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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for RBM28 |
 Gene summary |
| Gene information | Gene symbol | RBM28 | Gene ID | 55131 |
| Gene name | RNA binding motif protein 28 | |
| Synonyms | ANES | |
| Cytomap | 7q32.1 | |
| Type of gene | protein-coding | |
| Description | RNA-binding protein 282810480G15Rik | |
| Modification date | 20180523 | |
| UniProtAcc | Q9NW13 | |
| Context | PubMed: RBM28 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| 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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Exon skipping events across known transcript of Ensembl for RBM28 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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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Gene isoform structures and expression levels for RBM28 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for RBM28 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_479378 | 7 | 127950532:127950984:127953227:127953327:127954816:127955024 | 127953227:127953327 | ENSG00000106344.4 | ENST00000223073.2,ENST00000415472.2,ENST00000481788.1 |
| exon_skip_479380 | 7 | 127954816:127955073:127957711:127957786:127958009:127958159 | 127957711:127957786 | ENSG00000106344.4 | ENST00000223073.2,ENST00000415472.2 |
| exon_skip_479391 | 7 | 127964660:127964747:127965870:127965944:127970871:127970981 | 127965870:127965944 | ENSG00000106344.4 | ENST00000223073.2,ENST00000415472.2 |
| exon_skip_479392 | 7 | 127965870:127965944:127970871:127970981:127973343:127973416 | 127970871:127970981 | ENSG00000106344.4 | ENST00000223073.2,ENST00000415472.2 |
| exon_skip_479393 | 7 | 127970871:127970981:127973343:127973416:127975596:127975733 | 127973343:127973416 | ENSG00000106344.4 | ENST00000223073.2,ENST00000487602.1,ENST00000415472.2 |
| exon_skip_479395 | 7 | 127975900:127976096:127977184:127977256:127978303:127978396 | 127977184:127977256 | ENSG00000106344.4 | ENST00000223073.2 |
| exon_skip_479397 | 7 | 127977184:127977256:127978303:127978396:127978779:127978855 | 127978303:127978396 | ENSG00000106344.4 | ENST00000223073.2 |
| exon_skip_479398 | 7 | 127979686:127979845:127981171:127981273:127983729:127983924 | 127981171:127981273 | ENSG00000106344.4 | ENST00000459726.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for RBM28 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_479378 | 7 | 127950532:127950984:127953227:127953327:127954816:127955024 | 127953227:127953327 | ENSG00000106344.4 | ENST00000223073.2,ENST00000481788.1,ENST00000415472.2 |
| exon_skip_479380 | 7 | 127954816:127955073:127957711:127957786:127958009:127958159 | 127957711:127957786 | ENSG00000106344.4 | ENST00000223073.2,ENST00000415472.2 |
| exon_skip_479391 | 7 | 127964660:127964747:127965870:127965944:127970871:127970981 | 127965870:127965944 | ENSG00000106344.4 | ENST00000223073.2,ENST00000415472.2 |
| exon_skip_479392 | 7 | 127965870:127965944:127970871:127970981:127973343:127973416 | 127970871:127970981 | ENSG00000106344.4 | ENST00000223073.2,ENST00000415472.2 |
| exon_skip_479393 | 7 | 127970871:127970981:127973343:127973416:127975596:127975733 | 127973343:127973416 | ENSG00000106344.4 | ENST00000223073.2,ENST00000415472.2,ENST00000487602.1 |
| exon_skip_479396 | 7 | 127975900:127976096:127977184:127977256:127983729:127983924 | 127977184:127977256 | ENSG00000106344.4 | ENST00000415472.2 |
| exon_skip_479397 | 7 | 127977184:127977256:127978303:127978396:127978779:127978855 | 127978303:127978396 | ENSG00000106344.4 | ENST00000223073.2 |
| exon_skip_479398 | 7 | 127979686:127979845:127981171:127981273:127983729:127983924 | 127981171:127981273 | ENSG00000106344.4 | ENST00000459726.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for RBM28 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000223073 | 127953227 | 127953327 | Frame-shift |
| ENST00000223073 | 127965870 | 127965944 | Frame-shift |
| ENST00000223073 | 127970871 | 127970981 | Frame-shift |
| ENST00000223073 | 127973343 | 127973416 | Frame-shift |
| ENST00000223073 | 127957711 | 127957786 | In-frame |
| ENST00000223073 | 127977184 | 127977256 | In-frame |
| ENST00000223073 | 127978303 | 127978396 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000223073 | 127953227 | 127953327 | Frame-shift |
| ENST00000223073 | 127965870 | 127965944 | Frame-shift |
| ENST00000223073 | 127970871 | 127970981 | Frame-shift |
| ENST00000223073 | 127973343 | 127973416 | Frame-shift |
| ENST00000223073 | 127957711 | 127957786 | In-frame |
| ENST00000223073 | 127978303 | 127978396 | In-frame |
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Infer the effects of exon skipping event on protein functional features for RBM28 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| Loci of skipped exons in TCGA 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 |
| ENST00000223073 | 15524 | 759 | 127978303 | 127978396 | 564 | 656 | 149 | 180 |
| ENST00000223073 | 15524 | 759 | 127977184 | 127977256 | 657 | 728 | 180 | 204 |
| ENST00000223073 | 15524 | 759 | 127957711 | 127957786 | 1829 | 1903 | 571 | 596 |
| Loci of skipped exons in GTEx 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 |
| ENST00000223073 | 15524 | 759 | 127978303 | 127978396 | 564 | 656 | 149 | 180 |
| ENST00000223073 | 15524 | 759 | 127957711 | 127957786 | 1829 | 1903 | 571 | 596 |
| Lost protein functional features of individual exon skipping events in TCGA. |
| 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 |
| Q9NW13 | 149 | 180 | 39 | 179 | Alternative sequence | ID=VSP_046111;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NW13 | 149 | 180 | 2 | 759 | Chain | ID=PRO_0000081785;Note=RNA-binding protein 28 |
| Q9NW13 | 149 | 180 | 114 | 191 | Domain | Note=RRM 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
| Q9NW13 | 180 | 204 | 2 | 759 | Chain | ID=PRO_0000081785;Note=RNA-binding protein 28 |
| Q9NW13 | 180 | 204 | 114 | 191 | Domain | Note=RRM 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
| Q9NW13 | 571 | 596 | 2 | 759 | Chain | ID=PRO_0000081785;Note=RNA-binding protein 28 |
| Q9NW13 | 571 | 596 | 487 | 597 | Domain | Note=RRM 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
| Lost protein functional features of individual exon skipping events in GTEx. |
| 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 |
| Q9NW13 | 149 | 180 | 39 | 179 | Alternative sequence | ID=VSP_046111;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q9NW13 | 149 | 180 | 2 | 759 | Chain | ID=PRO_0000081785;Note=RNA-binding protein 28 |
| Q9NW13 | 149 | 180 | 114 | 191 | Domain | Note=RRM 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
| Q9NW13 | 571 | 596 | 2 | 759 | Chain | ID=PRO_0000081785;Note=RNA-binding protein 28 |
| Q9NW13 | 571 | 596 | 487 | 597 | Domain | Note=RRM 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
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SNVs in the skipped exons for RBM28 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - Differential PSIs between mutated versus non-mutated samples. |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_479378 | 127953228 | 127953327 | 127953286 | 127953286 | Frame_Shift_Del | T | - | p.K696fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_479378 | 127953228 | 127953327 | 127953286 | 127953286 | Frame_Shift_Del | T | - | p.K696fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_479393 | 127973344 | 127973416 | 127973349 | 127973349 | Frame_Shift_Del | A | - | p.F338fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_479393 | 127973344 | 127973416 | 127973361 | 127973361 | Frame_Shift_Del | C | - | p.G334fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_479397 | 127978304 | 127978396 | 127978357 | 127978357 | Frame_Shift_Del | T | - | p.N163fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_479397 | 127978304 | 127978396 | 127978371 | 127978371 | Frame_Shift_Del | A | - | p.F158fs |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_479397 | 127978304 | 127978396 | 127978371 | 127978371 | Frame_Shift_Del | A | - | p.F158fs |
| STAD | TCGA-BR-8360-01 | exon_skip_479393 | 127973344 | 127973416 | 127973348 | 127973349 | Frame_Shift_Ins | - | A | p.F338fs |
| STAD | TCGA-BR-8360-01 | exon_skip_479393 | 127973344 | 127973416 | 127973348 | 127973349 | Frame_Shift_Ins | - | A | p.I339fs |
| STAD | TCGA-BR-8360-01 | exon_skip_479393 | 127973344 | 127973416 | 127973349 | 127973350 | Frame_Shift_Ins | - | A | p.F338fs |
| HNSC | TCGA-MT-A7BN-01 | exon_skip_479380 | 127957712 | 127957786 | 127957756 | 127957756 | Nonsense_Mutation | G | A | p.R582* |
| LGG | TCGA-DU-6392-01 | exon_skip_479391 | 127965871 | 127965944 | 127965879 | 127965879 | Nonsense_Mutation | C | A | p.E399* |
| UCEC | TCGA-AP-A059-01 | exon_skip_479391 | 127965871 | 127965944 | 127965930 | 127965930 | Nonsense_Mutation | G | A | p.Q382* |
| UCEC | TCGA-D1-A16J-01 | exon_skip_479391 | 127965871 | 127965944 | 127965868 | 127965869 | Splice_Site | - | A | e11+2 |
| UCEC | TCGA-D1-A16J-01 | exon_skip_479391 | 127965871 | 127965944 | 127965868 | 127965869 | Splice_Site | - | A | p.E401_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| U118MG_CENTRAL_NERVOUS_SYSTEM | 127953228 | 127953327 | 127953292 | 127953292 | Missense_Mutation | G | A | p.P694L |
| JHUEM3_ENDOMETRIUM | 127957712 | 127957786 | 127957755 | 127957755 | Missense_Mutation | C | T | p.R582Q |
| NCIH2126_LUNG | 127965871 | 127965944 | 127965873 | 127965873 | Missense_Mutation | C | T | p.E401K |
| NCIH1573_LUNG | 127973344 | 127973416 | 127973391 | 127973391 | Missense_Mutation | C | G | p.K324N |
| WM1799_SKIN | 127977185 | 127977256 | 127977209 | 127977209 | Missense_Mutation | C | T | p.D197N |
| RERFLCKJ_LUNG | 127977185 | 127977256 | 127977209 | 127977209 | Missense_Mutation | C | T | p.D197N |
| LOVO_LARGE_INTESTINE | 127977185 | 127977256 | 127977254 | 127977254 | Missense_Mutation | G | A | p.R182W |
| AGS_STOMACH | 127978304 | 127978396 | 127978315 | 127978315 | Missense_Mutation | T | G | p.K177T |
| HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 127978304 | 127978396 | 127978317 | 127978317 | Missense_Mutation | C | T | p.M176I |
| KYAE1_OESOPHAGUS | 127978304 | 127978396 | 127978317 | 127978317 | Missense_Mutation | C | T | p.M176I |
| AGS_STOMACH | 127978304 | 127978396 | 127978325 | 127978325 | Missense_Mutation | T | G | p.M174L |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RBM28 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RBM28 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RBM28 |
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RelatedDrugs for RBM28 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for RBM28 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| RBM28 | C2677535 | Alopecia, Neurologic Defects, and Endocrinopathy Syndrome | 1 | CTD_human;ORPHANET;UNIPROT |
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