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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 LSM14B |
 Gene summary |
| Gene information | Gene symbol | LSM14B | Gene ID | 149986 |
| Gene name | LSM family member 14B | |
| Synonyms | C20orf40|FAM61B|FT005|LSM13|RAP55B|bA11M20.3 | |
| Cytomap | 20q13.33 | |
| Type of gene | protein-coding | |
| Description | protein LSM14 homolog BLSM14 homolog BLSM14B, SCD6 homolog BRNA-associated protein 55Bfamily with sequence similarity 61, member BhRAP55B | |
| Modification date | 20200327 | |
| UniProtAcc | ||
| Context |
| 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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Gene structures and expression levels for LSM14B |
| 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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ENSG00000149657
| 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. |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| 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 LSM14B |
| 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_111110 | chr20 | 62129785:62129952:62130219:62130296:62130530:62130605 | 62130219:62130296 |
| exon_skip_119777 | chr20 | 62124617:62124780:62126304:62126439:62127585:62127701 | 62126304:62126439 |
| exon_skip_137891 | chr20 | 62126340:62126439:62127585:62127701:62129785:62129952 | 62127585:62127701 |
| exon_skip_147370 | chr20 | 62126304:62126439:62129785:62129952:62130219:62130296 | 62129785:62129952 |
| exon_skip_168642 | chr20 | 62131356:62131506:62133290:62133475:62134163:62135374 | 62133290:62133475 |
| exon_skip_195124 | chr20 | 62129809:62129952:62130219:62130296:62130530:62130605 | 62130219:62130296 |
| exon_skip_208669 | chr20 | 62124617:62124780:62126304:62126439:62129785:62129952 | 62126304:62126439 |
| exon_skip_212817 | chr20 | 62127585:62127701:62129785:62129952:62130219:62130296 | 62129785:62129952 |
| exon_skip_235791 | chr20 | 62127590:62127701:62129785:62129952:62130219:62130296 | 62129785:62129952 |
| exon_skip_257549 | chr20 | 62126340:62126439:62129785:62129952:62130219:62130296 | 62129785:62129952 |
| exon_skip_284214 | chr20 | 62126304:62126439:62127585:62127701:62129785:62129952 | 62127585:62127701 |
| exon_skip_35540 | chr20 | 62124617:62124780:62126226:62126439:62129785:62129952 | 62126226:62126439 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_137891 | ROSMAP_DLPFC | 5.914218e-01 | 7.013913e-01 | -1.099695e-01 | 2.659928e-04 |
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Open reading frame (ORF) annotation in the exon skipping event for LSM14B |
| 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 |
| ENST00000279068 | 62133290 | 62133475 | 3UTR-3CDS |
| ENST00000279068 | 62126304 | 62126439 | Frame-shift |
| ENST00000279068 | 62129785 | 62129952 | In-frame |
| ENST00000279068 | 62130219 | 62130296 | 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 |
| ENST00000279068 | 62129785 | 62129952 | In-frame |
| ENST00000279068 | 62130219 | 62130296 | 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 |
| ENST00000279068 | 62126304 | 62126439 | Frame-shift |
| ENST00000279068 | 62129785 | 62129952 | In-frame |
| ENST00000279068 | 62130219 | 62130296 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LSM14B |
p-ENSG00000149657_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 |
| ENST00000279068 | 2565 | 385 | 62129785 | 62129952 | 589 | 755 | 143 | 198 |
| ENST00000279068 | 2565 | 385 | 62130219 | 62130296 | 757 | 833 | 199 | 224 |
| 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 |
| ENST00000279068 | 2565 | 385 | 62129785 | 62129952 | 589 | 755 | 143 | 198 |
| ENST00000279068 | 2565 | 385 | 62130219 | 62130296 | 757 | 833 | 199 | 224 |
| 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 |
| ENST00000279068 | 2565 | 385 | 62129785 | 62129952 | 589 | 755 | 143 | 198 |
| ENST00000279068 | 2565 | 385 | 62130219 | 62130296 | 757 | 833 | 199 | 224 |
| 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 |
| Q9BX40 | 143 | 198 | 143 | 220 | Alternative sequence | ID=VSP_014660;Note=In isoform 2. GAGFPSIPVGKSPMVEQAVQTGSADNLNAKKLLPGKGTTGTQLNGRQAQPSSKTASDVVQPAAVQAQGQVNDENRRPQ->EKLVSPPASAAASSPSSSPSPQPVSELDLSSEPQQLTAKGNSSLGELHAVLQTILRARGKAADRMTVAVADHLPSPCS;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334; |
| Q9BX40 | 143 | 198 | 2 | 385 | Chain | ID=PRO_0000187093;Note=Protein LSM14 homolog B |
| Q9BX40 | 143 | 198 | 154 | 154 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| Q9BX40 | 143 | 198 | 165 | 165 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q9BX40 | 199 | 224 | 143 | 220 | Alternative sequence | ID=VSP_014660;Note=In isoform 2. GAGFPSIPVGKSPMVEQAVQTGSADNLNAKKLLPGKGTTGTQLNGRQAQPSSKTASDVVQPAAVQAQGQVNDENRRPQ->EKLVSPPASAAASSPSSSPSPQPVSELDLSSEPQQLTAKGNSSLGELHAVLQTILRARGKAADRMTVAVADHLPSPCS;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334; |
| Q9BX40 | 199 | 224 | 2 | 385 | Chain | ID=PRO_0000187093;Note=Protein LSM14 homolog B |
| 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 |
| Q9BX40 | 143 | 198 | 143 | 220 | Alternative sequence | ID=VSP_014660;Note=In isoform 2. GAGFPSIPVGKSPMVEQAVQTGSADNLNAKKLLPGKGTTGTQLNGRQAQPSSKTASDVVQPAAVQAQGQVNDENRRPQ->EKLVSPPASAAASSPSSSPSPQPVSELDLSSEPQQLTAKGNSSLGELHAVLQTILRARGKAADRMTVAVADHLPSPCS;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334; |
| Q9BX40 | 143 | 198 | 2 | 385 | Chain | ID=PRO_0000187093;Note=Protein LSM14 homolog B |
| Q9BX40 | 143 | 198 | 154 | 154 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| Q9BX40 | 143 | 198 | 165 | 165 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q9BX40 | 199 | 224 | 143 | 220 | Alternative sequence | ID=VSP_014660;Note=In isoform 2. GAGFPSIPVGKSPMVEQAVQTGSADNLNAKKLLPGKGTTGTQLNGRQAQPSSKTASDVVQPAAVQAQGQVNDENRRPQ->EKLVSPPASAAASSPSSSPSPQPVSELDLSSEPQQLTAKGNSSLGELHAVLQTILRARGKAADRMTVAVADHLPSPCS;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334; |
| Q9BX40 | 199 | 224 | 2 | 385 | Chain | ID=PRO_0000187093;Note=Protein LSM14 homolog B |
| 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 |
| Q9BX40 | 143 | 198 | 143 | 220 | Alternative sequence | ID=VSP_014660;Note=In isoform 2. GAGFPSIPVGKSPMVEQAVQTGSADNLNAKKLLPGKGTTGTQLNGRQAQPSSKTASDVVQPAAVQAQGQVNDENRRPQ->EKLVSPPASAAASSPSSSPSPQPVSELDLSSEPQQLTAKGNSSLGELHAVLQTILRARGKAADRMTVAVADHLPSPCS;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334; |
| Q9BX40 | 143 | 198 | 2 | 385 | Chain | ID=PRO_0000187093;Note=Protein LSM14 homolog B |
| Q9BX40 | 143 | 198 | 154 | 154 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231;Dbxref=PMID:18669648,PMID:20068231 |
| Q9BX40 | 143 | 198 | 165 | 165 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q9BX40 | 199 | 224 | 143 | 220 | Alternative sequence | ID=VSP_014660;Note=In isoform 2. GAGFPSIPVGKSPMVEQAVQTGSADNLNAKKLLPGKGTTGTQLNGRQAQPSSKTASDVVQPAAVQAQGQVNDENRRPQ->EKLVSPPASAAASSPSSSPSPQPVSELDLSSEPQQLTAKGNSSLGELHAVLQTILRARGKAADRMTVAVADHLPSPCS;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334; |
| Q9BX40 | 199 | 224 | 2 | 385 | Chain | ID=PRO_0000187093;Note=Protein LSM14 homolog B |
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3'-UTR located exon skipping events that lost miRNA binding sites in LSM14B |
| 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 LSM14B |
| - 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 LSM14B |
| 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 LSM14B |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| DLPFC | exon_skip_257549 | rs6587299 | chr20:62223256 | 2.706876e-04 | 1.980573e-02 |
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Correlation with RNA binding proteins (RBPs) for LSM14B |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | SRSF4 | exon_skip_19997 | 4.013179e-01 | 4.219083e-06 |
| CB | RBM45 | exon_skip_119777 | 4.630178e-01 | 7.982757e-10 |
| CB | RBM45 | exon_skip_1714 | 4.319561e-01 | 2.320681e-07 |
| CB | PCBP2 | exon_skip_137891 | 4.108870e-01 | 7.460341e-08 |
| CB | NOVA1 | exon_skip_137891 | 4.342652e-01 | 1.071548e-08 |
| CB | NUP42 | exon_skip_220468 | 4.344005e-01 | 1.264487e-07 |
| CB | RALYL | exon_skip_220468 | 4.423805e-01 | 6.958339e-08 |
| CB | PCBP1 | exon_skip_257549 | -4.046813e-01 | 3.778898e-06 |
| CB | PCBP4 | exon_skip_257549 | 4.723363e-01 | 3.957489e-08 |
| CB | TRA2A | exon_skip_257549 | -5.215196e-01 | 7.304878e-10 |
| CB | NUP42 | exon_skip_257549 | 4.538118e-01 | 1.523365e-07 |
| CB | PCBP4 | exon_skip_11023 | 4.569464e-01 | 2.847380e-07 |
| CB | TRA2A | exon_skip_11023 | -5.128438e-01 | 4.635143e-09 |
| CB | NUP42 | exon_skip_11023 | 5.181678e-01 | 3.008863e-09 |
| CB | TARDBP | exon_skip_235791 | -4.550784e-01 | 1.675386e-09 |
| CB | PCBP1 | exon_skip_235791 | -4.416441e-01 | 5.629612e-09 |
| CB | PCBP4 | exon_skip_235791 | 6.147718e-01 | 6.695663e-18 |
| CB | TRA2A | exon_skip_235791 | -5.089112e-01 | 7.418592e-12 |
| CB | NUP42 | exon_skip_235791 | 4.735963e-01 | 2.885063e-10 |
| FL | SRSF2 | exon_skip_137891 | 4.018534e-01 | 4.536707e-07 |
| FL | ILF2 | exon_skip_137891 | 4.730717e-01 | 1.442409e-09 |
| FL | HNRNPK | exon_skip_137891 | 4.351057e-01 | 3.645579e-08 |
| HCC | ZNF638 | exon_skip_137891 | -4.630523e-01 | 7.335940e-16 |
| HCC | RBM6 | exon_skip_137891 | -6.128083e-01 | 1.948059e-29 |
| HCC | SRSF11 | exon_skip_137891 | -5.128822e-01 | 1.190567e-19 |
| HCC | HNRNPA2B1 | exon_skip_137891 | -4.547360e-01 | 2.753964e-15 |
| HCC | EIF4G2 | exon_skip_137891 | -5.227966e-01 | 1.757964e-20 |
| HCC | HNRNPF | exon_skip_137891 | -6.494998e-01 | 5.579404e-34 |
| IFG | IGF2BP2 | exon_skip_137891 | -4.000000e-01 | 3.493947e-02 |
| PCC | HNRNPF | exon_skip_137891 | -5.201495e-01 | 5.916194e-16 |
| STG | ILF2 | exon_skip_137891 | 4.188276e-01 | 4.653545e-04 |
| TC | SRSF2 | exon_skip_137891 | 5.351368e-01 | 4.369672e-13 |
| TC | MBNL1 | exon_skip_137891 | 4.177818e-01 | 4.718447e-08 |
| TC | ILF2 | exon_skip_137891 | 5.466734e-01 | 1.081161e-13 |
| TC | EIF4G2 | exon_skip_137891 | 4.026273e-01 | 1.567488e-07 |
| TC | PTBP3 | exon_skip_137891 | 4.533406e-01 | 2.211964e-09 |
| TC | NOVA1 | exon_skip_137891 | 7.031436e-01 | 7.097175e-25 |
| TC | RBFOX2 | exon_skip_79104 | 4.340702e-01 | 1.674797e-08 |
| TC | MSI1 | exon_skip_79104 | -4.004663e-01 | 2.428325e-07 |
| TC | RBM6 | exon_skip_79104 | -4.618158e-01 | 1.462621e-09 |
| TC | KHDRBS2 | exon_skip_79104 | 4.762158e-01 | 3.776762e-10 |
| TC | HNRNPA0 | exon_skip_79104 | 4.145661e-01 | 8.192782e-08 |
| TC | NUP42 | exon_skip_79104 | 4.162401e-01 | 7.177138e-08 |
| TC | RALYL | exon_skip_79104 | 4.398760e-01 | 1.023703e-08 |
| TC | HNRNPH2 | exon_skip_79104 | 4.214231e-01 | 4.742345e-08 |
| TC | NOVA1 | exon_skip_79104 | 5.577649e-01 | 4.734804e-14 |
| TC | NOVA1 | exon_skip_257549 | 4.302861e-01 | 3.893038e-08 |
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RelatedDrugs for LSM14B |
| 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 LSM14B |
| 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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