|
||||||
|
 | |
| |
| |
| 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 LARP4B |
 Gene summary |
| Gene information | Gene symbol | LARP4B | Gene ID | 23185 |
| Gene name | La ribonucleoprotein 4B | |
| Synonyms | KIAA0217|LARP5 | |
| Cytomap | 10p15.3 | |
| Type of gene | protein-coding | |
| Description | la-related protein 4BLa ribonucleoprotein domain family member 4BLa ribonucleoprotein domain family, member 5la-related protein 5 | |
| Modification date | 20200313 | |
| 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 |
Top |
Gene structures and expression levels for LARP4B |
| 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. |
 |
ENSG00000107929
| 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. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for LARP4B |
| 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_105670 | chr10 | 864241:864270:870009:870083:884447:884506 | 870009:870083 |
| exon_skip_127022 | chr10 | 864241:864270:870013:870083:884447:884506 | 870013:870083 |
| exon_skip_129597 | chr10 | 864241:864270:870013:870083:884447:884503 | 870013:870083 |
| exon_skip_139266 | chr10 | 842932:843068:844977:845055:863743:863883 | 844977:845055 |
| exon_skip_198222 | chr10 | 864241:864270:870009:870083:884447:884503 | 870009:870083 |
| exon_skip_258479 | chr10 | 807849:808272:812921:813213:814742:814850 | 812921:813213 |
| exon_skip_279961 | chr10 | 820800:820845:825065:825316:825764:825870 | 825065:825316 |
| exon_skip_71482 | chr10 | 806914:808272:812921:813213:814742:814850 | 812921:813213 |
| exon_skip_82843 | chr10 | 864154:864270:870009:870083:884447:884506 | 870009:870083 |
| 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 LARP4B |
| 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 |
| ENST00000316157 | 844977 | 845055 | Frame-shift |
| ENST00000612396 | 844977 | 845055 | Frame-shift |
| ENST00000316157 | 825065 | 825316 | In-frame |
| ENST00000612396 | 825065 | 825316 | 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 |
| ENST00000316157 | 844977 | 845055 | Frame-shift |
| ENST00000612396 | 844977 | 845055 | Frame-shift |
| 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 |
| ENST00000316157 | 844977 | 845055 | Frame-shift |
| ENST00000612396 | 844977 | 845055 | Frame-shift |
| ENST00000316157 | 825065 | 825316 | In-frame |
| ENST00000612396 | 825065 | 825316 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for LARP4B |
p-ENSG00000107929_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 |
| ENST00000316157 | 5659 | 738 | 825065 | 825316 | 1274 | 1524 | 411 | 494 |
| ENST00000612396 | 8563 | 738 | 825065 | 825316 | 1550 | 1800 | 411 | 494 |
| 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 |
| ENST00000316157 | 5659 | 738 | 825065 | 825316 | 1274 | 1524 | 411 | 494 |
| ENST00000612396 | 8563 | 738 | 825065 | 825316 | 1550 | 1800 | 411 | 494 |
| 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 |
| Q92615 | 411 | 494 | 1 | 738 | Chain | ID=PRO_0000281139;Note=La-related protein 4B |
| Q92615 | 411 | 494 | 1 | 738 | Chain | ID=PRO_0000281139;Note=La-related protein 4B |
| Q92615 | 411 | 494 | 419 | 419 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
| Q92615 | 411 | 494 | 419 | 419 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
| Q92615 | 411 | 494 | 424 | 424 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332;Dbxref=PMID:18669648,PMID:19690332 |
| Q92615 | 411 | 494 | 424 | 424 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332;Dbxref=PMID:18669648,PMID:19690332 |
| Q92615 | 411 | 494 | 434 | 434 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:16964243,ECO:0000244|PubMed:18669648;Dbxref=PMID:16964243,PMID:18669648 |
| Q92615 | 411 | 494 | 434 | 434 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:16964243,ECO:0000244|PubMed:18669648;Dbxref=PMID:16964243,PMID:18669648 |
| Q92615 | 411 | 494 | 451 | 451 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163 |
| Q92615 | 411 | 494 | 451 | 451 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163 |
| Q92615 | 411 | 494 | 488 | 488 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q92615 | 411 | 494 | 488 | 488 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q92615 | 411 | 494 | 493 | 493 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6A0A2 |
| Q92615 | 411 | 494 | 493 | 493 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6A0A2 |
| 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 |
| Q92615 | 411 | 494 | 1 | 738 | Chain | ID=PRO_0000281139;Note=La-related protein 4B |
| Q92615 | 411 | 494 | 1 | 738 | Chain | ID=PRO_0000281139;Note=La-related protein 4B |
| Q92615 | 411 | 494 | 419 | 419 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
| Q92615 | 411 | 494 | 419 | 419 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:24129315;Dbxref=PMID:24129315 |
| Q92615 | 411 | 494 | 424 | 424 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332;Dbxref=PMID:18669648,PMID:19690332 |
| Q92615 | 411 | 494 | 424 | 424 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:19690332;Dbxref=PMID:18669648,PMID:19690332 |
| Q92615 | 411 | 494 | 434 | 434 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:16964243,ECO:0000244|PubMed:18669648;Dbxref=PMID:16964243,PMID:18669648 |
| Q92615 | 411 | 494 | 434 | 434 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:16964243,ECO:0000244|PubMed:18669648;Dbxref=PMID:16964243,PMID:18669648 |
| Q92615 | 411 | 494 | 451 | 451 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163 |
| Q92615 | 411 | 494 | 451 | 451 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:23186163 |
| Q92615 | 411 | 494 | 488 | 488 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q92615 | 411 | 494 | 488 | 488 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q92615 | 411 | 494 | 493 | 493 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6A0A2 |
| Q92615 | 411 | 494 | 493 | 493 | Modified residue | Note=Omega-N-methylarginine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q6A0A2 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in LARP4B |
| 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 LARP4B |
| - 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 LARP4B |
| 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 LARP4B |
| 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 LARP4B |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
Top |
RelatedDrugs for LARP4B |
| 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 LARP4B |
| 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)
|