ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for PICALM

Gene summary

Gene information	Gene symbol	PICALM
	Gene ID	8301
	Gene name	phosphatidylinositol binding clathrin assembly protein
	Synonyms	CALM\|CLTH\|LAP
	Cytomap	11q14.2
	Type of gene	protein-coding
	Description	phosphatidylinositol-binding clathrin assembly proteinclathrin assembly lymphoid myeloid leukemia protein
	Modification date	20180523
	UniProtAcc	Q13492
	Context	PubMed: PICALM [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
PICALM	GO:0006898	receptor-mediated endocytosis	10436022
PICALM	GO:0032880	regulation of protein localization	10436022
PICALM	GO:0045893	positive regulation of transcription, DNA-templated	11425879
PICALM	GO:0048261	negative regulation of receptor-mediated endocytosis	10436022

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Exon skipping events across known transcript of Ensembl for PICALM from UCSC genome browser

Skipped exons in TCGA and GTEx 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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Gene isoform structures and expression levels for PICALM

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for PICALM

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_76491	11	85670079:85670103:85671717:85671820:85685750:85685855	85671717:85671820	ENSG00000073921.13	ENST00000530692.1
exon_skip_76494	11	85670079:85670103:85685750:85685855:85687665:85687725	85685750:85685855	ENSG00000073921.13	ENST00000532317.1,ENST00000526961.1,ENST00000526548.1,ENST00000526033.1,ENST00000528398.1,ENST00000529760.1,ENST00000393346.3
exon_skip_76495	11	85670079:85670103:85685750:85685855:85692171:85692271	85685750:85685855	ENSG00000073921.13	ENST00000356360.5,ENST00000532603.1
exon_skip_76498	11	85670079:85670103:85692171:85692271:85692787:85692818	85692171:85692271	ENSG00000073921.13	ENST00000529016.1
exon_skip_76500	11	85685824:85685855:85687665:85687725:85689112:85689136	85687665:85687725	ENSG00000073921.13	ENST00000532317.1,ENST00000526907.1,ENST00000526961.1,ENST00000529760.1,ENST00000530692.1
exon_skip_76501	11	85685824:85685855:85687665:85687725:85692171:85692271	85687665:85687725	ENSG00000073921.13	ENST00000526033.1,ENST00000528398.1,ENST00000393346.3
exon_skip_76504	11	85685824:85685855:85692171:85692271:85692787:85692818	85692171:85692271	ENSG00000073921.13	ENST00000356360.5,ENST00000532603.1
exon_skip_76505	11	85687691:85687725:85689112:85689136:85692171:85692271	85689112:85689136	ENSG00000073921.13	ENST00000532317.1,ENST00000526961.1,ENST00000529760.1,ENST00000530692.1
exon_skip_76509	11	85692914:85693031:85694908:85695016:85707868:85707972	85694908:85695016	ENSG00000073921.13	ENST00000529760.1
exon_skip_76512	11	85692914:85693046:85694908:85695016:85701292:85701301	85694908:85695016	ENSG00000073921.13	ENST00000356360.5,ENST00000526033.1,ENST00000393346.3
exon_skip_76513	11	85692914:85693046:85694908:85695016:85707868:85707972	85694908:85695016	ENSG00000073921.13	ENST00000532317.1,ENST00000529016.1,ENST00000528398.1
exon_skip_76519	11	85694908:85695016:85701292:85701421:85707868:85707972	85701292:85701421	ENSG00000073921.13	ENST00000526961.1,ENST00000526033.1
exon_skip_76520	11	85694908:85695016:85701292:85701442:85707868:85707972	85701292:85701442	ENSG00000073921.13	ENST00000530542.1,ENST00000356360.5,ENST00000393346.3
exon_skip_76523	11	85707868:85707972:85711685:85711822:85712077:85712184	85711685:85711822	ENSG00000073921.13	ENST00000532317.1,ENST00000530542.1,ENST00000529016.1,ENST00000356360.5,ENST00000526033.1,ENST00000528398.1,ENST00000529760.1,ENST00000393346.3
exon_skip_76525	11	85714408:85714494:85718584:85718626:85722072:85722178	85718584:85718626	ENSG00000073921.13	ENST00000532317.1,ENST00000356360.5,ENST00000534412.1,ENST00000526033.1,ENST00000528398.1,ENST00000393346.3
exon_skip_76526	11	85722154:85722179:85723323:85723435:85725912:85726006	85723323:85723435	ENSG00000073921.13	ENST00000532317.1,ENST00000531771.1,ENST00000356360.5,ENST00000531558.1,ENST00000534412.1,ENST00000526033.1,ENST00000528398.1,ENST00000393346.3
exon_skip_76527	11	85725912:85726006:85733409:85733512:85737333:85737409	85733409:85733512	ENSG00000073921.13	ENST00000532317.1,ENST00000525162.1,ENST00000356360.5,ENST00000528256.1,ENST00000526033.1,ENST00000528398.1,ENST00000531930.1,ENST00000393346.3
exon_skip_76528	11	85725912:85726006:85733409:85733512:85742510:85742653	85733409:85733512	ENSG00000073921.13	ENST00000532041.1
exon_skip_76533	11	85733420:85733512:85734458:85734584:85737333:85737409	85734458:85734584	ENSG00000073921.13	ENST00000528411.1
exon_skip_76534	11	85733420:85733512:85737333:85737409:85742510:85742653	85737333:85737409	ENSG00000073921.13	ENST00000532317.1,ENST00000525162.1,ENST00000356360.5,ENST00000528256.1,ENST00000526033.1,ENST00000528398.1,ENST00000531930.1,ENST00000393346.3
exon_skip_76536	11	85733420:85733512:85742510:85742653:85779692:85779775	85742510:85742653	ENSG00000073921.13	ENST00000532041.1
exon_skip_76537	11	85737333:85737409:85742510:85742653:85779692:85779775	85742510:85742653	ENSG00000073921.13	ENST00000356360.5,ENST00000528256.1,ENST00000526033.1,ENST00000528411.1,ENST00000531930.1,ENST00000393346.3
exon_skip_76539	11	85742510:85742653:85779692:85779775:85780761:85780853	85779692:85779775	ENSG00000073921.13	ENST00000531930.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for PICALM

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_76491	11	85670079:85670103:85671717:85671820:85685750:85685855	85671717:85671820	ENSG00000073921.13	ENST00000530692.1
exon_skip_76494	11	85670079:85670103:85685750:85685855:85687665:85687725	85685750:85685855	ENSG00000073921.13	ENST00000532317.1,ENST00000526033.1,ENST00000526548.1,ENST00000393346.3,ENST00000529760.1,ENST00000528398.1,ENST00000526961.1
exon_skip_76495	11	85670079:85670103:85685750:85685855:85692171:85692271	85685750:85685855	ENSG00000073921.13	ENST00000532603.1,ENST00000356360.5
exon_skip_76498	11	85670079:85670103:85692171:85692271:85692787:85692818	85692171:85692271	ENSG00000073921.13	ENST00000529016.1
exon_skip_76500	11	85685824:85685855:85687665:85687725:85689112:85689136	85687665:85687725	ENSG00000073921.13	ENST00000532317.1,ENST00000530692.1,ENST00000529760.1,ENST00000526961.1,ENST00000526907.1
exon_skip_76501	11	85685824:85685855:85687665:85687725:85692171:85692271	85687665:85687725	ENSG00000073921.13	ENST00000526033.1,ENST00000393346.3,ENST00000528398.1
exon_skip_76504	11	85685824:85685855:85692171:85692271:85692787:85692818	85692171:85692271	ENSG00000073921.13	ENST00000532603.1,ENST00000356360.5
exon_skip_76505	11	85687691:85687725:85689112:85689136:85692171:85692271	85689112:85689136	ENSG00000073921.13	ENST00000532317.1,ENST00000530692.1,ENST00000529760.1,ENST00000526961.1
exon_skip_76509	11	85692914:85693031:85694908:85695016:85707868:85707972	85694908:85695016	ENSG00000073921.13	ENST00000529760.1
exon_skip_76512	11	85692914:85693046:85694908:85695016:85701292:85701301	85694908:85695016	ENSG00000073921.13	ENST00000526033.1,ENST00000393346.3,ENST00000356360.5
exon_skip_76513	11	85692914:85693046:85694908:85695016:85707868:85707972	85694908:85695016	ENSG00000073921.13	ENST00000532317.1,ENST00000528398.1,ENST00000529016.1
exon_skip_76519	11	85694908:85695016:85701292:85701421:85707868:85707972	85701292:85701421	ENSG00000073921.13	ENST00000526033.1,ENST00000526961.1
exon_skip_76520	11	85694908:85695016:85701292:85701442:85707868:85707972	85701292:85701442	ENSG00000073921.13	ENST00000393346.3,ENST00000356360.5,ENST00000530542.1
exon_skip_76523	11	85707868:85707972:85711685:85711822:85712077:85712184	85711685:85711822	ENSG00000073921.13	ENST00000532317.1,ENST00000526033.1,ENST00000393346.3,ENST00000529760.1,ENST00000528398.1,ENST00000356360.5,ENST00000529016.1,ENST00000530542.1
exon_skip_76525	11	85714408:85714494:85718584:85718626:85722072:85722178	85718584:85718626	ENSG00000073921.13	ENST00000532317.1,ENST00000526033.1,ENST00000393346.3,ENST00000528398.1,ENST00000356360.5,ENST00000534412.1
exon_skip_76526	11	85722154:85722179:85723323:85723435:85725912:85726006	85723323:85723435	ENSG00000073921.13	ENST00000532317.1,ENST00000526033.1,ENST00000393346.3,ENST00000528398.1,ENST00000356360.5,ENST00000534412.1,ENST00000531771.1,ENST00000531558.1
exon_skip_76527	11	85725912:85726006:85733409:85733512:85737333:85737409	85733409:85733512	ENSG00000073921.13	ENST00000532317.1,ENST00000526033.1,ENST00000393346.3,ENST00000528398.1,ENST00000356360.5,ENST00000531930.1,ENST00000525162.1,ENST00000528256.1
exon_skip_76528	11	85725912:85726006:85733409:85733512:85742510:85742653	85733409:85733512	ENSG00000073921.13	ENST00000532041.1
exon_skip_76533	11	85733420:85733512:85734458:85734584:85737333:85737409	85734458:85734584	ENSG00000073921.13	ENST00000528411.1
exon_skip_76534	11	85733420:85733512:85737333:85737409:85742510:85742653	85737333:85737409	ENSG00000073921.13	ENST00000532317.1,ENST00000526033.1,ENST00000393346.3,ENST00000528398.1,ENST00000356360.5,ENST00000531930.1,ENST00000525162.1,ENST00000528256.1
exon_skip_76536	11	85733420:85733512:85742510:85742653:85779692:85779775	85742510:85742653	ENSG00000073921.13	ENST00000532041.1
exon_skip_76537	11	85737333:85737409:85742510:85742653:85779692:85779775	85742510:85742653	ENSG00000073921.13	ENST00000526033.1,ENST00000393346.3,ENST00000356360.5,ENST00000531930.1,ENST00000528256.1,ENST00000528411.1
exon_skip_76539	11	85742510:85742653:85779692:85779775:85780761:85780853	85779692:85779775	ENSG00000073921.13	ENST00000531930.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for PICALM

Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000393346	85711685	85711822	Frame-shift
ENST00000393346	85723323	85723435	Frame-shift
ENST00000393346	85733409	85733512	Frame-shift
ENST00000393346	85737333	85737409	Frame-shift
ENST00000393346	85742510	85742653	Frame-shift
ENST00000393346	85685750	85685855	In-frame
ENST00000393346	85687665	85687725	In-frame
ENST00000393346	85694908	85695016	In-frame
ENST00000393346	85701292	85701442	In-frame
ENST00000393346	85718584	85718626	In-frame

Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000393346	85711685	85711822	Frame-shift
ENST00000393346	85723323	85723435	Frame-shift
ENST00000393346	85733409	85733512	Frame-shift
ENST00000393346	85737333	85737409	Frame-shift
ENST00000393346	85742510	85742653	Frame-shift
ENST00000393346	85685750	85685855	In-frame
ENST00000393346	85687665	85687725	In-frame
ENST00000393346	85694908	85695016	In-frame
ENST00000393346	85701292	85701442	In-frame
ENST00000393346	85718584	85718626	In-frame

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Infer the effects of exon skipping event on protein functional features for PICALM

Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.

Loci of skipped exons in TCGA 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
ENST00000393346	2357	652	85718584	85718626	915	956	255	269
ENST00000393346	2357	652	85701292	85701442	1408	1557	419	469
ENST00000393346	2357	652	85694908	85695016	1558	1665	469	505
ENST00000393346	2357	652	85687665	85687725	1929	1988	593	613
ENST00000393346	2357	652	85685750	85685855	1989	2093	613	648

Loci of skipped exons in GTEx 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
ENST00000393346	2357	652	85718584	85718626	915	956	255	269
ENST00000393346	2357	652	85701292	85701442	1408	1557	419	469
ENST00000393346	2357	652	85694908	85695016	1558	1665	469	505
ENST00000393346	2357	652	85687665	85687725	1929	1988	593	613
ENST00000393346	2357	652	85685750	85685855	1989	2093	613	648

Lost protein functional features of individual exon skipping events in TCGA.

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
Q13492	255	269	2	652	Chain	ID=PRO_0000187062;Note=Phosphatidylinositol-binding clathrin assembly protein
Q13492	255	269	221	294	Region	Note=Interaction with PIMREG;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16491119;Dbxref=PMID:16491119
Q13492	419	469	420	469	Alternative sequence	ID=VSP_009607;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334
Q13492	419	469	420	426	Alternative sequence	ID=VSP_044568;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q13492	419	469	2	652	Chain	ID=PRO_0000187062;Note=Phosphatidylinositol-binding clathrin assembly protein
Q13492	469	505	420	469	Alternative sequence	ID=VSP_009607;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334
Q13492	469	505	2	652	Chain	ID=PRO_0000187062;Note=Phosphatidylinositol-binding clathrin assembly protein
Q13492	593	613	593	593	Alternative sequence	ID=VSP_009608;Note=In isoform 3. M->MNGMHFPQY;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q13492	593	613	594	613	Alternative sequence	ID=VSP_004067;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9737689;Dbxref=PMID:9737689
Q13492	593	613	2	652	Chain	ID=PRO_0000187062;Note=Phosphatidylinositol-binding clathrin assembly protein
Q13492	613	648	594	613	Alternative sequence	ID=VSP_004067;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9737689;Dbxref=PMID:9737689
Q13492	613	648	2	652	Chain	ID=PRO_0000187062;Note=Phosphatidylinositol-binding clathrin assembly protein
Q13492	613	648	641	641	Natural variant	ID=VAR_028195;Note=F->L;Dbxref=dbSNP:rs556337
Q13492	613	648	648	649	Site	Note=Breakpoint for translocation to form CALM/MLLT10 fusion protein

Lost protein functional features of individual exon skipping events in GTEx.

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
Q13492	255	269	2	652	Chain	ID=PRO_0000187062;Note=Phosphatidylinositol-binding clathrin assembly protein
Q13492	255	269	221	294	Region	Note=Interaction with PIMREG;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16491119;Dbxref=PMID:16491119
Q13492	419	469	420	469	Alternative sequence	ID=VSP_009607;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334
Q13492	419	469	420	426	Alternative sequence	ID=VSP_044568;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.3
Q13492	419	469	2	652	Chain	ID=PRO_0000187062;Note=Phosphatidylinositol-binding clathrin assembly protein
Q13492	469	505	420	469	Alternative sequence	ID=VSP_009607;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334
Q13492	469	505	2	652	Chain	ID=PRO_0000187062;Note=Phosphatidylinositol-binding clathrin assembly protein
Q13492	593	613	593	593	Alternative sequence	ID=VSP_009608;Note=In isoform 3. M->MNGMHFPQY;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q13492	593	613	594	613	Alternative sequence	ID=VSP_004067;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9737689;Dbxref=PMID:9737689
Q13492	593	613	2	652	Chain	ID=PRO_0000187062;Note=Phosphatidylinositol-binding clathrin assembly protein
Q13492	613	648	594	613	Alternative sequence	ID=VSP_004067;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9737689;Dbxref=PMID:9737689
Q13492	613	648	2	652	Chain	ID=PRO_0000187062;Note=Phosphatidylinositol-binding clathrin assembly protein
Q13492	613	648	641	641	Natural variant	ID=VAR_028195;Note=F->L;Dbxref=dbSNP:rs556337
Q13492	613	648	648	649	Site	Note=Breakpoint for translocation to form CALM/MLLT10 fusion protein

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SNVs in the skipped exons for PICALM

- Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.

- Differential PSIs between mutated versus non-mutated samples.

PICALM_COAD_exon_skip_76505_psi_boxplot.png
boxplot

PICALM_LUSC_exon_skip_76519_psi_boxplot.png
boxplot

PICALM_LUSC_exon_skip_76520_psi_boxplot.png
boxplot

PICALM_STAD_exon_skip_76505_psi_boxplot.png
boxplot

- Non-synonymous mutations located in the skipped exons in TCGA.

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
LIHC	TCGA-DD-A3A0-01	exon_skip_76494 exon_skip_76495	85685751	85685855	85685801	85685801	Frame_Shift_Del	G	-	p.Q625fs
HNSC	TCGA-F7-A50I-01	exon_skip_76504 exon_skip_76498	85692172	85692271	85692227	85692227	Frame_Shift_Del	C	-	p.G568fs
LUSC	TCGA-34-5231-01	exon_skip_76504 exon_skip_76498	85692172	85692271	85692259	85692259	Frame_Shift_Del	C	-	p.W564fs
LIHC	TCGA-DD-A1EG-01	exon_skip_76525	85718585	85718626	85718590	85718590	Frame_Shift_Del	A	-	p.S268fs
LIHC	TCGA-DD-A39Y-01	exon_skip_76534	85737334	85737409	85737346	85737346	Frame_Shift_Del	T	-	p.S113fs
LIHC	TCGA-DD-A3A0-01	exon_skip_76537 exon_skip_76536	85742511	85742653	85742592	85742592	Frame_Shift_Del	A	-	p.F64fs
BLCA	TCGA-ZF-AA5H-01	exon_skip_76519	85701293	85701421	85701319	85701320	Frame_Shift_Ins	-	T	p.R454fs
BLCA	TCGA-ZF-AA5H-01	exon_skip_76520	85701293	85701442	85701319	85701320	Frame_Shift_Ins	-	T	p.R454fs
UCEC	TCGA-B5-A0JZ-01	exon_skip_76534	85737334	85737409	85737353	85737354	Frame_Shift_Ins	-	A	p.L110fs
ESCA	TCGA-L5-A893-01	exon_skip_76494 exon_skip_76495	85685751	85685855	85685805	85685805	Nonsense_Mutation	G	T	p.Y630*
ESCA	TCGA-L5-A893-01	exon_skip_76494 exon_skip_76495	85685751	85685855	85685805	85685805	Nonsense_Mutation	G	T	p.Y630X
LUAD	TCGA-53-7626-01	exon_skip_76504 exon_skip_76498	85692172	85692271	85692255	85692255	Nonsense_Mutation	G	A	p.Q559*
LUAD	TCGA-53-7626-01	exon_skip_76504 exon_skip_76498	85692172	85692271	85692255	85692255	Nonsense_Mutation	G	A	p.Q566*
LUSC	TCGA-18-3410-01	exon_skip_76519	85701293	85701421	85701343	85701343	Nonsense_Mutation	G	C	p.S453*
LUSC	TCGA-18-3410-01	exon_skip_76520	85701293	85701442	85701343	85701343	Nonsense_Mutation	G	C	p.S453*
UCEC	TCGA-B5-A0JY-01	exon_skip_76526	85723324	85723435	85723423	85723423	Nonsense_Mutation	C	A	p.E187*
UCEC	TCGA-BS-A0UF-01	exon_skip_76526	85723324	85723435	85723423	85723423	Nonsense_Mutation	C	A	p.E187*
BLCA	TCGA-DK-A6B2-01	exon_skip_76527 exon_skip_76528	85733410	85733512	85733472	85733472	Nonsense_Mutation	A	T	p.Y130*
COAD	TCGA-F4-6856-01	exon_skip_76505	85689113	85689136	85689112	85689112	Splice_Site	C	T	.
STAD	TCGA-BR-4201-01	exon_skip_76505	85689113	85689136	85689112	85689112	Splice_Site	C	T	.
KIRC	TCGA-B0-4698-01	exon_skip_76525	85718585	85718626	85718627	85718627	Splice_Site	C	A	.

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons	Mutation description
	Sample: TCGA-18-3410-01
	Cancer type: LUSC
	ESID: exon_skip_76520
	Skipped exon start: 85701293
	Skipped exon end: 85701442
	Mutation start: 85701343
	Mutation end: 85701343
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: C
	AAchange: p.S453*
	Sample: TCGA-18-3410-01
	Cancer type: LUSC
	ESID: exon_skip_76519
	Skipped exon start: 85701293
	Skipped exon end: 85701421
	Mutation start: 85701343
	Mutation end: 85701343
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: C
	AAchange: p.S453*
exon_skip_76519_LUSC_TCGA-18-3410-01.png
exon_skip_76520_LUSC_TCGA-18-3410-01.png
	Sample: TCGA-18-3410-01
	Cancer type: LUSC
	ESID: exon_skip_76520
	Skipped exon start: 85701293
	Skipped exon end: 85701442
	Mutation start: 85701343
	Mutation end: 85701343
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: C
	AAchange: p.S453*
	Sample: TCGA-18-3410-01
	Cancer type: LUSC
	ESID: exon_skip_76519
	Skipped exon start: 85701293
	Skipped exon end: 85701421
	Mutation start: 85701343
	Mutation end: 85701343
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: C
	AAchange: p.S453*
exon_skip_76519_LUSC_TCGA-18-3410-01.png
exon_skip_76520_LUSC_TCGA-18-3410-01.png
	Sample: TCGA-F4-6856-01
	Cancer type: COAD
	ESID: exon_skip_76505
	Skipped exon start: 85689113
	Skipped exon end: 85689136
	Mutation start: 85689112
	Mutation end: 85689112
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: T
	AAchange: .
exon_skip_318867_COAD_TCGA-F4-6856-01.png
exon_skip_347508_COAD_TCGA-F4-6856-01.png
exon_skip_449553_COAD_TCGA-F4-6856-01.png
exon_skip_500368_COAD_TCGA-F4-6856-01.png
exon_skip_76505_COAD_TCGA-F4-6856-01.png

- 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
SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	85687666	85687725	85687718	85687718	Frame_Shift_Del	G	-	p.P596fs
LN215_CENTRAL_NERVOUS_SYSTEM	85718585	85718626	85718608	85718609	Frame_Shift_Del	CT	-	p.G262fs
OC316_OVARY	85737334	85737409	85737354	85737354	Frame_Shift_Del	A	-	p.L110fs
RKO_LARGE_INTESTINE	85685751	85685855	85685762	85685762	Missense_Mutation	A	G	p.S645P
KYSE140_OESOPHAGUS	85685751	85685855	85685813	85685813	Missense_Mutation	A	C	p.L628V
CW2_LARGE_INTESTINE	85692172	85692271	85692252	85692252	Missense_Mutation	G	A	p.P567S
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	85692172	85692271	85692263	85692263	Missense_Mutation	T	C	p.N563S
BICR18_UPPER_AERODIGESTIVE_TRACT	85692172	85692271	85692263	85692263	Missense_Mutation	T	C	p.N563S
KYSE180_OESOPHAGUS	85694909	85695016	85694971	85694971	Missense_Mutation	A	G	p.L485P
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	85694909	85695016	85694984	85694985	Missense_Mutation	GG	AA	p.P481S
HCT15_LARGE_INTESTINE	85701293	85701442	85701341	85701341	Missense_Mutation	C	A	p.D454Y
HCT15_LARGE_INTESTINE	85701293	85701421	85701341	85701341	Missense_Mutation	C	A	p.D454Y
HRT18_LARGE_INTESTINE	85701293	85701442	85701341	85701341	Missense_Mutation	C	A	p.D454Y
HRT18_LARGE_INTESTINE	85701293	85701421	85701341	85701341	Missense_Mutation	C	A	p.D454Y
THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	85701293	85701442	85701401	85701401	Missense_Mutation	G	C	p.P434A
THP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	85701293	85701421	85701401	85701401	Missense_Mutation	G	C	p.P434A
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	85701293	85701442	85701411	85701411	Missense_Mutation	A	C	p.D430E
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	85701293	85701421	85701411	85701411	Missense_Mutation	A	C	p.D430E
BICR18_UPPER_AERODIGESTIVE_TRACT	85701293	85701442	85701411	85701411	Missense_Mutation	A	C	p.D430E
BICR18_UPPER_AERODIGESTIVE_TRACT	85701293	85701421	85701411	85701411	Missense_Mutation	A	C	p.D430E
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	85701293	85701442	85701425	85701425	Missense_Mutation	C	G	p.V426L
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	85701293	85701421	85701425	85701425	Missense_Mutation	C	G	p.V426L
BICR18_UPPER_AERODIGESTIVE_TRACT	85701293	85701442	85701425	85701425	Missense_Mutation	C	G	p.V426L
BICR18_UPPER_AERODIGESTIVE_TRACT	85701293	85701421	85701425	85701425	Missense_Mutation	C	G	p.V426L
SNUC2A_LARGE_INTESTINE	85711686	85711822	85711699	85711699	Missense_Mutation	T	C	p.S381G
SLR24_KIDNEY	85711686	85711822	85711712	85711712	Missense_Mutation	T	C	p.I376M
SNU1040_LARGE_INTESTINE	85711686	85711822	85711762	85711762	Missense_Mutation	G	A	p.P360S
ATN1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	85718585	85718626	85718593	85718593	Missense_Mutation	G	A	p.L267F
HOP62_LUNG	85718585	85718626	85718614	85718614	Missense_Mutation	C	G	p.D260H
YT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	85723324	85723435	85723375	85723375	Missense_Mutation	C	T	p.D203N
HCC2998_LARGE_INTESTINE	85733410	85733512	85733423	85733423	Missense_Mutation	T	G	p.K147Q
HCT116_LARGE_INTESTINE	85733410	85733512	85733486	85733486	Missense_Mutation	G	A	p.R126W
SW948_LARGE_INTESTINE	85737334	85737409	85737367	85737367	Missense_Mutation	A	C	p.L106V
HEC251_ENDOMETRIUM	85742511	85742653	85742554	85742554	Missense_Mutation	T	G	p.K77T
HCC1438_LUNG	85742511	85742653	85742568	85742568	Missense_Mutation	C	A	p.W72C
KMRC1_KIDNEY	85742511	85742653	85742635	85742635	Missense_Mutation	T	C	p.N50S
NCIH2023_LUNG	85779693	85779775	85779770	85779770	Missense_Mutation	G	T	p.T18N

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PICALM

sQTL information located at the skipped exons.

Exon skip ID	Chromosome	Three exons	Skippped exon	ENST	Cancer type	SNP id	Location	DNA change (ref/var)	P-value
exon_skip_76504	11	85685824:85685855:85692171:85692271:85692787:85692818	85692171:85692271	ENST00000356360.5,ENST00000532603.1	LGG	rs76719109	chr11:85692181	A/C	1.30e-03
exon_skip_76498	11	85670079:85670103:85692171:85692271:85692787:85692818	85692171:85692271	ENST00000529016.1	LGG	rs76719109	chr11:85692181	A/C	1.30e-03

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PICALM

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PICALM

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RelatedDrugs for PICALM

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for PICALM

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
PICALM	C0002395	Alzheimer's Disease	2	CTD_human

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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