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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for RTN4 |
 Gene summary |
| Gene information | Gene symbol | RTN4 | Gene ID | 57142 |
| Gene name | reticulon 4 | |
| Synonyms | ASY|NI220/250|NOGO|NSP|NSP-CL|Nbla00271|Nbla10545|RTN-X|RTN4-A|RTN4-B1|RTN4-B2|RTN4-C | |
| Cytomap | 2p16.1 | |
| Type of gene | protein-coding | |
| Description | reticulon-4Human NogoAMy043 proteinfoocenneurite growth inhibitor 220neurite outgrowth inhibitorneuroendocrine-specific protein C homologreticulon 5 | |
| Modification date | 20200327 | |
| UniProtAcc | ||
| Context | - 16965550(Reticulons RTN3 and RTN4-B/C Interact With BACE1 and Inhibit Its Ability to Produce Amyloid Beta-Protein) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| RTN4 | GO:0030517 | negative regulation of axon extension | 10667797 |
| RTN4 | GO:0071787 | endoplasmic reticulum tubular network formation | 24262037|25612671 |
| RTN4 | GO:1905552 | positive regulation of protein localization to endoplasmic reticulum | 27353365 |
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Gene structures and expression levels for RTN4 |
| 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. |
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ENSG00000115310
| 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. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| CB | UP | ENST00000486085.5 | RTN4-214:protein_coding:RTN4 | 1.856166e+02 | 1.007225e+00 | 3.212105e-07 | 5.705643e-06 |
| CB | UP | ENST00000337526.11 | RTN4-202:protein_coding:RTN4 | 1.900132e+03 | 8.532699e-01 | 2.551597e-06 | 3.321260e-05 |
| TC | UP | ENST00000357732.8 | RTN4-204:protein_coding:RTN4 | 4.043529e+02 | 9.217151e-01 | 9.696681e-14 | 4.868017e-11 |
| 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 RTN4 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_102185 | chr2 | 54987491:54987698:55025086:55027485:55028164:55028220 | 55025086:55027485 |
| exon_skip_104563 | chr2 | 54973821:54973867:54974695:54974764:54982515:54982653 | 54974695:54974764 |
| exon_skip_105498 | chr2 | 54973138:54973198:54973563:54973621:54982515:54982653 | 54973563:54973621 |
| exon_skip_117613 | chr2 | 54987600:54987698:55025086:55027485:55028164:55028220 | 55025086:55027485 |
| exon_skip_162633 | chr2 | 54987600:54987698:55028164:55028220:55049745:55050214 | 55028164:55028220 |
| exon_skip_18975 | chr2 | 54973138:54973198:54973563:54973621:54973821:54973848 | 54973563:54973621 |
| exon_skip_191817 | chr2 | 54973563:54973621:54973821:54973867:54974695:54974764 | 54973821:54973867 |
| exon_skip_217824 | chr2 | 54987491:54987698:55028164:55028220:55049745:55049776 | 55028164:55028220 |
| exon_skip_220515 | chr2 | 54972814:54973198:54973563:54973621:54973821:54973867 | 54973563:54973621 |
| exon_skip_221473 | chr2 | 54972814:54973198:54973563:54973621:54982515:54982653 | 54973563:54973621 |
| exon_skip_234172 | chr2 | 54973563:54973621:54973821:54973867:54974695:54974757 | 54973821:54973867 |
| exon_skip_241538 | chr2 | 54987551:54987698:55025086:55027485:55028164:55028220 | 55025086:55027485 |
| exon_skip_245977 | chr2 | 54973821:54973867:54974695:54974764:54982515:54982603 | 54974695:54974764 |
| exon_skip_276062 | chr2 | 54973184:54973198:54973563:54973621:54973821:54973867 | 54973563:54973621 |
| exon_skip_282430 | chr2 | 54987491:54987698:55028164:55028220:55049745:55050214 | 55028164:55028220 |
| exon_skip_32287 | chr2 | 54972814:54973198:54973563:54973621:54982515:54982603 | 54973563:54973621 |
| exon_skip_38342 | chr2 | 54987491:54987698:55028164:55028220:55049745:55049792 | 55028164:55028220 |
| exon_skip_63482 | chr2 | 54973184:54973198:54973563:54973621:54982515:54982653 | 54973563:54973621 |
| 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 RTN4 |
| 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 |
| ENST00000337526 | 54973563 | 54973621 | Frame-shift |
| ENST00000337526 | 54973821 | 54973867 | Frame-shift |
| ENST00000337526 | 54974695 | 54974764 | Frame-shift |
| ENST00000337526 | 55025086 | 55027485 | 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 |
| ENST00000337526 | 54973563 | 54973621 | Frame-shift |
| ENST00000337526 | 54973821 | 54973867 | Frame-shift |
| ENST00000337526 | 54974695 | 54974764 | Frame-shift |
| ENST00000337526 | 55025086 | 55027485 | 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 |
| ENST00000337526 | 54973563 | 54973621 | Frame-shift |
| ENST00000337526 | 54973821 | 54973867 | Frame-shift |
| ENST00000337526 | 54974695 | 54974764 | Frame-shift |
| ENST00000337526 | 55025086 | 55027485 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RTN4 |
p-ENSG00000115310_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 |
| ENST00000337526 | 4807 | 1192 | 55025086 | 55027485 | 858 | 3256 | 204 | 1004 |
| 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 |
| ENST00000337526 | 4807 | 1192 | 55025086 | 55027485 | 858 | 3256 | 204 | 1004 |
| 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 |
| ENST00000337526 | 4807 | 1192 | 55025086 | 55027485 | 858 | 3256 | 204 | 1004 |
| 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 |
| Q9NQC3 | 204 | 1004 | 1 | 993 | Alternative sequence | ID=VSP_005652;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10667780,ECO:0000303|PubMed:10773680,ECO:0000303|PubMed:11042152,ECO:0000303 |
| Q9NQC3 | 204 | 1004 | 1 | 206 | Alternative sequence | ID=VSP_037112;Note=In isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11866689,ECO:0000303|PubMed:12488097;Dbxref=PMID:11866689,PMID:12488097 |
| Q9NQC3 | 204 | 1004 | 58 | 289 | Alternative sequence | ID=VSP_005654;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.9 |
| Q9NQC3 | 204 | 1004 | 186 | 1004 | Alternative sequence | ID=VSP_005655;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10667780,ECO:0000303|PubMed:10773680,ECO:0000303|PubMed:11126360,ECO:0000303|PubMed:1248 |
| Q9NQC3 | 204 | 1004 | 205 | 1004 | Alternative sequence | ID=VSP_037113;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12488097,ECO:0000303|PubMed:15489334;Dbxref=PMID:12488097,PMID:15489334 |
| Q9NQC3 | 204 | 1004 | 994 | 1004 | Alternative sequence | ID=VSP_005653;Note=In isoform 3. AIFSAELSKTS->MDGQKKNWKDK;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10667780,ECO:0000303|PubMed:10773680,ECO:0000303|PubMed:110 |
| Q9NQC3 | 204 | 1004 | 1 | 1192 | Chain | ID=PRO_0000168165;Note=Reticulon-4 |
| Q9NQC3 | 204 | 1004 | 361 | 361 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99P72 |
| Q9NQC3 | 204 | 1004 | 446 | 446 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9JK11 |
| Q9NQC3 | 204 | 1004 | 450 | 450 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9JK11 |
| Q9NQC3 | 204 | 1004 | 511 | 511 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99P72 |
| Q9NQC3 | 204 | 1004 | 749 | 749 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99P72 |
| Q9NQC3 | 204 | 1004 | 858 | 858 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9JK11 |
| Q9NQC3 | 204 | 1004 | 881 | 881 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99P72 |
| Q9NQC3 | 204 | 1004 | 991 | 991 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q9NQC3 | 204 | 1004 | 357 | 357 | Natural variant | ID=VAR_053633;Note=D->V;Dbxref=dbSNP:rs11677099 |
| Q9NQC3 | 204 | 1004 | 429 | 429 | Natural variant | ID=VAR_035904;Note=In a colorectal cancer sample%3B somatic mutation. L->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16959974;Dbxref=PMID:16959974 |
| Q9NQC3 | 204 | 1004 | 899 | 899 | Natural variant | ID=VAR_053634;Note=E->Q;Dbxref=dbSNP:rs6757519 |
| Q9NQC3 | 204 | 1004 | 920 | 920 | Natural variant | ID=VAR_053635;Note=S->C;Dbxref=dbSNP:rs6757705 |
| Q9NQC3 | 204 | 1004 | 458 | 458 | Sequence conflict | Note=S->P;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NQC3 | 204 | 1004 | 564 | 564 | Sequence conflict | Note=N->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NQC3 | 204 | 1004 | 1 | 1018 | 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 |
| Q9NQC3 | 204 | 1004 | 1 | 993 | Alternative sequence | ID=VSP_005652;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10667780,ECO:0000303|PubMed:10773680,ECO:0000303|PubMed:11042152,ECO:0000303 |
| Q9NQC3 | 204 | 1004 | 1 | 206 | Alternative sequence | ID=VSP_037112;Note=In isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11866689,ECO:0000303|PubMed:12488097;Dbxref=PMID:11866689,PMID:12488097 |
| Q9NQC3 | 204 | 1004 | 58 | 289 | Alternative sequence | ID=VSP_005654;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.9 |
| Q9NQC3 | 204 | 1004 | 186 | 1004 | Alternative sequence | ID=VSP_005655;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10667780,ECO:0000303|PubMed:10773680,ECO:0000303|PubMed:11126360,ECO:0000303|PubMed:1248 |
| Q9NQC3 | 204 | 1004 | 205 | 1004 | Alternative sequence | ID=VSP_037113;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12488097,ECO:0000303|PubMed:15489334;Dbxref=PMID:12488097,PMID:15489334 |
| Q9NQC3 | 204 | 1004 | 994 | 1004 | Alternative sequence | ID=VSP_005653;Note=In isoform 3. AIFSAELSKTS->MDGQKKNWKDK;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10667780,ECO:0000303|PubMed:10773680,ECO:0000303|PubMed:110 |
| Q9NQC3 | 204 | 1004 | 1 | 1192 | Chain | ID=PRO_0000168165;Note=Reticulon-4 |
| Q9NQC3 | 204 | 1004 | 361 | 361 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99P72 |
| Q9NQC3 | 204 | 1004 | 446 | 446 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9JK11 |
| Q9NQC3 | 204 | 1004 | 450 | 450 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9JK11 |
| Q9NQC3 | 204 | 1004 | 511 | 511 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99P72 |
| Q9NQC3 | 204 | 1004 | 749 | 749 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99P72 |
| Q9NQC3 | 204 | 1004 | 858 | 858 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9JK11 |
| Q9NQC3 | 204 | 1004 | 881 | 881 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99P72 |
| Q9NQC3 | 204 | 1004 | 991 | 991 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q9NQC3 | 204 | 1004 | 357 | 357 | Natural variant | ID=VAR_053633;Note=D->V;Dbxref=dbSNP:rs11677099 |
| Q9NQC3 | 204 | 1004 | 429 | 429 | Natural variant | ID=VAR_035904;Note=In a colorectal cancer sample%3B somatic mutation. L->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16959974;Dbxref=PMID:16959974 |
| Q9NQC3 | 204 | 1004 | 899 | 899 | Natural variant | ID=VAR_053634;Note=E->Q;Dbxref=dbSNP:rs6757519 |
| Q9NQC3 | 204 | 1004 | 920 | 920 | Natural variant | ID=VAR_053635;Note=S->C;Dbxref=dbSNP:rs6757705 |
| Q9NQC3 | 204 | 1004 | 458 | 458 | Sequence conflict | Note=S->P;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NQC3 | 204 | 1004 | 564 | 564 | Sequence conflict | Note=N->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NQC3 | 204 | 1004 | 1 | 1018 | 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 |
| Q9NQC3 | 204 | 1004 | 1 | 993 | Alternative sequence | ID=VSP_005652;Note=In isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10667780,ECO:0000303|PubMed:10773680,ECO:0000303|PubMed:11042152,ECO:0000303 |
| Q9NQC3 | 204 | 1004 | 1 | 206 | Alternative sequence | ID=VSP_037112;Note=In isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11866689,ECO:0000303|PubMed:12488097;Dbxref=PMID:11866689,PMID:12488097 |
| Q9NQC3 | 204 | 1004 | 58 | 289 | Alternative sequence | ID=VSP_005654;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|Ref.9 |
| Q9NQC3 | 204 | 1004 | 186 | 1004 | Alternative sequence | ID=VSP_005655;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10667780,ECO:0000303|PubMed:10773680,ECO:0000303|PubMed:11126360,ECO:0000303|PubMed:1248 |
| Q9NQC3 | 204 | 1004 | 205 | 1004 | Alternative sequence | ID=VSP_037113;Note=In isoform 5. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12488097,ECO:0000303|PubMed:15489334;Dbxref=PMID:12488097,PMID:15489334 |
| Q9NQC3 | 204 | 1004 | 994 | 1004 | Alternative sequence | ID=VSP_005653;Note=In isoform 3. AIFSAELSKTS->MDGQKKNWKDK;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:10667780,ECO:0000303|PubMed:10773680,ECO:0000303|PubMed:110 |
| Q9NQC3 | 204 | 1004 | 1 | 1192 | Chain | ID=PRO_0000168165;Note=Reticulon-4 |
| Q9NQC3 | 204 | 1004 | 361 | 361 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99P72 |
| Q9NQC3 | 204 | 1004 | 446 | 446 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9JK11 |
| Q9NQC3 | 204 | 1004 | 450 | 450 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9JK11 |
| Q9NQC3 | 204 | 1004 | 511 | 511 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99P72 |
| Q9NQC3 | 204 | 1004 | 749 | 749 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99P72 |
| Q9NQC3 | 204 | 1004 | 858 | 858 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q9JK11 |
| Q9NQC3 | 204 | 1004 | 881 | 881 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q99P72 |
| Q9NQC3 | 204 | 1004 | 991 | 991 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q9NQC3 | 204 | 1004 | 357 | 357 | Natural variant | ID=VAR_053633;Note=D->V;Dbxref=dbSNP:rs11677099 |
| Q9NQC3 | 204 | 1004 | 429 | 429 | Natural variant | ID=VAR_035904;Note=In a colorectal cancer sample%3B somatic mutation. L->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:16959974;Dbxref=PMID:16959974 |
| Q9NQC3 | 204 | 1004 | 899 | 899 | Natural variant | ID=VAR_053634;Note=E->Q;Dbxref=dbSNP:rs6757519 |
| Q9NQC3 | 204 | 1004 | 920 | 920 | Natural variant | ID=VAR_053635;Note=S->C;Dbxref=dbSNP:rs6757705 |
| Q9NQC3 | 204 | 1004 | 458 | 458 | Sequence conflict | Note=S->P;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NQC3 | 204 | 1004 | 564 | 564 | Sequence conflict | Note=N->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q9NQC3 | 204 | 1004 | 1 | 1018 | 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 RTN4 |
| 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 RTN4 |
| - 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 RTN4 |
| 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 RTN4 |
| 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 RTN4 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBFOX2 | exon_skip_102185 | 4.245668e-01 | 2.994787e-08 |
| CB | NOVA1 | exon_skip_102185 | 5.561868e-01 | 3.959857e-14 |
| FL | SRSF2 | exon_skip_102185 | 4.936072e-01 | 1.479978e-13 |
| FL | RBFOX2 | exon_skip_102185 | 5.643827e-01 | 4.753625e-18 |
| FL | ELAVL4 | exon_skip_102185 | 5.120126e-01 | 1.260314e-14 |
| FL | MBNL1 | exon_skip_102185 | 4.088424e-01 | 2.232656e-09 |
| FL | FXR2 | exon_skip_102185 | 5.202942e-01 | 3.960425e-15 |
| FL | PCBP1 | exon_skip_102185 | 4.918270e-01 | 1.863663e-13 |
| FL | ILF2 | exon_skip_102185 | 4.904753e-01 | 2.218172e-13 |
| FL | HNRNPK | exon_skip_102185 | 4.912990e-01 | 1.995014e-13 |
| FL | PCBP2 | exon_skip_102185 | 4.494651e-01 | 3.087214e-11 |
| FL | G3BP2 | exon_skip_102185 | 5.451075e-01 | 1.015655e-16 |
| FL | KHDRBS3 | exon_skip_102185 | 4.273541e-01 | 3.404872e-10 |
| FL | RBM24 | exon_skip_102185 | 5.213744e-01 | 3.397466e-15 |
| FL | HNRNPA0 | exon_skip_102185 | 5.677684e-01 | 2.719184e-18 |
| FL | PUF60 | exon_skip_102185 | 4.925846e-01 | 1.689789e-13 |
| FL | HNRNPC | exon_skip_102185 | 4.149347e-01 | 1.217564e-09 |
| FL | NUP42 | exon_skip_102185 | 4.275689e-01 | 3.329129e-10 |
| FL | RALYL | exon_skip_102185 | 4.800265e-01 | 8.308427e-13 |
| FL | EIF4G2 | exon_skip_102185 | 4.332837e-01 | 1.819071e-10 |
| FL | RBM42 | exon_skip_102185 | 4.044033e-01 | 3.446574e-09 |
| FL | HNRNPL | exon_skip_102185 | 5.269162e-01 | 1.533923e-15 |
| FL | CPEB2 | exon_skip_102185 | 4.220432e-01 | 5.908921e-10 |
| FL | CELF1 | exon_skip_102185 | 4.354899e-01 | 1.436164e-10 |
| FL | SRSF9 | exon_skip_102185 | 4.610056e-01 | 8.220791e-12 |
| FL | HNRNPH2 | exon_skip_102185 | 4.705901e-01 | 2.636430e-12 |
| FL | EIF4B | exon_skip_102185 | 4.243761e-01 | 4.643622e-10 |
| FL | SART3 | exon_skip_102185 | 4.133835e-01 | 1.422469e-09 |
| FL | NOVA1 | exon_skip_102185 | 5.158664e-01 | 7.382904e-15 |
| HCC | DAZAP1 | exon_skip_102185 | -4.322849e-01 | 1.014794e-13 |
| HCC | RBMS2 | exon_skip_102185 | -5.533529e-01 | 4.638075e-23 |
| HCC | RBFOX2 | exon_skip_102185 | 5.238795e-01 | 1.965756e-20 |
| HCC | MSI1 | exon_skip_102185 | -6.145660e-01 | 1.963676e-29 |
| HCC | PABPN1 | exon_skip_102185 | -4.325880e-01 | 9.712219e-14 |
| HCC | ZNF326 | exon_skip_102185 | -4.487367e-01 | 8.790646e-15 |
| HCC | SFPQ | exon_skip_102185 | -4.371720e-01 | 4.974757e-14 |
| HCC | RBM6 | exon_skip_102185 | -5.005260e-01 | 1.587512e-18 |
| HCC | SAMD4A | exon_skip_102185 | -5.846891e-01 | 3.732742e-26 |
| HCC | U2AF2 | exon_skip_102185 | -4.030544e-01 | 5.720226e-12 |
| HCC | RBM5 | exon_skip_102185 | -4.580920e-01 | 2.059958e-15 |
| HCC | RBM47 | exon_skip_102185 | -4.251547e-01 | 2.813552e-13 |
| HCC | KHDRBS3 | exon_skip_102185 | -4.145526e-01 | 1.226846e-12 |
| HCC | EIF4G2 | exon_skip_102185 | -4.547526e-01 | 3.475474e-15 |
| HCC | PTBP1 | exon_skip_102185 | -6.016621e-01 | 5.643407e-28 |
| HCC | SRSF4 | exon_skip_102185 | -4.531684e-01 | 4.445405e-15 |
| HCC | YBX2 | exon_skip_102185 | -4.067312e-01 | 3.518722e-12 |
| HCC | HNRNPF | exon_skip_102185 | -5.581787e-01 | 1.625454e-23 |
| IFG | PABPN1 | exon_skip_102185 | 4.096108e-01 | 3.041600e-02 |
| IFG | SFPQ | exon_skip_102185 | 4.535369e-01 | 1.535131e-02 |
| IFG | U2AF2 | exon_skip_102185 | 5.446836e-01 | 2.727367e-03 |
| IFG | CNOT4 | exon_skip_102185 | 4.835228e-01 | 9.141238e-03 |
| IFG | RBM5 | exon_skip_102185 | 4.381628e-01 | 1.969262e-02 |
| IFG | MBNL1 | exon_skip_102185 | 4.697347e-01 | 1.166656e-02 |
| IFG | HNRNPK | exon_skip_102185 | 4.161997e-01 | 2.759761e-02 |
| IFG | TRA2A | exon_skip_102185 | 4.406336e-01 | 1.893380e-02 |
| IFG | SF1 | exon_skip_102185 | 4.398100e-01 | 1.918402e-02 |
| IFG | ENOX1 | exon_skip_102185 | 6.511490e-01 | 1.749994e-04 |
| IFG | KHSRP | exon_skip_102185 | 5.142098e-01 | 5.121336e-03 |
| IFG | HNRNPA0 | exon_skip_102185 | 4.393303e-01 | 1.933100e-02 |
| IFG | HNRNPA2B1 | exon_skip_102185 | 4.623221e-01 | 1.324890e-02 |
| IFG | HNRNPDL | exon_skip_102185 | 4.733037e-01 | 1.096287e-02 |
| IFG | PUF60 | exon_skip_102185 | 4.483821e-01 | 1.670853e-02 |
| IFG | HNRNPAB | exon_skip_102185 | 4.063459e-01 | 3.189627e-02 |
| IFG | EIF4G2 | exon_skip_102185 | 5.869624e-01 | 1.025721e-03 |
| IFG | CPEB2 | exon_skip_102185 | 6.284177e-01 | 3.422882e-04 |
| IFG | CELF1 | exon_skip_102185 | 4.326720e-01 | 2.146852e-02 |
| IFG | PABPC1 | exon_skip_102185 | 4.085686e-01 | 3.088238e-02 |
| IFG | PABPC4 | exon_skip_102185 | 4.304757e-01 | 2.221464e-02 |
| IFG | SRSF1 | exon_skip_102185 | 4.631458e-01 | 1.306472e-02 |
| IFG | SRSF4 | exon_skip_102185 | 5.447700e-01 | 2.722270e-03 |
| IFG | SRSF9 | exon_skip_102185 | 4.911458e-01 | 7.954148e-03 |
| IFG | CPEB2 | exon_skip_282430 | -4.587157e-01 | 1.408098e-02 |
| IFG | SART3 | exon_skip_282430 | -4.083254e-01 | 3.099201e-02 |
| PCC | RBMS2 | exon_skip_102185 | -6.188090e-01 | 2.886234e-23 |
| PCC | RBFOX2 | exon_skip_102185 | 6.518068e-01 | 2.023129e-26 |
| PCC | MSI1 | exon_skip_102185 | -4.966173e-01 | 2.733680e-14 |
| PCC | ELAVL4 | exon_skip_102185 | 5.636639e-01 | 9.364532e-19 |
| PCC | RBM6 | exon_skip_102185 | -4.186164e-01 | 3.450957e-10 |
| PCC | SAMD4A | exon_skip_102185 | -5.334391e-01 | 1.280114e-16 |
| PCC | RBM47 | exon_skip_102185 | -4.471634e-01 | 1.433047e-11 |
| PCC | G3BP2 | exon_skip_102185 | 7.331572e-01 | 3.553271e-36 |
| PCC | ZFP36 | exon_skip_102185 | -4.224958e-01 | 2.278580e-10 |
| PCC | RALYL | exon_skip_102185 | 4.896769e-01 | 7.002919e-14 |
| PCC | PTBP1 | exon_skip_102185 | -5.879120e-01 | 1.240271e-20 |
| PCC | HNRNPF | exon_skip_102185 | -4.843820e-01 | 1.415163e-13 |
| PG | SRSF2 | exon_skip_102185 | 4.720220e-01 | 5.399614e-13 |
| PG | RBFOX2 | exon_skip_102185 | 5.772524e-01 | 5.756686e-20 |
| PG | ELAVL4 | exon_skip_102185 | 5.440048e-01 | 1.700344e-17 |
| PG | RBM25 | exon_skip_102185 | 4.364787e-01 | 3.933042e-11 |
| PG | ELAVL1 | exon_skip_102185 | 4.711774e-01 | 6.013971e-13 |
| PG | SFPQ | exon_skip_102185 | 4.000526e-01 | 1.957345e-09 |
| PG | SRSF11 | exon_skip_102185 | 4.615729e-01 | 2.006215e-12 |
| PG | TIA1 | exon_skip_102185 | 4.239295e-01 | 1.593695e-10 |
| PG | RBM3 | exon_skip_102185 | 4.556198e-01 | 4.155075e-12 |
| PG | MBNL1 | exon_skip_102185 | 4.701398e-01 | 6.862361e-13 |
| PG | TRNAU1AP | exon_skip_102185 | 4.198018e-01 | 2.493936e-10 |
| PG | FXR2 | exon_skip_102185 | 5.388097e-01 | 3.911047e-17 |
| PG | PCBP1 | exon_skip_102185 | 4.613815e-01 | 2.054186e-12 |
| PG | ILF2 | exon_skip_102185 | 5.140409e-01 | 1.714515e-15 |
| PG | HNRNPK | exon_skip_102185 | 5.275173e-01 | 2.277537e-16 |
| PG | PCBP2 | exon_skip_102185 | 4.575034e-01 | 3.305166e-12 |
| PG | RC3H1 | exon_skip_102185 | 4.219942e-01 | 1.967511e-10 |
| PG | G3BP2 | exon_skip_102185 | 6.007558e-01 | 6.870179e-22 |
| PG | KHDRBS2 | exon_skip_102185 | 4.456784e-01 | 1.358805e-11 |
| PG | KHDRBS3 | exon_skip_102185 | 4.709024e-01 | 6.228347e-13 |
| PG | RBM24 | exon_skip_102185 | 4.883083e-01 | 6.374047e-14 |
| PG | FUBP1 | exon_skip_102185 | 4.092841e-01 | 7.597408e-10 |
| PG | ENOX1 | exon_skip_102185 | 4.093566e-01 | 7.540283e-10 |
| PG | HNRNPA0 | exon_skip_102185 | 5.040816e-01 | 7.204055e-15 |
| PG | HNRNPDL | exon_skip_102185 | 4.470050e-01 | 1.162653e-11 |
| PG | PUF60 | exon_skip_102185 | 5.130791e-01 | 1.973499e-15 |
| PG | HNRNPD | exon_skip_102185 | 4.234408e-01 | 1.680989e-10 |
| PG | HNRNPC | exon_skip_102185 | 5.057282e-01 | 5.700253e-15 |
| PG | NUP42 | exon_skip_102185 | 4.280442e-01 | 1.013673e-10 |
| PG | RALYL | exon_skip_102185 | 5.231191e-01 | 4.444851e-16 |
| PG | EIF4G2 | exon_skip_102185 | 4.509536e-01 | 7.280857e-12 |
| PG | HNRNPL | exon_skip_102185 | 5.469617e-01 | 1.051550e-17 |
| PG | CPEB2 | exon_skip_102185 | 4.121247e-01 | 5.644861e-10 |
| PG | CELF1 | exon_skip_102185 | 5.139193e-01 | 1.745316e-15 |
| PG | RBM23 | exon_skip_102185 | 4.440021e-01 | 1.653087e-11 |
| PG | PABPC4 | exon_skip_102185 | 4.189417e-01 | 2.735752e-10 |
| PG | SRSF1 | exon_skip_102185 | 4.632453e-01 | 1.630968e-12 |
| PG | SRSF9 | exon_skip_102185 | 4.381943e-01 | 3.233710e-11 |
| PG | HNRNPH2 | exon_skip_102185 | 4.850123e-01 | 9.912918e-14 |
| PG | EIF4B | exon_skip_102185 | 4.645404e-01 | 1.388229e-12 |
| PG | SART3 | exon_skip_102185 | 5.049916e-01 | 6.330707e-15 |
| PG | NOVA1 | exon_skip_102185 | 4.948509e-01 | 2.615621e-14 |
| STG | TARDBP | exon_skip_102185 | 4.557471e-01 | 4.992533e-06 |
| STG | SRSF2 | exon_skip_102185 | 4.031179e-01 | 6.772456e-05 |
| STG | ZNF326 | exon_skip_102185 | 4.201498e-01 | 3.052558e-05 |
| STG | SFPQ | exon_skip_102185 | 4.031179e-01 | 6.772456e-05 |
| STG | HNRNPA0 | exon_skip_102185 | 4.557938e-01 | 4.980012e-06 |
| STG | NUP42 | exon_skip_102185 | 4.089116e-01 | 5.189320e-05 |
| STG | NOVA1 | exon_skip_102185 | 4.175133e-01 | 3.463101e-05 |
| TC | RALYL | exon_skip_73919 | -4.017235e-01 | 1.041738e-06 |
| TC | RBMS2 | exon_skip_241538 | -5.873046e-01 | 3.273041e-16 |
| TC | MSI1 | exon_skip_241538 | -6.066813e-01 | 1.852211e-17 |
| TC | SAMD4A | exon_skip_241538 | -4.951799e-01 | 2.803782e-11 |
| TC | PTBP1 | exon_skip_241538 | -4.781254e-01 | 1.616490e-10 |
| TC | NOVA1 | exon_skip_241538 | 5.837142e-01 | 5.457896e-16 |
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RelatedDrugs for RTN4 |
| 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 RTN4 |
| 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)
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