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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 SSB |
 Gene summary |
| Gene information | Gene symbol | SSB | Gene ID | 6741 |
| Gene name | Sjogren syndrome antigen B | |
| Synonyms | LARP3|La|La/SSB | |
| Cytomap | 2q31.1 | |
| Type of gene | protein-coding | |
| Description | lupus La proteinLa ribonucleoprotein domain family, member 3SS-BSS-B/La proteinautoantigen Lala autoantigenlupus La antigensjoegren syndrome type B antigen | |
| Modification date | 20180522 | |
| UniProtAcc | P05455 | |
| Context | PubMed: SSB [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 |
| SSB | GO:0075522 | IRES-dependent viral translational initiation | 12384597 |
| SSB | GO:1903608 | protein localization to cytoplasmic stress granule | 24965446 |
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Exon skipping events across known transcript of Ensembl for SSB 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 SSB |
| 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 SSB |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_330923 | 2 | 170655389:170655486:170657461:170657536:170661983:170662087 | 170657461:170657536 | ENSG00000138385.11 | ENST00000461708.1,ENST00000413002.1,ENST00000260956.4 |
| exon_skip_330927 | 2 | 170655389:170655486:170661983:170662087:170662174:170662349 | 170661983:170662087 | ENSG00000138385.11 | ENST00000417292.1 |
| exon_skip_330929 | 2 | 170657461:170657536:170661983:170662087:170662174:170662325 | 170661983:170662087 | ENSG00000138385.11 | ENST00000422006.1,ENST00000461708.1,ENST00000413002.1,ENST00000260956.4,ENST00000409333.1 |
| exon_skip_330933 | 2 | 170662174:170662349:170662507:170662623:170663294:170663400 | 170662507:170662623 | ENSG00000138385.11 | ENST00000413002.1 |
| exon_skip_330935 | 2 | 170663480:170663581:170664991:170665063:170665369:170665412 | 170664991:170665063 | ENSG00000138385.11 | ENST00000474273.1,ENST00000260956.4,ENST00000409333.1 |
| exon_skip_330937 | 2 | 170665369:170665412:170666792:170666933:170667367:170667398 | 170666792:170666933 | ENSG00000138385.11 | ENST00000490914.1,ENST00000260956.4,ENST00000409333.1 |
| exon_skip_330938 | 2 | 170666792:170666933:170667367:170667554:170667692:170667833 | 170667367:170667554 | ENSG00000138385.11 | ENST00000260956.4,ENST00000409333.1 |
| exon_skip_330940 | 2 | 170667367:170667554:170667692:170667833:170668177:170668574 | 170667692:170667833 | ENSG00000138385.11 | ENST00000260956.4,ENST00000409333.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for SSB |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_330923 | 2 | 170655389:170655486:170657461:170657536:170661983:170662087 | 170657461:170657536 | ENSG00000138385.11 | ENST00000260956.4,ENST00000413002.1,ENST00000461708.1 |
| exon_skip_330927 | 2 | 170655389:170655486:170661983:170662087:170662174:170662349 | 170661983:170662087 | ENSG00000138385.11 | ENST00000417292.1 |
| exon_skip_330929 | 2 | 170657461:170657536:170661983:170662087:170662174:170662325 | 170661983:170662087 | ENSG00000138385.11 | ENST00000422006.1,ENST00000260956.4,ENST00000413002.1,ENST00000461708.1,ENST00000409333.1 |
| exon_skip_330933 | 2 | 170662174:170662349:170662507:170662623:170663294:170663400 | 170662507:170662623 | ENSG00000138385.11 | ENST00000413002.1 |
| exon_skip_330935 | 2 | 170663480:170663581:170664991:170665063:170665369:170665412 | 170664991:170665063 | ENSG00000138385.11 | ENST00000260956.4,ENST00000409333.1,ENST00000474273.1 |
| exon_skip_330937 | 2 | 170665369:170665412:170666792:170666933:170667367:170667398 | 170666792:170666933 | ENSG00000138385.11 | ENST00000260956.4,ENST00000409333.1,ENST00000490914.1 |
| exon_skip_330938 | 2 | 170666792:170666933:170667367:170667554:170667692:170667833 | 170667367:170667554 | ENSG00000138385.11 | ENST00000260956.4,ENST00000409333.1 |
| exon_skip_330940 | 2 | 170667367:170667554:170667692:170667833:170668177:170668574 | 170667692:170667833 | ENSG00000138385.11 | ENST00000260956.4,ENST00000409333.1 |
| 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 SSB |
| 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 |
| ENST00000260956 | 170657461 | 170657536 | 5CDS-5UTR |
| ENST00000260956 | 170661983 | 170662087 | Frame-shift |
| ENST00000409333 | 170661983 | 170662087 | Frame-shift |
| ENST00000260956 | 170667367 | 170667554 | Frame-shift |
| ENST00000409333 | 170667367 | 170667554 | Frame-shift |
| ENST00000260956 | 170664991 | 170665063 | In-frame |
| ENST00000409333 | 170664991 | 170665063 | In-frame |
| ENST00000260956 | 170666792 | 170666933 | In-frame |
| ENST00000409333 | 170666792 | 170666933 | In-frame |
| ENST00000260956 | 170667692 | 170667833 | In-frame |
| ENST00000409333 | 170667692 | 170667833 | 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 |
| ENST00000260956 | 170657461 | 170657536 | 5CDS-5UTR |
| ENST00000260956 | 170661983 | 170662087 | Frame-shift |
| ENST00000409333 | 170661983 | 170662087 | Frame-shift |
| ENST00000260956 | 170667367 | 170667554 | Frame-shift |
| ENST00000409333 | 170667367 | 170667554 | Frame-shift |
| ENST00000260956 | 170664991 | 170665063 | In-frame |
| ENST00000409333 | 170664991 | 170665063 | In-frame |
| ENST00000260956 | 170666792 | 170666933 | In-frame |
| ENST00000409333 | 170666792 | 170666933 | In-frame |
| ENST00000260956 | 170667692 | 170667833 | In-frame |
| ENST00000409333 | 170667692 | 170667833 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SSB |
| 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 |
| ENST00000260956 | 1726 | 408 | 170666792 | 170666933 | 844 | 984 | 223 | 270 |
| ENST00000409333 | 1799 | 408 | 170666792 | 170666933 | 917 | 1057 | 223 | 270 |
| ENST00000260956 | 1726 | 408 | 170667692 | 170667833 | 1172 | 1312 | 332 | 379 |
| ENST00000409333 | 1799 | 408 | 170667692 | 170667833 | 1245 | 1385 | 332 | 379 |
| 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 |
| ENST00000260956 | 1726 | 408 | 170666792 | 170666933 | 844 | 984 | 223 | 270 |
| ENST00000409333 | 1799 | 408 | 170666792 | 170666933 | 917 | 1057 | 223 | 270 |
| ENST00000260956 | 1726 | 408 | 170667692 | 170667833 | 1172 | 1312 | 332 | 379 |
| ENST00000409333 | 1799 | 408 | 170667692 | 170667833 | 1245 | 1385 | 332 | 379 |
| 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 |
| P05455 | 223 | 270 | 233 | 239 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 233 | 239 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 259 | 263 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 259 | 263 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 269 | 277 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 269 | 277 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 1 | 408 | Chain | ID=PRO_0000207599;Note=Lupus La protein |
| P05455 | 223 | 270 | 1 | 408 | Chain | ID=PRO_0000207599;Note=Lupus La protein |
| P05455 | 223 | 270 | 246 | 252 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 246 | 252 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 225 | 225 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P05455 | 223 | 270 | 225 | 225 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P05455 | 332 | 379 | 1 | 408 | Chain | ID=PRO_0000207599;Note=Lupus La protein |
| P05455 | 332 | 379 | 1 | 408 | Chain | ID=PRO_0000207599;Note=Lupus La protein |
| P05455 | 332 | 379 | 341 | 341 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P32067 |
| P05455 | 332 | 379 | 341 | 341 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P32067 |
| P05455 | 332 | 379 | 360 | 360 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P05455 | 332 | 379 | 360 | 360 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P05455 | 332 | 379 | 362 | 362 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| P05455 | 332 | 379 | 362 | 362 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| P05455 | 332 | 379 | 366 | 366 | Modified residue | Note=Phosphoserine%3B by CK2;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:17081983,ECO:0000244|PubMed:18318008,ECO:0000244|PubMed:18669648,ECO:0000244 |
| P05455 | 332 | 379 | 366 | 366 | Modified residue | Note=Phosphoserine%3B by CK2;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:17081983,ECO:0000244|PubMed:18318008,ECO:0000244|PubMed:18669648,ECO:0000244 |
| 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 |
| P05455 | 223 | 270 | 233 | 239 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 233 | 239 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 259 | 263 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 259 | 263 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 269 | 277 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 269 | 277 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 1 | 408 | Chain | ID=PRO_0000207599;Note=Lupus La protein |
| P05455 | 223 | 270 | 1 | 408 | Chain | ID=PRO_0000207599;Note=Lupus La protein |
| P05455 | 223 | 270 | 246 | 252 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 246 | 252 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OWX |
| P05455 | 223 | 270 | 225 | 225 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P05455 | 223 | 270 | 225 | 225 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| P05455 | 332 | 379 | 1 | 408 | Chain | ID=PRO_0000207599;Note=Lupus La protein |
| P05455 | 332 | 379 | 1 | 408 | Chain | ID=PRO_0000207599;Note=Lupus La protein |
| P05455 | 332 | 379 | 341 | 341 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P32067 |
| P05455 | 332 | 379 | 341 | 341 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:P32067 |
| P05455 | 332 | 379 | 360 | 360 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P05455 | 332 | 379 | 360 | 360 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| P05455 | 332 | 379 | 362 | 362 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| P05455 | 332 | 379 | 362 | 362 | Modified residue | Note=Phosphothreonine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24275569;Dbxref=PMID:24275569 |
| P05455 | 332 | 379 | 366 | 366 | Modified residue | Note=Phosphoserine%3B by CK2;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:17081983,ECO:0000244|PubMed:18318008,ECO:0000244|PubMed:18669648,ECO:0000244 |
| P05455 | 332 | 379 | 366 | 366 | Modified residue | Note=Phosphoserine%3B by CK2;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244|PubMed:17081983,ECO:0000244|PubMed:18318008,ECO:0000244|PubMed:18669648,ECO:0000244 |
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SNVs in the skipped exons for SSB |
| - 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 |
| HNSC | TCGA-CR-6493-01 | exon_skip_330935 | 170664992 | 170665063 | 170665008 | 170665008 | Frame_Shift_Del | A | - | p.K191fs |
| HNSC | TCGA-CR-6493-01 | exon_skip_330935 | 170664992 | 170665063 | 170665008 | 170665008 | Frame_Shift_Del | A | - | p.K192fs |
| PCPG | TCGA-RW-A686-06 | exon_skip_330935 | 170664992 | 170665063 | 170665008 | 170665008 | Frame_Shift_Del | A | - | p.K192fs |
| STAD | TCGA-B7-A5TI-01 | exon_skip_330935 | 170664992 | 170665063 | 170665008 | 170665008 | Frame_Shift_Del | A | - | p.K192fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_330938 | 170667368 | 170667554 | 170667387 | 170667387 | Frame_Shift_Del | A | - | p.E277fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_330938 | 170667368 | 170667554 | 170667489 | 170667489 | Frame_Shift_Del | A | - | p.E311fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_330938 | 170667368 | 170667554 | 170667489 | 170667489 | Frame_Shift_Del | A | - | p.E311fs |
| PRAD | TCGA-HC-7080-01 | exon_skip_330938 | 170667368 | 170667554 | 170667531 | 170667531 | Frame_Shift_Del | C | - | p.S325fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_330940 | 170667693 | 170667833 | 170667776 | 170667776 | Frame_Shift_Del | A | - | p.K361fs |
| LUAD | TCGA-95-7567-01 | exon_skip_330935 | 170664992 | 170665063 | 170665007 | 170665008 | Frame_Shift_Ins | - | A | p.A190fs |
| LUAD | TCGA-95-7567-01 | exon_skip_330935 | 170664992 | 170665063 | 170665007 | 170665008 | Frame_Shift_Ins | - | A | p.AK190fs |
| BLCA | TCGA-DK-A6AW-01 | exon_skip_330937 | 170666793 | 170666933 | 170666805 | 170666805 | Nonsense_Mutation | G | T | p.E228* |
| - 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 |
| TGBC11TKB_STOMACH | 170664992 | 170665063 | 170665007 | 170665008 | Frame_Shift_Ins | - | A | p.K191fs |
| HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 170666793 | 170666933 | 170666838 | 170666838 | Missense_Mutation | G | A | p.D239N |
| SKMEL2_SKIN | 170666793 | 170666933 | 170666907 | 170666907 | Missense_Mutation | A | T | p.I262L |
| SNU1040_LARGE_INTESTINE | 170666793 | 170666933 | 170666916 | 170666916 | Missense_Mutation | G | A | p.V265I |
| OC316_OVARY | 170667368 | 170667554 | 170667397 | 170667397 | Missense_Mutation | G | T | p.K280N |
| OC314_OVARY | 170667368 | 170667554 | 170667397 | 170667397 | Missense_Mutation | G | T | p.K280N |
| EN_ENDOMETRIUM | 170667368 | 170667554 | 170667534 | 170667534 | Missense_Mutation | T | C | p.L326P |
| SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 170667693 | 170667833 | 170667731 | 170667731 | Missense_Mutation | G | A | p.A346T |
| BC3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 170667693 | 170667833 | 170667744 | 170667744 | Missense_Mutation | C | T | p.S350F |
| KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 170667693 | 170667833 | 170667788 | 170667788 | Missense_Mutation | G | A | p.A365T |
| HS939T_SKIN | 170667693 | 170667833 | 170667807 | 170667807 | Missense_Mutation | A | G | p.D371G |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SSB |
| 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 SSB |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SSB |
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RelatedDrugs for SSB |
| 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 SSB |
| 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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