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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 LCA5L |
Gene summary |
Gene information | Gene symbol | LCA5L | Gene ID | 150082 |
Gene name | lebercilin LCA5 like | |
Synonyms | C21orf13 | |
Cytomap | 21q22.2 | |
Type of gene | protein-coding | |
Description | lebercilin-like proteinLCA5L, lebercilin likeleber congenital amaurosis 5-like protein | |
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 |
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Gene structures and expression levels for LCA5L |
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. |
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 | DOWN | ENST00000448288.6 | LCA5L-210:protein_coding:LCA5L | 3.231276e+00 | -2.004312e+00 | 1.612103e-05 | 1.580507e-04 |
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 LCA5L |
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_10630 | chr21 | 39423245:39423490:39428172:39428503:39429131:39429211 | 39428172:39428503 |
exon_skip_130229 | chr21 | 39429188:39429211:39435420:39435542:39444135:39444201 | 39435420:39435542 |
exon_skip_166932 | chr21 | 39429188:39429211:39435420:39435573:39444135:39444201 | 39435420:39435573 |
exon_skip_17891 | chr21 | 39429188:39429211:39435420:39435573:39445725:39445761 | 39435420:39435573 |
exon_skip_188013 | chr21 | 39423420:39423490:39428172:39428503:39429131:39429211 | 39428172:39428503 |
exon_skip_19659 | chr21 | 39435420:39435573:39444135:39444201:39445725:39445761 | 39444135:39444201 |
exon_skip_224106 | chr21 | 39420706:39420843:39422976:39423490:39428172:39428503 | 39422976:39423490 |
exon_skip_87285 | chr21 | 39411718:39411802:39420706:39420843:39422976:39423083 | 39420706:39420843 |
exon_skip_87982 | chr21 | 39429188:39429211:39444135:39444201:39445725:39445752 | 39444135:39444201 |
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 |
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Open reading frame (ORF) annotation in the exon skipping event for LCA5L |
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 |
ENST00000288350 | 39428172 | 39428503 | 3UTR-3CDS |
ENST00000358268 | 39428172 | 39428503 | 3UTR-3CDS |
ENST00000288350 | 39435420 | 39435573 | 3UTR-3UTR |
ENST00000288350 | 39444135 | 39444201 | 3UTR-3UTR |
ENST00000288350 | 39420706 | 39420843 | In-frame |
ENST00000358268 | 39420706 | 39420843 | In-frame |
ENST00000380671 | 39420706 | 39420843 | 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 |
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 |
ENST00000288350 | 39428172 | 39428503 | 3UTR-3CDS |
ENST00000358268 | 39428172 | 39428503 | 3UTR-3CDS |
ENST00000288350 | 39435420 | 39435573 | 3UTR-3UTR |
ENST00000288350 | 39422976 | 39423490 | Frame-shift |
ENST00000358268 | 39422976 | 39423490 | Frame-shift |
ENST00000288350 | 39420706 | 39420843 | In-frame |
ENST00000358268 | 39420706 | 39420843 | In-frame |
ENST00000380671 | 39420706 | 39420843 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LCA5L |
p-ENSG00000157578_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 |
ENST00000288350 | 2433 | 670 | 39420706 | 39420843 | 1203 | 1339 | 279 | 324 |
ENST00000358268 | 2581 | 670 | 39420706 | 39420843 | 1367 | 1503 | 279 | 324 |
ENST00000380671 | 2097 | 670 | 39420706 | 39420843 | 867 | 1003 | 279 | 324 |
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 |
ENST00000288350 | 2433 | 670 | 39420706 | 39420843 | 1203 | 1339 | 279 | 324 |
ENST00000358268 | 2581 | 670 | 39420706 | 39420843 | 1367 | 1503 | 279 | 324 |
ENST00000380671 | 2097 | 670 | 39420706 | 39420843 | 867 | 1003 | 279 | 324 |
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 |
O95447 | 279 | 324 | 1 | 670 | Chain | ID=PRO_0000079507;Note=Lebercilin-like protein |
O95447 | 279 | 324 | 1 | 670 | Chain | ID=PRO_0000079507;Note=Lebercilin-like protein |
O95447 | 279 | 324 | 1 | 670 | Chain | ID=PRO_0000079507;Note=Lebercilin-like protein |
O95447 | 279 | 324 | 305 | 336 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
O95447 | 279 | 324 | 305 | 336 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
O95447 | 279 | 324 | 305 | 336 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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 |
O95447 | 279 | 324 | 1 | 670 | Chain | ID=PRO_0000079507;Note=Lebercilin-like protein |
O95447 | 279 | 324 | 1 | 670 | Chain | ID=PRO_0000079507;Note=Lebercilin-like protein |
O95447 | 279 | 324 | 1 | 670 | Chain | ID=PRO_0000079507;Note=Lebercilin-like protein |
O95447 | 279 | 324 | 305 | 336 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
O95447 | 279 | 324 | 305 | 336 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
O95447 | 279 | 324 | 305 | 336 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in LCA5L |
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 |
Mayo | ENST00000288350 | 39435420 | 39435573 | hsa-miR-3613-3p | chr21:39435522-39435529 | 8mer-1a | chr21:39435506-39435529 | 148.00 | -5.89 |
Mayo | ENST00000288350 | 39435420 | 39435573 | hsa-miR-9500 | chr21:39435438-39435445 | 8mer-1a | chr21:39435426-39435445 | 146.00 | -12.50 |
ROSMAP | ENST00000288350 | 39444135 | 39444201 | hsa-miR-3166 | chr21:39444167-39444174 | 8mer-1a | chr21:39444167-39444187 | 159.00 | -15.66 |
ROSMAP | ENST00000288350 | 39435420 | 39435573 | hsa-miR-3613-3p | chr21:39435522-39435529 | 8mer-1a | chr21:39435506-39435529 | 148.00 | -5.89 |
ROSMAP | ENST00000288350 | 39444135 | 39444201 | hsa-miR-4708-5p | chr21:39444172-39444179 | 8mer-1a | chr21:39444167-39444187 | 159.00 | -15.66 |
ROSMAP | ENST00000288350 | 39435420 | 39435573 | hsa-miR-9500 | chr21:39435438-39435445 | 8mer-1a | chr21:39435426-39435445 | 146.00 | -12.50 |
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SNVs in the skipped exons for LCA5L |
- 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 LCA5L |
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 LCA5L |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for LCA5L |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for LCA5L |
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 LCA5L |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |