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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 CLTCL1 |
Gene summary |
Gene information | Gene symbol | CLTCL1 | Gene ID | 8218 |
Gene name | clathrin heavy chain like 1 | |
Synonyms | CHC22|CLH22|CLTCL|CLTD | |
Cytomap | 22q11.21 | |
Type of gene | protein-coding | |
Description | clathrin heavy chain 2CLH-22Clathrin, heavy polypeptide Dclathrin heavy chain on chromosome 22clathrin, heavy polypeptide-like 1 | |
Modification date | 20200313 | |
UniProtAcc | A0A087WV74, | |
Context |
Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
Gene | GO ID | GO term | PubMed ID |
CLTCL1 | GO:0000278 | mitotic cell cycle | 19509056 |
CLTCL1 | GO:0000278 | mitotic cell cycle | 20065094 |
CLTCL1 | GO:0006898 | receptor-mediated endocytosis | 19509056 |
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Gene structures and expression levels for CLTCL1 |
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 | ENST00000622493.4 | CLTCL1-212:protein_coding:CLTCL1 | 4.721474e+01 | -1.472636e+00 | 1.792510e-08 | 4.955858e-07 |
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 CLTCL1 |
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_126578 | chr22 | 19223891:19224054:19225453:19225633:19226219:19226320 | 19225453:19225633 |
exon_skip_161075 | chr22 | 19183495:19183611:19187558:19187728:19187981:19188091 | 19187558:19187728 |
exon_skip_197138 | chr22 | 19201391:19201493:19208154:19208311:19208922:19209114 | 19208154:19208311 |
exon_skip_218907 | chr22 | 19183476:19183611:19187558:19187728:19187981:19188091 | 19187558:19187728 |
exon_skip_228557 | chr22 | 19201391:19201493:19208154:19208311:19208922:19209327 | 19208154:19208311 |
exon_skip_233449 | chr22 | 19183495:19183611:19187981:19188091:19191304:19191435 | 19187981:19188091 |
exon_skip_239137 | chr22 | 19183476:19183611:19184396:19184536:19187558:19187728 | 19184396:19184536 |
exon_skip_253255 | chr22 | 19183414:19183611:19187981:19188091:19191304:19191435 | 19187981:19188091 |
exon_skip_289192 | chr22 | 19179775:19179969:19180199:19180238:19180731:19180806 | 19180199:19180238 |
exon_skip_74434 | chr22 | 19183476:19183611:19187981:19188091:19191304:19191435 | 19187981:19188091 |
exon_skip_92805 | chr22 | 19196489:19196656:19199734:19199841:19201329:19201493 | 19199734:19199841 |
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 CLTCL1 |
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 |
ENST00000427926 | 19180199 | 19180238 | 5CDS-5UTR |
ENST00000427926 | 19208154 | 19208311 | Frame-shift |
ENST00000427926 | 19225453 | 19225633 | Frame-shift |
ENST00000427926 | 19187558 | 19187728 | In-frame |
ENST00000427926 | 19199734 | 19199841 | 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 |
ENST00000427926 | 19208154 | 19208311 | Frame-shift |
ENST00000427926 | 19187558 | 19187728 | 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 |
ENST00000427926 | 19180199 | 19180238 | 5CDS-5UTR |
ENST00000427926 | 19208154 | 19208311 | Frame-shift |
ENST00000427926 | 19225453 | 19225633 | Frame-shift |
ENST00000427926 | 19187558 | 19187728 | In-frame |
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Infer the effects of exon skipping event on protein functional features for CLTCL1 |
p-ENSG00000070371_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 |
ENST00000427926 | 5530 | 1640 | 19199734 | 19199841 | 3839 | 3945 | 1255 | 1290 |
ENST00000427926 | 5530 | 1640 | 19187558 | 19187728 | 4508 | 4677 | 1478 | 1534 |
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 |
ENST00000427926 | 5530 | 1640 | 19187558 | 19187728 | 4508 | 4677 | 1478 | 1534 |
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 |
ENST00000427926 | 5530 | 1640 | 19187558 | 19187728 | 4508 | 4677 | 1478 | 1534 |
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 |
P53675 | 1255 | 1290 | 2 | 1640 | Chain | ID=PRO_0000205786;Note=Clathrin heavy chain 2 |
P53675 | 1255 | 1290 | 524 | 1640 | Region | Note=Heavy chain arm |
P53675 | 1255 | 1290 | 639 | 1640 | Region | Note=Proximal segment |
P53675 | 1255 | 1290 | 1213 | 1522 | Region | Note=Involved in binding clathrin light chain;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
P53675 | 1255 | 1290 | 1128 | 1269 | Repeat | Note=CHCR 5 |
P53675 | 1255 | 1290 | 1274 | 1420 | Repeat | Note=CHCR 6 |
P53675 | 1478 | 1534 | 1479 | 1535 | Alternative sequence | ID=VSP_001100;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:8733129,ECO:0000303|PubMed:8844170;Dbxref=PMID:14702039,PMID:8733129,PMID:8844170 |
P53675 | 1478 | 1534 | 2 | 1640 | Chain | ID=PRO_0000205786;Note=Clathrin heavy chain 2 |
P53675 | 1478 | 1534 | 1487 | 1487 | Modified residue | Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q68FD5 |
P53675 | 1478 | 1534 | 1494 | 1494 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q00610 |
P53675 | 1478 | 1534 | 1501 | 1501 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q00610 |
P53675 | 1478 | 1534 | 524 | 1640 | Region | Note=Heavy chain arm |
P53675 | 1478 | 1534 | 639 | 1640 | Region | Note=Proximal segment |
P53675 | 1478 | 1534 | 1213 | 1522 | Region | Note=Involved in binding clathrin light chain;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
P53675 | 1478 | 1534 | 1423 | 1566 | Repeat | Note=CHCR 7 |
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 |
P53675 | 1478 | 1534 | 1479 | 1535 | Alternative sequence | ID=VSP_001100;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:8733129,ECO:0000303|PubMed:8844170;Dbxref=PMID:14702039,PMID:8733129,PMID:8844170 |
P53675 | 1478 | 1534 | 2 | 1640 | Chain | ID=PRO_0000205786;Note=Clathrin heavy chain 2 |
P53675 | 1478 | 1534 | 1487 | 1487 | Modified residue | Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q68FD5 |
P53675 | 1478 | 1534 | 1494 | 1494 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q00610 |
P53675 | 1478 | 1534 | 1501 | 1501 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q00610 |
P53675 | 1478 | 1534 | 524 | 1640 | Region | Note=Heavy chain arm |
P53675 | 1478 | 1534 | 639 | 1640 | Region | Note=Proximal segment |
P53675 | 1478 | 1534 | 1213 | 1522 | Region | Note=Involved in binding clathrin light chain;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
P53675 | 1478 | 1534 | 1423 | 1566 | Repeat | Note=CHCR 7 |
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 |
P53675 | 1478 | 1534 | 1479 | 1535 | Alternative sequence | ID=VSP_001100;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:14702039,ECO:0000303|PubMed:8733129,ECO:0000303|PubMed:8844170;Dbxref=PMID:14702039,PMID:8733129,PMID:8844170 |
P53675 | 1478 | 1534 | 2 | 1640 | Chain | ID=PRO_0000205786;Note=Clathrin heavy chain 2 |
P53675 | 1478 | 1534 | 1487 | 1487 | Modified residue | Note=Phosphotyrosine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q68FD5 |
P53675 | 1478 | 1534 | 1494 | 1494 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q00610 |
P53675 | 1478 | 1534 | 1501 | 1501 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q00610 |
P53675 | 1478 | 1534 | 524 | 1640 | Region | Note=Heavy chain arm |
P53675 | 1478 | 1534 | 639 | 1640 | Region | Note=Proximal segment |
P53675 | 1478 | 1534 | 1213 | 1522 | Region | Note=Involved in binding clathrin light chain;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
P53675 | 1478 | 1534 | 1423 | 1566 | Repeat | Note=CHCR 7 |
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3'-UTR located exon skipping events that lost miRNA binding sites in CLTCL1 |
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 CLTCL1 |
- 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 CLTCL1 |
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 CLTCL1 |
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 CLTCL1 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for CLTCL1 |
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 CLTCL1 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |