|
||||||
|
 | |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| 3'-UTR located exon skipping events lost miRNA binding sites |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| |
| |
|
Gene summary for LSM14A |
 Gene summary |
| Gene information | Gene symbol | LSM14A | Gene ID | 26065 |
| Gene name | LSM14A mRNA processing body assembly factor | |
| Synonyms | C19orf13|FAM61A|RAP55|RAP55A | |
| Cytomap | 19q13.11 | |
| Type of gene | protein-coding | |
| Description | protein LSM14 homolog ALSM14 homolog ALSM14A, SCD6 homolog ARNA-associated protein 55RNA-associated protein 55AalphaSNBPfamily with sequence similarity 61, member AhRAP55hRAP55Aprotein SCD6 homologputative alpha-synuclein-binding protein | |
| 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 |
| LSM14A | GO:0033962 | cytoplasmic mRNA processing body assembly | 16484376 |
Top |
Gene structures and expression levels for LSM14A |
| 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. |
 |
ENSG00000257103
| 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 |
| CB | UP | ENST00000586157.2 | LSM14A-205:protein_coding:LSM14A | 7.741312e+01 | 9.759113e-01 | 1.008321e-05 | 1.061608e-04 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for LSM14A |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
 |
| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_107046 | chr19 | 34196634:34196763:34215124:34215300:34215596:34215661 | 34215124:34215300 |
| exon_skip_108646 | chr19 | 34196634:34196763:34208929:34209051:34215596:34215661 | 34208929:34209051 |
| exon_skip_146501 | chr19 | 34209036:34209051:34215596:34215661:34219391:34219573 | 34215596:34215661 |
| exon_skip_155978 | chr19 | 34196634:34196763:34208929:34209051:34215124:34215300 | 34208929:34209051 |
| exon_skip_169594 | chr19 | 34215596:34215661:34219391:34219573:34219706:34219877 | 34219391:34219573 |
| exon_skip_178842 | chr19 | 34194478:34194641:34196634:34196763:34208929:34209051 | 34196634:34196763 |
| exon_skip_187081 | chr19 | 34194478:34194641:34195219:34195320:34196634:34196666 | 34195219:34195320 |
| exon_skip_189073 | chr19 | 34194478:34194641:34196634:34196763:34208929:34209011 | 34196634:34196763 |
| exon_skip_206495 | chr19 | 34196667:34196763:34208929:34209051:34215124:34215300 | 34208929:34209051 |
| exon_skip_227039 | chr19 | 34196634:34196763:34208929:34209051:34215124:34215217 | 34208929:34209051 |
| exon_skip_24414 | chr19 | 34221507:34221738:34226408:34226464:34227365:34227390 | 34226408:34226464 |
| exon_skip_249391 | chr19 | 34208929:34209051:34215596:34215661:34219391:34219573 | 34215596:34215661 |
| exon_skip_260924 | chr19 | 34221507:34221738:34226408:34226464:34227365:34227617 | 34226408:34226464 |
| exon_skip_267781 | chr19 | 34208936:34209051:34215124:34215300:34215596:34215657 | 34215124:34215300 |
| exon_skip_270626 | chr19 | 34208929:34209051:34215124:34215300:34215596:34215661 | 34215124:34215300 |
| exon_skip_286824 | chr19 | 34209036:34209051:34215124:34215300:34215596:34215661 | 34215124:34215300 |
| exon_skip_348 | chr19 | 34221507:34221738:34226408:34226464:34227365:34227413 | 34226408:34226464 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
Top |
Open reading frame (ORF) annotation in the exon skipping event for LSM14A |
| 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 |
| 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 |
| 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 |
Top |
Infer the effects of exon skipping event on protein functional features for LSM14A |
p-ENSG00000257103_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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in LSM14A |
| 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 |
Top |
SNVs in the skipped exons for LSM14A |
| - 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 |
Top |
AD stage-associated exon skippint events for LSM14A |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LSM14A |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for LSM14A |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | NUP42 | exon_skip_348 | 5.618487e-01 | 1.306453e-14 |
| CB | RALYL | exon_skip_348 | 4.898000e-01 | 5.664819e-11 |
| CB | SRSF9 | exon_skip_348 | 4.615944e-01 | 9.130249e-10 |
Top |
RelatedDrugs for LSM14A |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for LSM14A |
| 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)
|