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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 RTN1 |
Gene summary |
Gene information | Gene symbol | RTN1 | Gene ID | 6252 |
Gene name | reticulon 1 | |
Synonyms | NSP | |
Cytomap | 14q23.1 | |
Type of gene | protein-coding | |
Description | reticulon-1neuroendocrine-specific protein | |
Modification date | 20200320 | |
UniProtAcc | ||
Context | - 28623007(Gene Networks in Neurodegenerative Disorders) |
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 RTN1 |
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 |
PCC | UP | ENST00000474911.5 | RTN1-205:retained_intron:RTN1 | 3.388490e+02 | 1.545878e+00 | 4.189920e-05 | 3.405941e-03 |
STG | DOWN | ENST00000267484.10 | RTN1-201:protein_coding:RTN1 | 6.562039e+02 | -8.801238e-01 | 1.828651e-05 | 3.967998e-03 |
PG | DOWN | ENST00000342503.8 | RTN1-202:protein_coding:RTN1 | 8.755085e+02 | -9.870628e-01 | 5.594615e-06 | 3.284252e-04 |
CB | UP | ENST00000557422.1 | RTN1-208:lncRNA:RTN1 | 1.284160e+02 | 1.615458e+00 | 5.317694e-11 | 3.760125e-09 |
TC | DOWN | ENST00000395090.5 | RTN1-203:protein_coding:RTN1 | 1.579850e+02 | -1.956908e+00 | 8.649117e-11 | 1.706941e-08 |
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 RTN1 |
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_117050 | chr14 | 59603892:59603921:59605368:59605506:59607285:59607492 | 59605368:59605506 |
exon_skip_138647 | chr14 | 59603852:59603921:59605368:59605506:59607285:59607297 | 59605368:59605506 |
exon_skip_14908 | chr14 | 59607475:59607492:59610122:59610232:59630446:59630609 | 59610122:59610232 |
exon_skip_149799 | chr14 | 59726919:59727668:59745708:59746481:59870390:59870420 | 59745708:59746481 |
exon_skip_158653 | chr14 | 59607285:59607492:59610122:59610232:59630446:59630475 | 59610122:59610232 |
exon_skip_203048 | chr14 | 59607285:59607492:59610122:59610232:59630446:59630609 | 59610122:59610232 |
exon_skip_204866 | chr14 | 59607482:59607492:59610122:59610232:59630446:59630609 | 59610122:59610232 |
exon_skip_214064 | chr14 | 59603065:59603123:59603212:59603258:59603852:59603921 | 59603212:59603258 |
exon_skip_276713 | chr14 | 59603066:59603123:59603212:59603258:59603852:59603921 | 59603212:59603258 |
exon_skip_281183 | chr14 | 59603852:59603921:59605368:59605506:59607285:59607492 | 59605368:59605506 |
exon_skip_39802 | chr14 | 59603852:59603921:59607285:59607492:59630446:59630609 | 59607285:59607492 |
exon_skip_58752 | chr14 | 59605383:59605506:59607285:59607492:59630446:59630609 | 59607285:59607492 |
exon_skip_72443 | chr14 | 59603852:59603921:59605368:59605506:59607285:59607430 | 59605368:59605506 |
exon_skip_90700 | chr14 | 59603852:59603921:59605368:59605506:59607285:59607404 | 59605368:59605506 |
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 RTN1 |
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 |
ENST00000267484 | 59603212 | 59603258 | Frame-shift |
ENST00000267484 | 59605368 | 59605506 | Frame-shift |
ENST00000267484 | 59745708 | 59746481 | 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 |
ENST00000267484 | 59605368 | 59605506 | 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 |
ENST00000267484 | 59603212 | 59603258 | Frame-shift |
ENST00000267484 | 59605368 | 59605506 | Frame-shift |
ENST00000267484 | 59745708 | 59746481 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RTN1 |
p-ENSG00000139970_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 |
ENST00000267484 | 3452 | 776 | 59745708 | 59746481 | 578 | 1350 | 80 | 338 |
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 |
ENST00000267484 | 3452 | 776 | 59745708 | 59746481 | 578 | 1350 | 80 | 338 |
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 |
Q16799 | 80 | 338 | 1 | 568 | Alternative sequence | ID=VSP_005645;Note=In isoform RTN1-C. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:7685762;Dbxref=PMID:15489334,PMID:7685762 |
Q16799 | 80 | 338 | 1 | 420 | Alternative sequence | ID=VSP_005644;Note=In isoform RTN1-B. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7685762;Dbxref=PMID:7685762 |
Q16799 | 80 | 338 | 1 | 776 | Chain | ID=PRO_0000168158;Note=Reticulon-1 |
Q16799 | 80 | 338 | 327 | 327 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q64548 |
Q16799 | 80 | 338 | 247 | 247 | Natural variant | ID=VAR_053630;Note=G->E;Dbxref=dbSNP:rs35645652 |
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 |
Q16799 | 80 | 338 | 1 | 568 | Alternative sequence | ID=VSP_005645;Note=In isoform RTN1-C. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:15489334,ECO:0000303|PubMed:7685762;Dbxref=PMID:15489334,PMID:7685762 |
Q16799 | 80 | 338 | 1 | 420 | Alternative sequence | ID=VSP_005644;Note=In isoform RTN1-B. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:7685762;Dbxref=PMID:7685762 |
Q16799 | 80 | 338 | 1 | 776 | Chain | ID=PRO_0000168158;Note=Reticulon-1 |
Q16799 | 80 | 338 | 327 | 327 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q64548 |
Q16799 | 80 | 338 | 247 | 247 | Natural variant | ID=VAR_053630;Note=G->E;Dbxref=dbSNP:rs35645652 |
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3'-UTR located exon skipping events that lost miRNA binding sites in RTN1 |
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 RTN1 |
- 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 RTN1 |
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 RTN1 |
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 RTN1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | NUP42 | exon_skip_27655 | 4.067087e-01 | 1.080563e-06 |
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RelatedDrugs for RTN1 |
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 RTN1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |