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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 RAB11FIP3 |
Gene summary |
Gene information | Gene symbol | RAB11FIP3 | Gene ID | 9727 |
Gene name | RAB11 family interacting protein 3 | |
Synonyms | CART1|FIP3-Rab11|Rab11-FIP3 | |
Cytomap | 16p13.3 | |
Type of gene | protein-coding | |
Description | rab11 family-interacting protein 3EF hands-containing Rab-interacting proteinMU-MB-17.148RAB11 family interacting protein 3 (class II)arfophilin-1cytoplasmic adaptor for RAR and TReferin | |
Modification date | 20200313 | |
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 |
RAB11FIP3 | GO:0032456 | endocytic recycling | 17394487 |
RAB11FIP3 | GO:0070164 | negative regulation of adiponectin secretion | 24040321 |
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Gene structures and expression levels for RAB11FIP3 |
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. |
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 | ENST00000450428.5 | RAB11FIP3-205:protein_coding:RAB11FIP3 | 4.819026e+02 | -1.134379e+00 | 3.319311e-10 | 1.751661e-08 |
TC | DOWN | ENST00000483002.1 | RAB11FIP3-209:retained_intron:RAB11FIP3 | 8.404965e-01 | -1.139250e+00 | 7.890210e-03 | 4.702859e-02 |
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 RAB11FIP3 |
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_115513 | chr16 | 461404:461497:471295:471389:482525:482736 | 471295:471389 |
exon_skip_161417 | chr16 | 503004:503097:505524:505627:510660:510800 | 505524:505627 |
exon_skip_207668 | chr16 | 519754:519891:520122:520277:520459:520599 | 520122:520277 |
exon_skip_216500 | chr16 | 471295:471389:482525:482736:488851:489000 | 482525:482736 |
exon_skip_277052 | chr16 | 488942:489000:496824:496859:503004:503063 | 496824:496859 |
exon_skip_293656 | chr16 | 519754:519891:520122:520277:520459:520552 | 520122:520277 |
exon_skip_293851 | chr16 | 491134:491268:496824:496859:503004:503063 | 496824:496859 |
exon_skip_5086 | chr16 | 482657:482736:488851:489000:496824:496859 | 488851:489000 |
exon_skip_73141 | chr16 | 519763:519891:520122:520277:520459:520599 | 520122:520277 |
exon_skip_93805 | chr16 | 488942:489000:491134:491268:496824:496859 | 491134:491268 |
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 |
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Open reading frame (ORF) annotation in the exon skipping event for RAB11FIP3 |
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 |
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 |
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Infer the effects of exon skipping event on protein functional features for RAB11FIP3 |
p-ENSG00000090565_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 |
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 |
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3'-UTR located exon skipping events that lost miRNA binding sites in RAB11FIP3 |
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 |
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SNVs in the skipped exons for RAB11FIP3 |
- 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 RAB11FIP3 |
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 RAB11FIP3 |
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 RAB11FIP3 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | SRSF2 | exon_skip_93805 | 4.209352e-01 | 3.298900e-08 |
CB | TIA1 | exon_skip_93805 | 5.057675e-01 | 1.045529e-11 |
CB | MATR3 | exon_skip_93805 | 4.488692e-01 | 2.952786e-09 |
CB | HNRNPK | exon_skip_93805 | 5.497193e-01 | 6.171146e-14 |
CB | PCBP2 | exon_skip_93805 | 6.170006e-01 | 4.714939e-18 |
CB | NUP42 | exon_skip_93805 | 5.014159e-01 | 1.671501e-11 |
CB | RALYL | exon_skip_93805 | 6.308981e-01 | 4.963486e-19 |
CB | PTBP3 | exon_skip_93805 | 4.200484e-01 | 3.549067e-08 |
CB | HNRNPL | exon_skip_93805 | 5.172777e-01 | 2.925787e-12 |
CB | PABPC1 | exon_skip_93805 | 4.531177e-01 | 2.006158e-09 |
DLPFC | KHDRBS2 | exon_skip_93805 | 7.537334e-01 | 3.868195e-64 |
FL | SRSF2 | exon_skip_93805 | 4.856443e-01 | 1.229194e-12 |
FL | MATR3 | exon_skip_93805 | 4.824462e-01 | 1.808987e-12 |
FL | HNRNPK | exon_skip_93805 | 4.392407e-01 | 2.301554e-10 |
FL | KHDRBS3 | exon_skip_93805 | 5.305405e-01 | 3.463782e-15 |
FL | RBM24 | exon_skip_93805 | 4.656767e-01 | 1.286698e-11 |
FL | RALYL | exon_skip_93805 | 4.972197e-01 | 2.933770e-13 |
FL | HNRNPL | exon_skip_93805 | 4.749859e-01 | 4.387442e-12 |
FL | NOVA1 | exon_skip_93805 | 4.721947e-01 | 6.078495e-12 |
HCC | TIA1 | exon_skip_93805 | -5.126261e-01 | 1.071196e-19 |
HCC | IGF2BP2 | exon_skip_93805 | -4.057281e-01 | 3.052907e-12 |
HCC | TRNAU1AP | exon_skip_93805 | -4.642232e-01 | 5.368097e-16 |
HCC | RBM47 | exon_skip_93805 | -4.334719e-01 | 6.218840e-14 |
HCC | KHDRBS3 | exon_skip_93805 | -4.851977e-01 | 1.578226e-17 |
HCC | PTBP1 | exon_skip_93805 | -6.954860e-01 | 8.694377e-41 |
HCC | PABPC1 | exon_skip_93805 | -4.440972e-01 | 1.270531e-14 |
IFG | IGF2BP2 | exon_skip_93805 | -4.400250e-01 | 1.911846e-02 |
IFG | RBM47 | exon_skip_93805 | -4.391966e-01 | 1.937216e-02 |
IFG | KHDRBS2 | exon_skip_93805 | 4.700479e-01 | 1.160333e-02 |
IFG | KHDRBS3 | exon_skip_93805 | 4.033705e-01 | 3.329537e-02 |
IFG | RALYL | exon_skip_93805 | 4.000642e-01 | 3.490756e-02 |
IFG | PTBP1 | exon_skip_93805 | -5.500258e-01 | 2.427244e-03 |
PCC | RALYL | exon_skip_93805 | 4.244737e-01 | 9.034295e-11 |
PCC | PTBP1 | exon_skip_93805 | -5.900921e-01 | 1.816061e-21 |
PG | TARDBP | exon_skip_93805 | 4.362108e-01 | 3.802187e-09 |
PG | SRSF2 | exon_skip_93805 | 4.638947e-01 | 2.721425e-10 |
PG | TIA1 | exon_skip_93805 | 4.353431e-01 | 4.114310e-09 |
PG | MATR3 | exon_skip_93805 | 6.151804e-01 | 9.147780e-19 |
PG | TRNAU1AP | exon_skip_93805 | 4.497003e-01 | 1.083400e-09 |
PG | HNRNPK | exon_skip_93805 | 4.943293e-01 | 1.126505e-11 |
PG | KHDRBS2 | exon_skip_93805 | 6.634873e-01 | 1.510744e-22 |
PG | KHDRBS3 | exon_skip_93805 | 6.942939e-01 | 2.384560e-25 |
PG | RBM24 | exon_skip_93805 | 6.101907e-01 | 2.067670e-18 |
PG | NUP42 | exon_skip_93805 | 5.020110e-01 | 4.792704e-12 |
PG | RALYL | exon_skip_93805 | 6.981362e-01 | 1.007045e-25 |
PG | HNRNPL | exon_skip_93805 | 5.343948e-01 | 1.022540e-13 |
PG | NOVA1 | exon_skip_93805 | 6.004235e-01 | 9.794070e-18 |
STG | IGF2BP2 | exon_skip_93805 | -4.430216e-01 | 2.177131e-05 |
STG | RALYL | exon_skip_93805 | 4.256970e-01 | 4.873222e-05 |
TC | SRSF2 | exon_skip_93805 | 5.057655e-01 | 8.993823e-12 |
TC | MATR3 | exon_skip_93805 | 7.380107e-01 | 8.712878e-29 |
TC | KHDRBS2 | exon_skip_93805 | 8.477069e-01 | 2.335503e-45 |
TC | KHDRBS3 | exon_skip_93805 | 7.611078e-01 | 1.635219e-31 |
TC | RBM24 | exon_skip_93805 | 7.983334e-01 | 1.256143e-36 |
TC | PPRC1 | exon_skip_93805 | 4.059922e-01 | 1.001893e-07 |
TC | NUP42 | exon_skip_93805 | 6.955111e-01 | 1.877890e-24 |
TC | RALYL | exon_skip_93805 | 8.973629e-01 | 5.190787e-58 |
TC | PTBP1 | exon_skip_93805 | -4.291539e-01 | 1.493690e-08 |
TC | PTBP3 | exon_skip_93805 | 4.780914e-01 | 1.621994e-10 |
TC | NOVA1 | exon_skip_93805 | 6.450621e-01 | 3.380928e-20 |
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RelatedDrugs for RAB11FIP3 |
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 RAB11FIP3 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |