|
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 RFTN1 |
Gene summary |
Gene information | Gene symbol | RFTN1 | Gene ID | 23180 |
Gene name | raftlin, lipid raft linker 1 | |
Synonyms | MIG2|PIB10|PIG9|RAFTLIN | |
Cytomap | 3p24.3 | |
Type of gene | protein-coding | |
Description | raftlincell migration-inducing gene 2 proteinproliferation-inducing protein 10proliferation-inducing protein 9raft-linking protein | |
Modification date | 20200313 | |
UniProtAcc | C9JHG2, | |
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 RFTN1 |
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 |
Landscape of isoform expressions across multiple brain tissues between AD and control. |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for RFTN1 |
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_102732 | chr3 | 16357932:16358047:16370076:16370279:16377718:16378102 | 16370076:16370279 |
exon_skip_145839 | chr3 | 16323376:16323457:16326773:16326876:16357932:16358047 | 16326773:16326876 |
exon_skip_184812 | chr3 | 16317175:16317232:16323376:16323457:16326773:16326867 | 16323376:16323457 |
exon_skip_20917 | chr3 | 16409473:16409483:16433851:16434037:16493725:16493877 | 16433851:16434037 |
exon_skip_260606 | chr3 | 16433851:16434037:16493725:16493877:16513442:16513522 | 16493725:16493877 |
exon_skip_67927 | chr3 | 16433851:16434037:16471961:16472118:16472519:16472599 | 16471961:16472118 |
exon_skip_74750 | chr3 | 16326773:16326876:16357932:16358047:16370076:16370279 | 16357932:16358047 |
exon_skip_8217 | chr3 | 16433851:16434037:16493725:16493877:16513442:16513465 | 16493725:16493877 |
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 RFTN1 |
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 |
ENST00000334133 | 16493725 | 16493877 | 3UTR-3CDS |
ENST00000334133 | 16323376 | 16323457 | Frame-shift |
ENST00000334133 | 16326773 | 16326876 | Frame-shift |
ENST00000334133 | 16357932 | 16358047 | 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 |
ENST00000334133 | 16357932 | 16358047 | 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 |
ENST00000334133 | 16493725 | 16493877 | 3UTR-3CDS |
ENST00000334133 | 16326773 | 16326876 | Frame-shift |
ENST00000334133 | 16357932 | 16358047 | Frame-shift |
ENST00000334133 | 16433851 | 16434037 | Frame-shift |
ENST00000334133 | 16370076 | 16370279 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for RFTN1 |
p-ENSG00000131378_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 |
ENST00000334133 | 2999 | 578 | 16370076 | 16370279 | 1100 | 1302 | 275 | 343 |
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 |
Q14699 | 275 | 343 | 2 | 578 | Chain | ID=PRO_0000050718;Note=Raftlin |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in RFTN1 |
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 RFTN1 |
- 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 RFTN1 |
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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RFTN1 |
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 RFTN1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for RFTN1 |
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 RFTN1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |