF4 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_324653 | 32517246 | 32517417 | 32517380 | 32517380 | Frame_Shift_Del | T | - | p.L123fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_324653 | 32517246 | 32517417 | 32517380 | 32517380 | Frame_Shift_Del | T | - | p.L123fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_324659 | 32526451 | 32526564 | 32526490 | 32526490 | Frame_Shift_Del | T | - | p.L176fs |
| UCEC | TCGA-AP-A056-01 | exon_skip_324648 | 32515552 | 32515705 | 32515564 | 32515564 | Nonsense_Mutation | C | A | p.S31* |
| STAD | TCGA-BR-8680-01 | exon_skip_324648 | 32515552 | 32515705 | 32515614 | 32515614 | Nonsense_Mutation | G | T | p.E48* |
| STAD | TCGA-BR-8680-01 | exon_skip_324648 | 32515552 | 32515705 | 32515614 | 32515614 | Nonsense_Mutation | G | T | p.E48X |
| UCEC | TCGA-AP-A0LM-01 | exon_skip_324656 exon_skip_324655 | 32523303 | 32523380 | 32523378 | 32523378 | Nonsense_Mutation | G | T | p.E161* |
| LUSC | TCGA-37-3789-01 | exon_skip_324653 | 32517246 | 32517417 | 32517245 | 32517245 | Splice_Site | G | T | p.L78_splice |
| STAD | TCGA-CD-A4MI-01 | exon_skip_324653 | 32517246 | 32517417 | 32517418 | 32517418 | Splice_Site | G | A | p.R135_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-BR-8680-01 |
| Cancer type: STAD | |
| ESID: exon_skip_324648 | |
| Skipped exon start: 32515552 | |
| Skipped exon end: 32515705 | |
| Mutation start: 32515614 | |
| Mutation end: 32515614 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: T | |
| AAchange: p.E48X | |
| Sample: TCGA-BR-8680-01 |
| Cancer type: STAD | |
| ESID: exon_skip_324648 | |
| Skipped exon start: 32515552 | |
| Skipped exon end: 32515705 | |
| Mutation start: 32515614 | |
| Mutation end: 32515614 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: T | |
| AAchange: p.E48* | |
exon_skip_106946_STAD_TCGA-BR-8680-01.png | |
exon_skip_107215_STAD_TCGA-BR-8680-01.png | |
exon_skip_122567_STAD_TCGA-BR-8680-01.png | |
exon_skip_122573_STAD_TCGA-BR-8680-01.png | |
exon_skip_144294_STAD_TCGA-BR-8680-01.png | |
exon_skip_26878_STAD_TCGA-BR-8680-01.png | |
exon_skip_30156_STAD_TCGA-BR-8680-01.png | |
exon_skip_324648_STAD_TCGA-BR-8680-01.png | |
exon_skip_326437_STAD_TCGA-BR-8680-01.png | |
exon_skip_326558_STAD_TCGA-BR-8680-01.png | |
exon_skip_326569_STAD_TCGA-BR-8680-01.png | |
exon_skip_328488_STAD_TCGA-BR-8680-01.png | |
exon_skip_335090_STAD_TCGA-BR-8680-01.png | |
exon_skip_389166_STAD_TCGA-BR-8680-01.png | |
exon_skip_40432_STAD_TCGA-BR-8680-01.png | |
exon_skip_40460_STAD_TCGA-BR-8680-01.png | |
exon_skip_40461_STAD_TCGA-BR-8680-01.png | |
exon_skip_436498_STAD_TCGA-BR-8680-01.png | |
exon_skip_466512_STAD_TCGA-BR-8680-01.png | |
exon_skip_478774_STAD_TCGA-BR-8680-01.png | |
exon_skip_484956_STAD_TCGA-BR-8680-01.png | |
exon_skip_64135_STAD_TCGA-BR-8680-01.png | |
exon_skip_64136_STAD_TCGA-BR-8680-01.png | |
exon_skip_64137_STAD_TCGA-BR-8680-01.png | |
exon_skip_69365_STAD_TCGA-BR-8680-01.png | |
exon_skip_69375_STAD_TCGA-BR-8680-01.png | |
exon_skip_75101_STAD_TCGA-BR-8680-01.png | |
| - 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 |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 32515552 | 32515705 | 32515598 | 32515599 | In_Frame_Ins | - | GTAAGC | p.42_43insVS |
| SW756_CERVIX | 32515552 | 32515705 | 32515564 | 32515564 | Missense_Mutation | C | T | p.S31L |
| LB771HNC_UPPER_AERODIGESTIVE_TRACT | 32515552 | 32515705 | 32515573 | 32515573 | Missense_Mutation | C | A | p.S34Y |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32515552 | 32515705 | 32515679 | 32515679 | Missense_Mutation | T | G | p.D69E |
| NCIH2110_LUNG | 32515552 | 32515705 | 32515699 | 32515699 | Missense_Mutation | C | T | p.P76L |
| RL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32517246 | 32517417 | 32517283 | 32517283 | Missense_Mutation | A | C | p.K91Q |
| SNU1040_LARGE_INTESTINE | 32517246 | 32517417 | 32517304 | 32517304 | Missense_Mutation | C | T | p.P98S |
| HCT15_LARGE_INTESTINE | 32517246 | 32517417 | 32517332 | 32517332 | Missense_Mutation | A | G | p.Q107R |
| L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32517246 | 32517417 | 32517379 | 32517379 | Missense_Mutation | C | G | p.L123V |
| SH4_SKIN | 32523303 | 32523380 | 32523309 | 32523309 | Missense_Mutation | T | C | p.S138P |
| HT115_LARGE_INTESTINE | 32526451 | 32526564 | 32526511 | 32526511 | Missense_Mutation | G | A | p.A182T |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 32526451 | 32526564 | 32526517 | 32526517 | Missense_Mutation | G | A | p.V184I |
| JHUEM2_ENDOMETRIUM | 32526451 | 32526564 | 32526559 | 32526559 | Missense_Mutation | A | G | p.I198V |
| SNU119_OVARY | 32526451 | 32526564 | 32526559 | 32526559 | Missense_Mutation | A | G | p.I198V |
| KPNYS_AUTONOMIC_GANGLIA | 32526451 | 32526564 | 32526559 | 32526559 | Missense_Mutation | A | G | p.I198V |
| JHUEM7_ENDOMETRIUM | 32515552 | 32515705 | 32515614 | 32515614 | Nonsense_Mutation | G | T | p.E48* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for YIPF4 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for YIPF4 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for YIPF4 |
Top |
RelatedDrugs for YIPF4 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for YIPF4 |
| 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)
|