|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for LSM1 |
 Gene summary |
| Gene information | Gene symbol | LSM1 | Gene ID | 27257 |
| Gene name | LSM1 homolog, mRNA degradation associated | |
| Synonyms | CASM|YJL124C | |
| Cytomap | 8p11.23 | |
| Type of gene | protein-coding | |
| Description | U6 snRNA-associated Sm-like protein LSm1LSM1 homolog, U6 small nuclear RNA associatedLSM1 mRNA degradation associatedLSM1, U6 small nuclear RNA associatedLSM1-like protein U6 small nuclear RNA associatedcancer-associated Sm proteincancer-associated | |
| Modification date | 20180523 | |
| UniProtAcc | O15116 | |
| Context | PubMed: LSM1 [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 |
Top |
Exon skipping events across known transcript of Ensembl for LSM1 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. |
 |
Top |
Gene isoform structures and expression levels for LSM1 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for LSM1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_489166 | 8 | 38021127:38021358:38027319:38027435:38029482:38029546 | 38027319:38027435 | ENSG00000175324.5 | ENST00000520286.1,ENST00000311351.4,ENST00000522515.1 |
| exon_skip_489170 | 8 | 38021127:38021358:38029482:38029551:38033792:38034006 | 38029482:38029551 | ENSG00000175324.5 | ENST00000520755.1 |
| exon_skip_489172 | 8 | 38027319:38027435:38028460:38028530:38029482:38029546 | 38028460:38028530 | ENSG00000175324.5 | ENST00000523511.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for LSM1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_489166 | 8 | 38021127:38021358:38027319:38027435:38029482:38029546 | 38027319:38027435 | ENSG00000175324.5 | ENST00000311351.4,ENST00000522515.1,ENST00000520286.1 |
| exon_skip_489170 | 8 | 38021127:38021358:38029482:38029551:38033792:38034006 | 38029482:38029551 | ENSG00000175324.5 | ENST00000520755.1 |
| exon_skip_489172 | 8 | 38027319:38027435:38028460:38028530:38029482:38029546 | 38028460:38028530 | ENSG00000175324.5 | ENST00000523511.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for LSM1 |
| 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 |
| ENST00000311351 | 38027319 | 38027435 | Frame-shift |
| 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 |
| ENST00000311351 | 38027319 | 38027435 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for LSM1 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| 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 |
| 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 |
| 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 |
| 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 |
Top |
SNVs in the skipped exons for LSM1 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - Differential PSIs between mutated versus non-mutated samples. |
LSM1_COAD_exon_skip_489166_psi_boxplot.png |
LSM1_KIRP_exon_skip_489166_psi_boxplot.png |
LSM1_LIHC_exon_skip_489166_psi_boxplot.png |
LSM1_STAD_exon_skip_489166_psi_boxplot.png |
| - 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-G3-A3CJ-01 | exon_skip_489166 | 38027320 | 38027435 | 38027386 | 38027386 | Frame_Shift_Del | T | - | p.K55fs |
| UCEC | TCGA-BG-A0MQ-01 | exon_skip_489170 | 38029483 | 38029551 | 38029503 | 38029503 | Frame_Shift_Del | A | - | p.L32fs |
| COAD | TCGA-AA-3713-01 | exon_skip_489166 | 38027320 | 38027435 | 38027409 | 38027409 | Nonsense_Mutation | C | A | p.E48X |
| KIRP | TCGA-B9-A69E-01 | exon_skip_489166 | 38027320 | 38027435 | 38027436 | 38027436 | Splice_Site | C | - | p.A39_splice |
| STAD | TCGA-VQ-A8P2-01 | exon_skip_489166 | 38027320 | 38027435 | 38027436 | 38027436 | Splice_Site | C | T | . |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-B9-A69E-01 |
| Cancer type: KIRP | |
| ESID: exon_skip_489166 | |
| Skipped exon start: 38027320 | |
| Skipped exon end: 38027435 | |
| Mutation start: 38027436 | |
| Mutation end: 38027436 | |
| Mutation type: Splice_Site | |
| Reference seq: C | |
| Mutation seq: - | |
| AAchange: p.A39_splice | |
exon_skip_489166_KIRP_TCGA-B9-A69E-01.png | |
 | Sample: TCGA-AA-3713-01 |
| Cancer type: COAD | |
| ESID: exon_skip_489166 | |
| Skipped exon start: 38027320 | |
| Skipped exon end: 38027435 | |
| Mutation start: 38027409 | |
| Mutation end: 38027409 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: C | |
| Mutation seq: A | |
| AAchange: p.E48X | |
exon_skip_133096_COAD_TCGA-AA-3713-01.png | |
exon_skip_26067_COAD_TCGA-AA-3713-01.png | |
exon_skip_37475_COAD_TCGA-AA-3713-01.png | |
exon_skip_450406_COAD_TCGA-AA-3713-01.png | |
exon_skip_461886_COAD_TCGA-AA-3713-01.png | |
exon_skip_468121_COAD_TCGA-AA-3713-01.png | |
exon_skip_489166_COAD_TCGA-AA-3713-01.png | |
exon_skip_49506_COAD_TCGA-AA-3713-01.png | |
exon_skip_51251_COAD_TCGA-AA-3713-01.png | |
exon_skip_517478_COAD_TCGA-AA-3713-01.png | |
exon_skip_62245_COAD_TCGA-AA-3713-01.png | |
exon_skip_73552_COAD_TCGA-AA-3713-01.png | |
| - 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 |
| 42MGBA_CENTRAL_NERVOUS_SYSTEM | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| 639V_URINARY_TRACT | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| C32_SKIN | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| CFPAC1_PANCREAS | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| CH157MN_CENTRAL_NERVOUS_SYSTEM | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| COV318_OVARY | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| G292CLONEA141B1_BONE | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| GP2D_LARGE_INTESTINE | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| HCC515_LUNG | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| HLF_LIVER | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| HS688AT_FIBROBLAST | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| HS698T_FIBROBLAST | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| HS863T_FIBROBLAST | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| HT1197_URINARY_TRACT | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| KP4_PANCREAS | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| KS1_CENTRAL_NERVOUS_SYSTEM | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| LU99_LUNG | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| M07E_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| MCF7_BREAST | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| NCIH1781_LUNG | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| NCIH1930_LUNG | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| NCIH1944_LUNG | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| NCIH2081_LUNG | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| NCIH727_LUNG | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| NUDUL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| OE21_OESOPHAGUS | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| OUMS23_LARGE_INTESTINE | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| PANC0213_PANCREAS | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| PECAPJ49_UPPER_AERODIGESTIVE_TRACT | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| QGP1_PANCREAS | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| SNUC4_LARGE_INTESTINE | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| T173_FIBROBLAST | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| TE6_OESOPHAGUS | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| TT_THYROID | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| WM2664_SKIN | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| ZR7530_BREAST | 38027320 | 38027435 | 38027385 | 38027386 | Frame_Shift_Ins | - | T | p.Y56fs |
| CORL321_PLEURA | 38027320 | 38027435 | 38027369 | 38027369 | Missense_Mutation | C | T | p.R61Q |
| WSUNHL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 38027320 | 38027435 | 38027390 | 38027390 | Missense_Mutation | T | C | p.K54R |
| SW48_LARGE_INTESTINE | 38027320 | 38027435 | 38027397 | 38027397 | Missense_Mutation | C | T | p.V52M |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 38027320 | 38027435 | 38027434 | 38027434 | Splice_Site | T | A | p.A39A |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LSM1 |
| 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 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LSM1 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LSM1 |
Top |
RelatedDrugs for LSM1 |
| 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 |
Top |
RelatedDiseases for LSM1 |
| 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)
|