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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 RTN3 |
Gene summary |
Gene information | Gene symbol | RTN3 | Gene ID | 10313 |
Gene name | reticulon 3 | |
Synonyms | ASYIP|HAP|NSPL2|NSPLII|RTN3-A1 | |
Cytomap | 11q13.1 | |
Type of gene | protein-coding | |
Description | reticulon-3ASY interacting proteinNSP-like protein 2NSP-like protein IIhomolog of ASY proteinneuroendocrine-specific protein-like 2neuroendocrine-specific protein-like II | |
Modification date | 20200327 | |
UniProtAcc | ||
Context | - 27883331(Effects of Altered RTN3 Expression on BACE1 Activity and Alzheimer's Neuritic Plaques) |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
RTN3 | GO:0071787 | endoplasmic reticulum tubular network formation | 25612671 |
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Gene structures and expression levels for RTN3 |
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 |
PG | DOWN | ENST00000545432.5 | RTN3-214:protein_coding:RTN3 | 2.772795e+00 | -9.141061e-01 | 1.317319e-04 | 3.365350e-03 |
PG | DOWN | ENST00000234347.10 | PRTN3-201:protein_coding:PRTN3 | 1.619879e+00 | -9.268314e-01 | 5.060568e-04 | 8.907658e-03 |
CB | UP | ENST00000543123.1 | RTN3-212:retained_intron:RTN3 | 5.120522e+01 | 8.456341e-01 | 1.243067e-12 | 1.786756e-10 |
CB | UP | ENST00000354497.4 | RTN3-204:protein_coding:RTN3 | 2.665876e+01 | 2.058503e+00 | 5.087756e-12 | 5.699529e-10 |
CB | UP | ENST00000536011.5 | RTN3-207:nonsense_mediated_decay:RTN3 | 5.376241e+00 | 2.627848e+00 | 4.602197e-10 | 2.306029e-08 |
CB | UP | ENST00000543552.5 | RTN3-213:protein_coding:RTN3 | 2.547356e+00 | 8.815397e-01 | 1.113831e-03 | 5.654789e-03 |
TC | DOWN | ENST00000234347.10 | PRTN3-201:protein_coding:PRTN3 | 1.065023e+01 | -8.270473e-01 | 8.650290e-04 | 8.833044e-03 |
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 RTN3 |
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_102867 | chr11 | 63753662:63753708:63756112:63756170:63758156:63758240 | 63756112:63756170 |
exon_skip_105577 | chr11 | 63681718:63681778:63746947:63747024:63749991:63750198 | 63746947:63747024 |
exon_skip_10647 | chr11 | 63681573:63681778:63746947:63747024:63749991:63750056 | 63746947:63747024 |
exon_skip_111759 | chr11 | 63753662:63753708:63756112:63756170:63758156:63758196 | 63756112:63756170 |
exon_skip_112570 | chr11 | 63750075:63750198:63756112:63756170:63758156:63758421 | 63756112:63756170 |
exon_skip_115006 | chr11 | 63753662:63753708:63756112:63756170:63758156:63758228 | 63756112:63756170 |
exon_skip_118400 | chr11 | 63681597:63681778:63704851:63704907:63718981:63719189 | 63704851:63704907 |
exon_skip_134894 | chr11 | 63681597:63681778:63704851:63704907:63718702:63721032 | 63704851:63704907 |
exon_skip_136874 | chr11 | 63681573:63681778:63718702:63721032:63749991:63750056 | 63718702:63721032 |
exon_skip_13831 | chr11 | 63681573:63681778:63704851:63704907:63718702:63721032 | 63704851:63704907 |
exon_skip_140859 | chr11 | 63753662:63753708:63756112:63756170:63758156:63758177 | 63756112:63756170 |
exon_skip_145285 | chr11 | 63681573:63681778:63718981:63721032:63749991:63750056 | 63718981:63721032 |
exon_skip_146554 | chr11 | 63681573:63681778:63704851:63704907:63718981:63719189 | 63704851:63704907 |
exon_skip_146845 | chr11 | 63681573:63681778:63704851:63704907:63749991:63750197 | 63704851:63704907 |
exon_skip_149971 | chr11 | 63681573:63681778:63749991:63750198:63756112:63756170 | 63749991:63750198 |
exon_skip_160375 | chr11 | 63681718:63681778:63704851:63704907:63749991:63750198 | 63704851:63704907 |
exon_skip_168608 | chr11 | 63749991:63750198:63756112:63756170:63758156:63758184 | 63756112:63756170 |
exon_skip_177360 | chr11 | 63681573:63681778:63704851:63704907:63749991:63750056 | 63704851:63704907 |
exon_skip_180808 | chr11 | 63681573:63681778:63718981:63721032:63749991:63750197 | 63718981:63721032 |
exon_skip_185561 | chr11 | 63681573:63681778:63749991:63750198:63753069:63753138 | 63749991:63750198 |
exon_skip_187953 | chr11 | 63750136:63750198:63752507:63752645:63753069:63753138 | 63752507:63752645 |
exon_skip_189506 | chr11 | 63681458:63681778:63746947:63747024:63749991:63750198 | 63746947:63747024 |
exon_skip_193411 | chr11 | 63681718:63681778:63718702:63721032:63749991:63750198 | 63718702:63721032 |
exon_skip_193979 | chr11 | 63750075:63750198:63752507:63752645:63753069:63753138 | 63752507:63752645 |
exon_skip_194807 | chr11 | 63750075:63750198:63756112:63756170:63758156:63758225 | 63756112:63756170 |
exon_skip_203781 | chr11 | 63681573:63681778:63718981:63721032:63749991:63750198 | 63718981:63721032 |
exon_skip_207991 | chr11 | 63681573:63681778:63718702:63721032:63749991:63750198 | 63718702:63721032 |
exon_skip_214509 | chr11 | 63681474:63681778:63704851:63704907:63713971:63714479 | 63704851:63704907 |
exon_skip_220985 | chr11 | 63681573:63681778:63718702:63721032:63749991:63750197 | 63718702:63721032 |
exon_skip_225573 | chr11 | 63704851:63704907:63718702:63721032:63749991:63750198 | 63718702:63721032 |
exon_skip_231525 | chr11 | 63681718:63681778:63718981:63721032:63749991:63750198 | 63718981:63721032 |
exon_skip_233521 | chr11 | 63704880:63704907:63718702:63721032:63749991:63750198 | 63718702:63721032 |
exon_skip_257322 | chr11 | 63749991:63750198:63756112:63756170:63758156:63758421 | 63756112:63756170 |
exon_skip_259406 | chr11 | 63681718:63681778:63704851:63704907:63718702:63721032 | 63704851:63704907 |
exon_skip_261656 | chr11 | 63681573:63681778:63746947:63747024:63749991:63750198 | 63746947:63747024 |
exon_skip_265007 | chr11 | 63704851:63704907:63718702:63721032:63749991:63750056 | 63718702:63721032 |
exon_skip_265377 | chr11 | 63704851:63704907:63718702:63721032:63749991:63750197 | 63718702:63721032 |
exon_skip_265430 | chr11 | 63681718:63681778:63704851:63704907:63718981:63719189 | 63704851:63704907 |
exon_skip_275159 | chr11 | 63753662:63753708:63756112:63756170:63758156:63758168 | 63756112:63756170 |
exon_skip_276513 | chr11 | 63753662:63753708:63756112:63756170:63758156:63758421 | 63756112:63756170 |
exon_skip_288472 | chr11 | 63681458:63681778:63746947:63747024:63749991:63750197 | 63746947:63747024 |
exon_skip_31543 | chr11 | 63750075:63750198:63756112:63756170:63758156:63758392 | 63756112:63756170 |
exon_skip_32816 | chr11 | 63753681:63753708:63756112:63756170:63758156:63758421 | 63756112:63756170 |
exon_skip_34660 | chr11 | 63752507:63752645:63753069:63753138:63753662:63753708 | 63753069:63753138 |
exon_skip_37484 | chr11 | 63749991:63750198:63753069:63753138:63753662:63753708 | 63753069:63753138 |
exon_skip_38960 | chr11 | 63681483:63681778:63704851:63704907:63718702:63719994 | 63704851:63704907 |
exon_skip_67936 | chr11 | 63681573:63681778:63749991:63750198:63756112:63756168 | 63749991:63750198 |
exon_skip_8534 | chr11 | 63753662:63753708:63756112:63756170:63758156:63758184 | 63756112:63756170 |
exon_skip_89864 | chr11 | 63681573:63681778:63704851:63704907:63749991:63750198 | 63704851:63704907 |
exon_skip_92724 | chr11 | 63752588:63752645:63753069:63753138:63753662:63753708 | 63753069:63753138 |
exon_skip_9344 | chr11 | 63750075:63750198:63752507:63752645:63753069:63753137 | 63752507:63752645 |
exon_skip_95254 | chr11 | 63750075:63750198:63753069:63753138:63753662:63753708 | 63753069:63753138 |
exon_skip_95479 | chr11 | 63681573:63681778:63704851:63704907:63713971:63714166 | 63704851:63704907 |
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 RTN3 |
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 |
ENST00000377819 | 63752507 | 63752645 | Frame-shift |
ENST00000377819 | 63753069 | 63753138 | Frame-shift |
ENST00000377819 | 63756112 | 63756170 | Frame-shift |
ENST00000377819 | 63704851 | 63704907 | In-frame |
ENST00000377819 | 63718702 | 63721032 | 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 |
ENST00000377819 | 63752507 | 63752645 | Frame-shift |
ENST00000377819 | 63753069 | 63753138 | Frame-shift |
ENST00000377819 | 63756112 | 63756170 | Frame-shift |
ENST00000377819 | 63704851 | 63704907 | In-frame |
ENST00000377819 | 63718702 | 63721032 | In-frame |
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 |
ENST00000377819 | 63752507 | 63752645 | Frame-shift |
ENST00000377819 | 63753069 | 63753138 | Frame-shift |
ENST00000377819 | 63756112 | 63756170 | Frame-shift |
ENST00000377819 | 63704851 | 63704907 | In-frame |
ENST00000377819 | 63718702 | 63721032 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RTN3 |
p-ENSG00000133318_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 |
ENST00000377819 | 4954 | 1032 | 63704851 | 63704907 | 298 | 353 | 48 | 66 |
ENST00000377819 | 4954 | 1032 | 63718702 | 63721032 | 355 | 2684 | 67 | 843 |
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 |
ENST00000377819 | 4954 | 1032 | 63704851 | 63704907 | 298 | 353 | 48 | 66 |
ENST00000377819 | 4954 | 1032 | 63718702 | 63721032 | 355 | 2684 | 67 | 843 |
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 |
ENST00000377819 | 4954 | 1032 | 63704851 | 63704907 | 298 | 353 | 48 | 66 |
ENST00000377819 | 4954 | 1032 | 63718702 | 63721032 | 355 | 2684 | 67 | 843 |
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 |
O95197 | 48 | 66 | 48 | 843 | Alternative sequence | ID=VSP_045319;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
O95197 | 48 | 66 | 48 | 159 | Alternative sequence | ID=VSP_047008;Note=In isoform 7. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
O95197 | 48 | 66 | 48 | 66 | Alternative sequence | ID=VSP_023759;Note=In isoform 2%2C isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10331947,ECO:0000303|PubMed:12811824,ECO:0000303|PubMed:14986 |
O95197 | 48 | 66 | 2 | 1032 | Chain | ID=PRO_0000168163;Note=Reticulon-3 |
O95197 | 48 | 66 | 2 | 863 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
O95197 | 67 | 843 | 48 | 843 | Alternative sequence | ID=VSP_045319;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
O95197 | 67 | 843 | 48 | 159 | Alternative sequence | ID=VSP_047008;Note=In isoform 7. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
O95197 | 67 | 843 | 67 | 843 | Alternative sequence | ID=VSP_023760;Note=In isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10331947,ECO:0000303|PubMed:12811824,ECO:0000303|PubMed:14702 |
O95197 | 67 | 843 | 2 | 1032 | Chain | ID=PRO_0000168163;Note=Reticulon-3 |
O95197 | 67 | 843 | 229 | 229 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
O95197 | 67 | 843 | 243 | 243 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ES97 |
O95197 | 67 | 843 | 246 | 246 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
O95197 | 67 | 843 | 283 | 283 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6RJR6 |
O95197 | 67 | 843 | 316 | 316 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
O95197 | 67 | 843 | 453 | 453 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
O95197 | 67 | 843 | 649 | 649 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
O95197 | 67 | 843 | 650 | 650 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
O95197 | 67 | 843 | 735 | 735 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ES97 |
O95197 | 67 | 843 | 501 | 501 | Natural variant | ID=VAR_057713;Note=D->H;Dbxref=dbSNP:rs7936660 |
O95197 | 67 | 843 | 2 | 863 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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 |
O95197 | 48 | 66 | 48 | 843 | Alternative sequence | ID=VSP_045319;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
O95197 | 48 | 66 | 48 | 159 | Alternative sequence | ID=VSP_047008;Note=In isoform 7. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
O95197 | 48 | 66 | 48 | 66 | Alternative sequence | ID=VSP_023759;Note=In isoform 2%2C isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10331947,ECO:0000303|PubMed:12811824,ECO:0000303|PubMed:14986 |
O95197 | 48 | 66 | 2 | 1032 | Chain | ID=PRO_0000168163;Note=Reticulon-3 |
O95197 | 48 | 66 | 2 | 863 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
O95197 | 67 | 843 | 48 | 843 | Alternative sequence | ID=VSP_045319;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
O95197 | 67 | 843 | 48 | 159 | Alternative sequence | ID=VSP_047008;Note=In isoform 7. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
O95197 | 67 | 843 | 67 | 843 | Alternative sequence | ID=VSP_023760;Note=In isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10331947,ECO:0000303|PubMed:12811824,ECO:0000303|PubMed:14702 |
O95197 | 67 | 843 | 2 | 1032 | Chain | ID=PRO_0000168163;Note=Reticulon-3 |
O95197 | 67 | 843 | 229 | 229 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
O95197 | 67 | 843 | 243 | 243 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ES97 |
O95197 | 67 | 843 | 246 | 246 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
O95197 | 67 | 843 | 283 | 283 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6RJR6 |
O95197 | 67 | 843 | 316 | 316 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
O95197 | 67 | 843 | 453 | 453 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
O95197 | 67 | 843 | 649 | 649 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
O95197 | 67 | 843 | 650 | 650 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
O95197 | 67 | 843 | 735 | 735 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ES97 |
O95197 | 67 | 843 | 501 | 501 | Natural variant | ID=VAR_057713;Note=D->H;Dbxref=dbSNP:rs7936660 |
O95197 | 67 | 843 | 2 | 863 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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 |
O95197 | 48 | 66 | 48 | 843 | Alternative sequence | ID=VSP_045319;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
O95197 | 48 | 66 | 48 | 159 | Alternative sequence | ID=VSP_047008;Note=In isoform 7. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
O95197 | 48 | 66 | 48 | 66 | Alternative sequence | ID=VSP_023759;Note=In isoform 2%2C isoform 3 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10331947,ECO:0000303|PubMed:12811824,ECO:0000303|PubMed:14986 |
O95197 | 48 | 66 | 2 | 1032 | Chain | ID=PRO_0000168163;Note=Reticulon-3 |
O95197 | 48 | 66 | 2 | 863 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
O95197 | 67 | 843 | 48 | 843 | Alternative sequence | ID=VSP_045319;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
O95197 | 67 | 843 | 48 | 159 | Alternative sequence | ID=VSP_047008;Note=In isoform 7. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
O95197 | 67 | 843 | 67 | 843 | Alternative sequence | ID=VSP_023760;Note=In isoform 3%2C isoform 4 and isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10331947,ECO:0000303|PubMed:12811824,ECO:0000303|PubMed:14702 |
O95197 | 67 | 843 | 2 | 1032 | Chain | ID=PRO_0000168163;Note=Reticulon-3 |
O95197 | 67 | 843 | 229 | 229 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
O95197 | 67 | 843 | 243 | 243 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ES97 |
O95197 | 67 | 843 | 246 | 246 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
O95197 | 67 | 843 | 283 | 283 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6RJR6 |
O95197 | 67 | 843 | 316 | 316 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
O95197 | 67 | 843 | 453 | 453 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
O95197 | 67 | 843 | 649 | 649 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
O95197 | 67 | 843 | 650 | 650 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:18669648;Dbxref=PMID:18669648 |
O95197 | 67 | 843 | 735 | 735 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9ES97 |
O95197 | 67 | 843 | 501 | 501 | Natural variant | ID=VAR_057713;Note=D->H;Dbxref=dbSNP:rs7936660 |
O95197 | 67 | 843 | 2 | 863 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in RTN3 |
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 RTN3 |
- 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 RTN3 |
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 |
ADstage | MSBB | IFG | exon_skip_32816 | -3.740026e-01 | 4.992285e-02 | chr11 | + | 63753681 | 63753708 | 63756112 | 63756170 | 63758156 | 63758421 |
CDR | MSBB | IFG | exon_skip_269471 | 4.414395e-01 | 1.869158e-02 | chr11 | + | 63681573 | 63681778 | 63720850 | 63721032 | 63749991 | 63750198 |
CDR | MSBB | STG | exon_skip_207991 | -3.387609e-01 | 8.953760e-04 | chr11 | + | 63681573 | 63681778 | 63718702 | 63721032 | 63749991 | 63750198 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RTN3 |
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 RTN3 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | TIA1 | exon_skip_89864 | 4.888531e-01 | 6.244899e-11 |
CB | TARDBP | exon_skip_225573 | 5.133544e-01 | 2.163232e-11 |
CB | RBFOX2 | exon_skip_225573 | 4.507434e-01 | 8.002701e-09 |
CB | ZNF326 | exon_skip_225573 | 4.788417e-01 | 6.524704e-10 |
CB | ELAVL1 | exon_skip_225573 | 4.473021e-01 | 1.071344e-08 |
CB | SAMD4A | exon_skip_225573 | 5.839233e-01 | 5.437846e-15 |
CB | CNOT4 | exon_skip_225573 | 5.275818e-01 | 4.735110e-12 |
CB | MATR3 | exon_skip_225573 | 4.612732e-01 | 3.211738e-09 |
CB | RC3H1 | exon_skip_225573 | 4.469442e-01 | 1.104142e-08 |
CB | G3BP2 | exon_skip_225573 | 4.362988e-01 | 2.665166e-08 |
CB | QKI | exon_skip_225573 | 4.227772e-01 | 7.820552e-08 |
CB | SF1 | exon_skip_225573 | 4.025285e-01 | 3.598398e-07 |
CB | FUBP1 | exon_skip_225573 | 4.348803e-01 | 2.990419e-08 |
CB | KHSRP | exon_skip_225573 | 4.340175e-01 | 3.206557e-08 |
CB | PUM1 | exon_skip_225573 | 4.140968e-01 | 1.523199e-07 |
CB | HNRNPA2B1 | exon_skip_225573 | 5.051125e-01 | 5.053187e-11 |
CB | CELF1 | exon_skip_225573 | 4.178085e-01 | 1.148040e-07 |
CB | SRSF1 | exon_skip_225573 | 5.016686e-01 | 7.155462e-11 |
CB | RBM41 | exon_skip_225573 | 5.089257e-01 | 3.422311e-11 |
CB | HNRNPF | exon_skip_225573 | 4.555272e-01 | 5.306007e-09 |
CB | RBM6 | exon_skip_8534 | -5.789801e-01 | 1.305265e-15 |
CB | RBM3 | exon_skip_8534 | 5.481940e-01 | 7.468684e-14 |
CB | PCBP1 | exon_skip_8534 | -4.235234e-01 | 2.661897e-08 |
DLPFC | ELAVL4 | exon_skip_160375 | 7.094974e-01 | 1.690486e-38 |
DLPFC | TIA1 | exon_skip_160375 | 4.615158e-01 | 3.199539e-14 |
DLPFC | PUF60 | exon_skip_160375 | 5.961663e-01 | 8.917816e-25 |
DLPFC | RALYL | exon_skip_160375 | 6.582318e-01 | 1.484941e-31 |
DLPFC | PTBP3 | exon_skip_160375 | 5.323690e-01 | 3.463292e-19 |
DLPFC | EWSR1 | exon_skip_160375 | 5.574229e-01 | 3.069562e-21 |
DLPFC | DAZAP1 | exon_skip_265377 | -6.467080e-01 | 2.612477e-32 |
DLPFC | TARDBP | exon_skip_265377 | -4.684781e-01 | 1.209982e-15 |
DLPFC | SRSF2 | exon_skip_265377 | -5.488918e-01 | 6.147346e-22 |
DLPFC | MSI1 | exon_skip_265377 | -5.473778e-01 | 8.381115e-22 |
DLPFC | PABPN1 | exon_skip_265377 | -6.497947e-01 | 1.063676e-32 |
DLPFC | ELAVL4 | exon_skip_265377 | -4.542144e-01 | 1.086844e-14 |
DLPFC | RBM25 | exon_skip_265377 | -6.255054e-01 | 9.556307e-30 |
DLPFC | ZNF326 | exon_skip_265377 | -4.673552e-01 | 1.443628e-15 |
DLPFC | ELAVL1 | exon_skip_265377 | -4.216516e-01 | 1.129261e-12 |
DLPFC | SFPQ | exon_skip_265377 | -5.621288e-01 | 3.821151e-23 |
DLPFC | RBM6 | exon_skip_265377 | -6.076084e-01 | 9.896786e-28 |
DLPFC | SRSF11 | exon_skip_265377 | -5.658661e-01 | 1.704845e-23 |
DLPFC | U2AF2 | exon_skip_265377 | -5.811400e-01 | 5.648921e-25 |
DLPFC | RBM5 | exon_skip_265377 | -5.855033e-01 | 2.064597e-25 |
DLPFC | RBM3 | exon_skip_265377 | -5.063597e-01 | 2.109351e-18 |
DLPFC | MATR3 | exon_skip_265377 | -4.208923e-01 | 1.251100e-12 |
DLPFC | TRNAU1AP | exon_skip_265377 | -6.289062e-01 | 3.823505e-30 |
DLPFC | PCBP1 | exon_skip_265377 | -5.073707e-01 | 1.760920e-18 |
DLPFC | ILF2 | exon_skip_265377 | -4.665087e-01 | 1.648431e-15 |
DLPFC | HNRNPK | exon_skip_265377 | -4.031327e-01 | 1.278473e-11 |
DLPFC | PCBP4 | exon_skip_265377 | -6.561378e-01 | 1.623590e-33 |
DLPFC | UNK | exon_skip_265377 | -5.493292e-01 | 5.619171e-22 |
DLPFC | TRA2A | exon_skip_265377 | -5.015151e-01 | 4.969379e-18 |
DLPFC | PCBP2 | exon_skip_265377 | -4.318625e-01 | 2.776451e-13 |
DLPFC | SNRPA | exon_skip_265377 | -6.437955e-01 | 6.041730e-32 |
DLPFC | SF1 | exon_skip_265377 | -5.647979e-01 | 2.149426e-23 |
DLPFC | KHDRBS3 | exon_skip_265377 | -4.795993e-01 | 2.032391e-16 |
DLPFC | HNRNPA1 | exon_skip_265377 | -4.511590e-01 | 1.716619e-14 |
DLPFC | RBM24 | exon_skip_265377 | -4.353171e-01 | 1.708688e-13 |
DLPFC | FUBP3 | exon_skip_265377 | -4.277744e-01 | 4.896626e-13 |
DLPFC | FUBP1 | exon_skip_265377 | -5.421529e-01 | 2.413455e-21 |
DLPFC | KHSRP | exon_skip_265377 | -5.601261e-01 | 5.864133e-23 |
DLPFC | HNRNPA0 | exon_skip_265377 | -5.174828e-01 | 2.798809e-19 |
DLPFC | HNRNPA1L2 | exon_skip_265377 | -5.637536e-01 | 2.693732e-23 |
DLPFC | HNRNPA2B1 | exon_skip_265377 | -4.440512e-01 | 4.884906e-14 |
DLPFC | HNRNPDL | exon_skip_265377 | -5.036219e-01 | 3.429176e-18 |
DLPFC | RBM45 | exon_skip_265377 | -4.300428e-01 | 3.577511e-13 |
DLPFC | PUF60 | exon_skip_265377 | -6.147110e-01 | 1.626095e-28 |
DLPFC | HNRNPAB | exon_skip_265377 | -5.063929e-01 | 2.096911e-18 |
DLPFC | HNRNPD | exon_skip_265377 | -5.539398e-01 | 2.162250e-22 |
DLPFC | NUP42 | exon_skip_265377 | -4.790380e-01 | 2.227346e-16 |
DLPFC | RALYL | exon_skip_265377 | -4.444385e-01 | 4.617225e-14 |
DLPFC | PTBP1 | exon_skip_265377 | -5.787257e-01 | 9.795644e-25 |
DLPFC | HNRNPL | exon_skip_265377 | -5.837612e-01 | 3.091344e-25 |
DLPFC | PABPC3 | exon_skip_265377 | -4.005783e-01 | 1.766171e-11 |
DLPFC | CELF1 | exon_skip_265377 | -6.120378e-01 | 3.226096e-28 |
DLPFC | RBM23 | exon_skip_265377 | -4.822780e-01 | 1.309642e-16 |
DLPFC | PABPC1 | exon_skip_265377 | -5.126067e-01 | 6.846334e-19 |
DLPFC | PABPC4 | exon_skip_265377 | -5.701411e-01 | 6.687541e-24 |
DLPFC | EWSR1 | exon_skip_265377 | -6.129582e-01 | 2.550102e-28 |
DLPFC | SRSF1 | exon_skip_265377 | -4.359243e-01 | 1.568060e-13 |
DLPFC | SRSF4 | exon_skip_265377 | -5.867283e-01 | 1.552118e-25 |
DLPFC | SRSF9 | exon_skip_265377 | -5.644235e-01 | 2.330820e-23 |
DLPFC | SRSF5 | exon_skip_265377 | -5.528777e-01 | 2.697906e-22 |
DLPFC | HNRNPH2 | exon_skip_265377 | -4.105242e-01 | 4.940843e-12 |
DLPFC | YBX2 | exon_skip_265377 | -5.982053e-01 | 1.009354e-26 |
DLPFC | ESRP1 | exon_skip_265377 | -4.464011e-01 | 3.466355e-14 |
DLPFC | ZCRB1 | exon_skip_265377 | -5.599838e-01 | 6.044597e-23 |
DLPFC | HNRNPF | exon_skip_265377 | -4.069202e-01 | 7.877534e-12 |
DLPFC | SART3 | exon_skip_265377 | -5.890877e-01 | 8.928502e-26 |
DLPFC | NOVA1 | exon_skip_265377 | -5.587384e-01 | 7.876940e-23 |
HCC | RBMS2 | exon_skip_89864 | -5.721531e-01 | 4.740866e-25 |
HCC | TIA1 | exon_skip_89864 | -4.470915e-01 | 9.004020e-15 |
HCC | TRNAU1AP | exon_skip_89864 | -4.019542e-01 | 5.520427e-12 |
HCC | FUBP1 | exon_skip_89864 | -4.290928e-01 | 1.306168e-13 |
IFG | ELAVL4 | exon_skip_225573 | 4.974765e-01 | 8.284434e-03 |
IFG | SRSF2 | exon_skip_41244 | -4.446158e-01 | 2.014474e-02 |
IFG | ILF2 | exon_skip_41244 | -5.345793e-01 | 4.070538e-03 |
IFG | ZCRB1 | exon_skip_41244 | -4.436978e-01 | 2.043443e-02 |
PCC | RBMS2 | exon_skip_177360 | -4.595868e-01 | 1.399391e-12 |
PCC | ELAVL4 | exon_skip_177360 | 5.634403e-01 | 2.514164e-19 |
PCC | RALYL | exon_skip_177360 | 4.624221e-01 | 9.784847e-13 |
PCC | RBM3 | exon_skip_111918 | -4.120812e-01 | 2.611505e-09 |
PG | ELAVL4 | exon_skip_177360 | 4.074476e-01 | 2.125335e-09 |
STG | ELAVL4 | exon_skip_89864 | 5.060151e-01 | 2.288801e-07 |
STG | PUF60 | exon_skip_89864 | 4.092989e-01 | 4.627096e-05 |
STG | RALYL | exon_skip_89864 | 4.971535e-01 | 3.994218e-07 |
STG | SFPQ | exon_skip_225573 | 4.118365e-01 | 3.592373e-04 |
STG | TIA1 | exon_skip_225573 | 4.219274e-01 | 2.475170e-04 |
STG | RBM24 | exon_skip_225573 | 4.327908e-01 | 1.635628e-04 |
STG | RBM45 | exon_skip_225573 | 4.392338e-01 | 1.270793e-04 |
TC | RBFOX2 | exon_skip_233521 | 7.369997e-01 | 2.847752e-26 |
TC | ELAVL4 | exon_skip_233521 | 6.850362e-01 | 1.491481e-21 |
TC | CNOT4 | exon_skip_233521 | 4.040118e-01 | 4.258956e-07 |
TC | MATR3 | exon_skip_233521 | 5.684915e-01 | 7.164868e-14 |
TC | G3BP2 | exon_skip_233521 | 6.351840e-01 | 7.259851e-18 |
TC | KHDRBS2 | exon_skip_233521 | 6.611022e-01 | 1.075154e-19 |
TC | KHDRBS3 | exon_skip_233521 | 5.834859e-01 | 1.086302e-14 |
TC | RBM24 | exon_skip_233521 | 5.396471e-01 | 2.088327e-12 |
TC | HNRNPA0 | exon_skip_233521 | 5.496727e-01 | 6.708002e-13 |
TC | PUM1 | exon_skip_233521 | 6.228496e-01 | 4.700346e-17 |
TC | HNRNPD | exon_skip_233521 | 5.018221e-01 | 1.099598e-10 |
TC | NUP42 | exon_skip_233521 | 5.340481e-01 | 3.874570e-12 |
TC | RALYL | exon_skip_233521 | 6.092171e-01 | 3.372428e-16 |
TC | PTBP3 | exon_skip_233521 | 5.640123e-01 | 1.235919e-13 |
TC | CELF1 | exon_skip_233521 | 5.029241e-01 | 9.863222e-11 |
TC | CPEB1 | exon_skip_233521 | 4.393006e-01 | 2.904390e-08 |
TC | HNRNPH2 | exon_skip_233521 | 5.662080e-01 | 9.470370e-14 |
TC | ESRP1 | exon_skip_233521 | 4.716640e-01 | 1.863307e-09 |
TC | NOVA1 | exon_skip_233521 | 4.434467e-01 | 2.075355e-08 |
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RelatedDrugs for RTN3 |
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 RTN3 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |