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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 BMS1 |
 Gene summary |
| Gene information | Gene symbol | BMS1 | Gene ID | 9790 |
| Gene name | BMS1, ribosome biogenesis factor | |
| Synonyms | ACC|BMS1L | |
| Cytomap | 10q11.21 | |
| Type of gene | protein-coding | |
| Description | ribosome biogenesis protein BMS1 homologBMS1 homolog, ribosome assembly proteinBMS1-like, ribosome assembly proteinribosome assembly protein BMS1 homolog | |
| Modification date | 20180523 | |
| UniProtAcc | Q14692 | |
| Context | PubMed: BMS1 [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 BMS1 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 BMS1 |
| 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 BMS1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_40897 | 10 | 43282615:43282695:43285770:43285959:43287074:43287217 | 43285770:43285959 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40898 | 10 | 43285770:43285959:43287074:43287217:43287940:43288062 | 43287074:43287217 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40902 | 10 | 43293915:43294073:43297584:43297666:43312046:43312120 | 43297584:43297666 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40905 | 10 | 43297584:43297666:43312046:43312120:43312765:43312942 | 43312046:43312120 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40910 | 10 | 43312765:43312942:43315683:43315872:43315955:43316136 | 43315683:43315872 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40911 | 10 | 43315955:43316136:43316381:43316440:43317509:43317632 | 43316381:43316440 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40912 | 10 | 43316381:43316440:43317509:43317632:43318565:43318713 | 43317509:43317632 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40914 | 10 | 43317509:43317632:43318565:43318713:43319056:43319232 | 43318565:43318713 | ENSG00000165733.7 | ENST00000374518.5 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for BMS1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_40897 | 10 | 43282615:43282695:43285770:43285959:43287074:43287217 | 43285770:43285959 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40898 | 10 | 43285770:43285959:43287074:43287217:43287940:43288062 | 43287074:43287217 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40902 | 10 | 43293915:43294073:43297584:43297666:43312046:43312120 | 43297584:43297666 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40905 | 10 | 43297584:43297666:43312046:43312120:43312765:43312942 | 43312046:43312120 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40910 | 10 | 43312765:43312942:43315683:43315872:43315955:43316136 | 43315683:43315872 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40911 | 10 | 43315955:43316136:43316381:43316440:43317509:43317632 | 43316381:43316440 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40912 | 10 | 43316381:43316440:43317509:43317632:43318565:43318713 | 43317509:43317632 | ENSG00000165733.7 | ENST00000374518.5 |
| exon_skip_40914 | 10 | 43317509:43317632:43318565:43318713:43319056:43319232 | 43318565:43318713 | ENSG00000165733.7 | ENST00000374518.5 |
| 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 BMS1 |
| 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 |
| ENST00000374518 | 43287074 | 43287217 | Frame-shift |
| ENST00000374518 | 43297584 | 43297666 | Frame-shift |
| ENST00000374518 | 43312046 | 43312120 | Frame-shift |
| ENST00000374518 | 43316381 | 43316440 | Frame-shift |
| ENST00000374518 | 43318565 | 43318713 | Frame-shift |
| ENST00000374518 | 43285770 | 43285959 | In-frame |
| ENST00000374518 | 43315683 | 43315872 | In-frame |
| ENST00000374518 | 43317509 | 43317632 | 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 |
| ENST00000374518 | 43287074 | 43287217 | Frame-shift |
| ENST00000374518 | 43297584 | 43297666 | Frame-shift |
| ENST00000374518 | 43312046 | 43312120 | Frame-shift |
| ENST00000374518 | 43316381 | 43316440 | Frame-shift |
| ENST00000374518 | 43318565 | 43318713 | Frame-shift |
| ENST00000374518 | 43285770 | 43285959 | In-frame |
| ENST00000374518 | 43315683 | 43315872 | In-frame |
| ENST00000374518 | 43317509 | 43317632 | In-frame |
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Infer the effects of exon skipping event on protein functional features for BMS1 |
| 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 |
| ENST00000374518 | 7770 | 1282 | 43285770 | 43285959 | 511 | 699 | 149 | 212 |
| ENST00000374518 | 7770 | 1282 | 43315683 | 43315872 | 2644 | 2832 | 860 | 923 |
| ENST00000374518 | 7770 | 1282 | 43317509 | 43317632 | 3073 | 3195 | 1003 | 1044 |
| 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 |
| ENST00000374518 | 7770 | 1282 | 43285770 | 43285959 | 511 | 699 | 149 | 212 |
| ENST00000374518 | 7770 | 1282 | 43315683 | 43315872 | 2644 | 2832 | 860 | 923 |
| ENST00000374518 | 7770 | 1282 | 43317509 | 43317632 | 3073 | 3195 | 1003 | 1044 |
| 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 |
| Q14692 | 149 | 212 | 1 | 1282 | Chain | ID=PRO_0000195004;Note=Ribosome biogenesis protein BMS1 homolog |
| Q14692 | 149 | 212 | 80 | 246 | Domain | Note=Bms1-type G |
| Q14692 | 149 | 212 | 188 | 188 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q14692 | 860 | 923 | 1 | 1282 | Chain | ID=PRO_0000195004;Note=Ribosome biogenesis protein BMS1 homolog |
| Q14692 | 860 | 923 | 884 | 884 | Natural variant | ID=VAR_057506;Note=M->V;Dbxref=dbSNP:rs2419109 |
| Q14692 | 1003 | 1044 | 1 | 1282 | Chain | ID=PRO_0000195004;Note=Ribosome biogenesis protein BMS1 homolog |
| 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 |
| Q14692 | 149 | 212 | 1 | 1282 | Chain | ID=PRO_0000195004;Note=Ribosome biogenesis protein BMS1 homolog |
| Q14692 | 149 | 212 | 80 | 246 | Domain | Note=Bms1-type G |
| Q14692 | 149 | 212 | 188 | 188 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q14692 | 860 | 923 | 1 | 1282 | Chain | ID=PRO_0000195004;Note=Ribosome biogenesis protein BMS1 homolog |
| Q14692 | 860 | 923 | 884 | 884 | Natural variant | ID=VAR_057506;Note=M->V;Dbxref=dbSNP:rs2419109 |
| Q14692 | 1003 | 1044 | 1 | 1282 | Chain | ID=PRO_0000195004;Note=Ribosome biogenesis protein BMS1 homolog |
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SNVs in the skipped exons for BMS1 |
| - 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_40897 | 43285771 | 43285959 | 43285795 | 43285795 | Frame_Shift_Del | T | - | p.F158fs |
| KIRC | TCGA-BP-5177-01 | exon_skip_40910 | 43315684 | 43315872 | 43315792 | 43315792 | Frame_Shift_Del | T | - | p.E896fs |
| KIRC | TCGA-BP-5177-01 | exon_skip_40910 | 43315684 | 43315872 | 43315792 | 43315792 | Frame_Shift_Del | T | - | p.F897fs |
| SKCM | TCGA-FW-A3R5-06 | exon_skip_40897 | 43285771 | 43285959 | 43285837 | 43285837 | Nonsense_Mutation | C | T | p.Q172* |
| ACC | TCGA-OR-A5J5-01 | exon_skip_40897 | 43285771 | 43285959 | 43285924 | 43285924 | Nonsense_Mutation | C | T | p.R201* |
| ACC | TCGA-OR-A5J5-01 | exon_skip_40897 | 43285771 | 43285959 | 43285924 | 43285924 | Nonsense_Mutation | C | T | p.R201X |
| UCEC | TCGA-BS-A0UF-01 | exon_skip_40910 | 43315684 | 43315872 | 43315744 | 43315744 | Nonsense_Mutation | C | T | p.R881* |
| UVM | TCGA-VD-A8KE-01 | exon_skip_40914 | 43318566 | 43318713 | 43318659 | 43318659 | Nonsense_Mutation | C | T | p.R1076X |
| UCS | TCGA-N7-A4Y8-01 | exon_skip_40912 | 43317510 | 43317632 | 43317508 | 43317508 | Splice_Site | A | G | . |
| - 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 |
| MDAPCA2B_PROSTATE | 43285771 | 43285959 | 43285784 | 43285784 | Missense_Mutation | T | C | p.I154T |
| M980513_SKIN | 43285771 | 43285959 | 43285790 | 43285790 | Missense_Mutation | C | T | p.A156V |
| HUCCT1_BILIARY_TRACT | 43285771 | 43285959 | 43285814 | 43285814 | Missense_Mutation | C | G | p.T164R |
| HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43285771 | 43285959 | 43285861 | 43285861 | Missense_Mutation | A | C | p.M180L |
| HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43285771 | 43285959 | 43285882 | 43285882 | Missense_Mutation | G | A | p.D187N |
| CL40_LARGE_INTESTINE | 43285771 | 43285959 | 43285882 | 43285882 | Missense_Mutation | G | A | p.D187N |
| HEC108_ENDOMETRIUM | 43285771 | 43285959 | 43285891 | 43285891 | Missense_Mutation | A | G | p.K190E |
| TCYIK_CERVIX | 43287075 | 43287217 | 43287112 | 43287112 | Missense_Mutation | G | T | p.G225V |
| HEP3B217_LIVER | 43287075 | 43287217 | 43287186 | 43287186 | Missense_Mutation | C | G | p.Q250E |
| J82_URINARY_TRACT | 43287075 | 43287217 | 43287213 | 43287213 | Missense_Mutation | G | A | p.D259N |
| HEC1A_ENDOMETRIUM | 43297585 | 43297666 | 43297616 | 43297616 | Missense_Mutation | C | T | p.T760I |
| HEC1_ENDOMETRIUM | 43297585 | 43297666 | 43297616 | 43297616 | Missense_Mutation | C | T | p.T760I |
| HEC1B_ENDOMETRIUM | 43297585 | 43297666 | 43297616 | 43297616 | Missense_Mutation | C | T | p.T760I |
| HEC108_ENDOMETRIUM | 43297585 | 43297666 | 43297624 | 43297624 | Missense_Mutation | T | C | p.W763R |
| HEC6_ENDOMETRIUM | 43297585 | 43297666 | 43297650 | 43297650 | Missense_Mutation | G | T | p.K771N |
| HCC461_LUNG | 43315684 | 43315872 | 43315718 | 43315718 | Missense_Mutation | A | G | p.E872G |
| DMS79_LUNG | 43315684 | 43315872 | 43315720 | 43315720 | Missense_Mutation | G | T | p.A873S |
| JHH5_LIVER | 43315684 | 43315872 | 43315840 | 43315840 | Missense_Mutation | G | A | p.G913S |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43315684 | 43315872 | 43315857 | 43315857 | Missense_Mutation | T | A | p.N918K |
| SNU349_KIDNEY | 43316382 | 43316440 | 43316417 | 43316417 | Missense_Mutation | A | G | p.I996V |
| SNU175_LARGE_INTESTINE | 43316382 | 43316440 | 43316427 | 43316427 | Missense_Mutation | T | G | p.V999G |
| PANC1_PANCREAS | 43317510 | 43317632 | 43317520 | 43317520 | Missense_Mutation | G | A | p.R1007Q |
| KP1N_PANCREAS | 43317510 | 43317632 | 43317520 | 43317520 | Missense_Mutation | G | A | p.R1007Q |
| SNU1040_LARGE_INTESTINE | 43317510 | 43317632 | 43317597 | 43317597 | Missense_Mutation | C | T | p.P1033S |
| KARPAS1106P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43317510 | 43317632 | 43317603 | 43317603 | Missense_Mutation | A | G | p.K1035E |
| HEC251_ENDOMETRIUM | 43317510 | 43317632 | 43317625 | 43317625 | Missense_Mutation | T | G | p.F1042C |
| DSH1_URINARY_TRACT | 43318566 | 43318713 | 43318668 | 43318668 | Missense_Mutation | G | A | p.E1079K |
| SNU81_LARGE_INTESTINE | 43315684 | 43315872 | 43315744 | 43315744 | Nonsense_Mutation | C | T | p.R881* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for BMS1 |
| 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 BMS1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BMS1 |
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RelatedDrugs for BMS1 |
| 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 BMS1 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| BMS1 | C0282160 | Aplasia Cutis Congenita | 1 | ORPHANET;UNIPROT |
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