ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for TPCN2

Gene summary

Gene information	Gene symbol	TPCN2
	Gene ID	219931
	Gene name	two pore segment channel 2
	Synonyms	SHEP10\|TPC2
	Cytomap	11q13.3
	Type of gene	protein-coding
	Description	two pore calcium channel protein 2voltage-dependent calcium channel protein TPC2
	Modification date	20180522
	UniProtAcc	Q8NHX9
	Context	PubMed: TPCN2 [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
TPCN2	GO:0006874	cellular calcium ion homeostasis	19387438

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Exon skipping events across known transcript of Ensembl for TPCN2 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 TPCN2

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 TPCN2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_62568	11	68816497:68816574:68821500:68821565:68825045:68825162	68821500:68821565	ENSG00000162341.11	ENST00000535009.1
exon_skip_62575	11	68821500:68821565:68822188:68822265:68822642:68822820	68822188:68822265	ENSG00000162341.11	ENST00000294309.3,ENST00000542467.1
exon_skip_62579	11	68821500:68821565:68825045:68825162:68830351:68830458	68825045:68825162	ENSG00000162341.11	ENST00000535009.1
exon_skip_62580	11	68822188:68822265:68822642:68822820:68825045:68825162	68822642:68822820	ENSG00000162341.11	ENST00000294309.3,ENST00000542467.1
exon_skip_62584	11	68830351:68830458:68831362:68831435:68834970:68835073	68831362:68831435	ENSG00000162341.11	ENST00000442692.2,ENST00000294309.3,ENST00000542467.1,ENST00000535009.1
exon_skip_62597	11	68831362:68831435:68834970:68835073:68837897:68837963	68834970:68835073	ENSG00000162341.11	ENST00000442692.2,ENST00000294309.3,ENST00000542467.1,ENST00000535009.1
exon_skip_62608	11	68838823:68838888:68839390:68839491:68845949:68846069	68839390:68839491	ENSG00000162341.11	ENST00000442692.2
exon_skip_62610	11	68839390:68839491:68840094:68840176:68840382:68840469	68840094:68840176	ENSG00000162341.11	ENST00000294309.3,ENST00000542467.1,ENST00000535009.1
exon_skip_62613	11	68840094:68840176:68840382:68840469:68845949:68846069	68840382:68840469	ENSG00000162341.11	ENST00000294309.3,ENST00000542467.1,ENST00000535009.1
exon_skip_62623	11	68846359:68846488:68847301:68847351:68848867:68848967	68847301:68847351	ENSG00000162341.11	ENST00000294309.3
exon_skip_62626	11	68846359:68846488:68848867:68848967:68851412:68851484	68848867:68848967	ENSG00000162341.11	ENST00000442692.2
exon_skip_62638	11	68848867:68848967:68851412:68851484:68852677:68852754	68851412:68851484	ENSG00000162341.11	ENST00000294309.3
exon_skip_62642	11	68851412:68851484:68852677:68852754:68853138:68853220	68852677:68852754	ENSG00000162341.11	ENST00000294309.3
exon_skip_62644	11	68853315:68853398:68853990:68854072:68854579:68854674	68853990:68854072	ENSG00000162341.11	ENST00000442692.2,ENST00000294309.3
exon_skip_62645	11	68853990:68854072:68854579:68854674:68855342:68855671	68854579:68854674	ENSG00000162341.11	ENST00000442692.2,ENST00000294309.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for TPCN2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_62568	11	68816497:68816574:68821500:68821565:68825045:68825162	68821500:68821565	ENSG00000162341.11	ENST00000535009.1
exon_skip_62575	11	68821500:68821565:68822188:68822265:68822642:68822820	68822188:68822265	ENSG00000162341.11	ENST00000294309.3,ENST00000542467.1
exon_skip_62579	11	68821500:68821565:68825045:68825162:68830351:68830458	68825045:68825162	ENSG00000162341.11	ENST00000535009.1
exon_skip_62580	11	68822188:68822265:68822642:68822820:68825045:68825162	68822642:68822820	ENSG00000162341.11	ENST00000294309.3,ENST00000542467.1
exon_skip_62584	11	68830351:68830458:68831362:68831435:68834970:68835073	68831362:68831435	ENSG00000162341.11	ENST00000294309.3,ENST00000535009.1,ENST00000542467.1,ENST00000442692.2
exon_skip_62597	11	68831362:68831435:68834970:68835073:68837897:68837963	68834970:68835073	ENSG00000162341.11	ENST00000294309.3,ENST00000535009.1,ENST00000542467.1,ENST00000442692.2
exon_skip_62608	11	68838823:68838888:68839390:68839491:68845949:68846069	68839390:68839491	ENSG00000162341.11	ENST00000442692.2
exon_skip_62610	11	68839390:68839491:68840094:68840176:68840382:68840469	68840094:68840176	ENSG00000162341.11	ENST00000294309.3,ENST00000535009.1,ENST00000542467.1
exon_skip_62613	11	68840094:68840176:68840382:68840469:68845949:68846069	68840382:68840469	ENSG00000162341.11	ENST00000294309.3,ENST00000535009.1,ENST00000542467.1
exon_skip_62623	11	68846359:68846488:68847301:68847351:68848867:68848967	68847301:68847351	ENSG00000162341.11	ENST00000294309.3
exon_skip_62626	11	68846359:68846488:68848867:68848967:68851412:68851484	68848867:68848967	ENSG00000162341.11	ENST00000442692.2
exon_skip_62638	11	68848867:68848967:68851412:68851484:68852677:68852754	68851412:68851484	ENSG00000162341.11	ENST00000294309.3
exon_skip_62642	11	68851412:68851484:68852677:68852754:68853138:68853220	68852677:68852754	ENSG00000162341.11	ENST00000294309.3
exon_skip_62644	11	68853315:68853398:68853990:68854072:68854579:68854674	68853990:68854072	ENSG00000162341.11	ENST00000294309.3,ENST00000442692.2
exon_skip_62645	11	68853990:68854072:68854579:68854674:68855342:68855671	68854579:68854674	ENSG00000162341.11	ENST00000294309.3,ENST00000442692.2

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 TPCN2

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
ENST00000294309	68822188	68822265	Frame-shift
ENST00000294309	68822642	68822820	Frame-shift
ENST00000294309	68831362	68831435	Frame-shift
ENST00000294309	68834970	68835073	Frame-shift
ENST00000294309	68840094	68840176	Frame-shift
ENST00000294309	68847301	68847351	Frame-shift
ENST00000294309	68852677	68852754	Frame-shift
ENST00000294309	68853990	68854072	Frame-shift
ENST00000294309	68854579	68854674	Frame-shift
ENST00000294309	68840382	68840469	In-frame
ENST00000294309	68851412	68851484	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
ENST00000294309	68822188	68822265	Frame-shift
ENST00000294309	68822642	68822820	Frame-shift
ENST00000294309	68831362	68831435	Frame-shift
ENST00000294309	68834970	68835073	Frame-shift
ENST00000294309	68840094	68840176	Frame-shift
ENST00000294309	68847301	68847351	Frame-shift
ENST00000294309	68852677	68852754	Frame-shift
ENST00000294309	68853990	68854072	Frame-shift
ENST00000294309	68854579	68854674	Frame-shift
ENST00000294309	68840382	68840469	In-frame
ENST00000294309	68851412	68851484	In-frame

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Infer the effects of exon skipping event on protein functional features for TPCN2

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
ENST00000294309	2948	752	68840382	68840469	1245	1331	381	410
ENST00000294309	2948	752	68851412	68851484	1791	1862	563	587

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
ENST00000294309	2948	752	68840382	68840469	1245	1331	381	410
ENST00000294309	2948	752	68851412	68851484	1791	1862	563	587

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
Q8NHX9	381	410	1	752	Chain	ID=PRO_0000276856;Note=Two pore calcium channel protein 2
Q8NHX9	381	410	311	436	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NHX9	563	587	1	752	Chain	ID=PRO_0000276856;Note=Two pore calcium channel protein 2
Q8NHX9	563	587	564	564	Natural variant	ID=VAR_030493;Note=L->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:17974005,ECO:0000269\|PubMed:19387438;Dbxref=dbSNP:rs2376558,PMID:15489334,PMID:17974005,PMID:19387438
Q8NHX9	563	587	576	580	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NHX9	563	587	555	575	Transmembrane	Note=Helical%3B Name%3DS4 of repeat II;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NHX9	563	587	581	601	Transmembrane	Note=Helical%3B Name%3DS5 of repeat II;Ontology_term=ECO:0000255;evidence=ECO:0000255

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
Q8NHX9	381	410	1	752	Chain	ID=PRO_0000276856;Note=Two pore calcium channel protein 2
Q8NHX9	381	410	311	436	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NHX9	563	587	1	752	Chain	ID=PRO_0000276856;Note=Two pore calcium channel protein 2
Q8NHX9	563	587	564	564	Natural variant	ID=VAR_030493;Note=L->P;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15489334,ECO:0000269\|PubMed:17974005,ECO:0000269\|PubMed:19387438;Dbxref=dbSNP:rs2376558,PMID:15489334,PMID:17974005,PMID:19387438
Q8NHX9	563	587	576	580	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NHX9	563	587	555	575	Transmembrane	Note=Helical%3B Name%3DS4 of repeat II;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8NHX9	563	587	581	601	Transmembrane	Note=Helical%3B Name%3DS5 of repeat II;Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for TPCN2

- 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.

- 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
STAD	TCGA-D7-8572-01	exon_skip_62580	68822643	68822820	68822739	68822751	Frame_Shift_Del	TCCCTGGGAGCCG	-	p.116_120del
LIHC	TCGA-G3-A3CJ-01	exon_skip_62579	68825046	68825162	68825076	68825076	Frame_Shift_Del	A	-	p.K154fs
LIHC	TCGA-DD-A3A0-01	exon_skip_62608	68839391	68839491	68839426	68839426	Frame_Shift_Del	G	-	p.L332fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_62608	68839391	68839491	68839465	68839465	Frame_Shift_Del	G	-	p.V345fs
LIHC	TCGA-DD-A3A1-01	exon_skip_62610	68840095	68840176	68840108	68840108	Frame_Shift_Del	C	-	p.P359fs
COAD	TCGA-G4-6297-01	exon_skip_62642	68852678	68852754	68852702	68852703	Frame_Shift_Ins	-	T	p.I596fs
PRAD	TCGA-HC-A6AS-01	exon_skip_62580	68822643	68822820	68822730	68822730	Nonsense_Mutation	C	A	p.Y113*
PRAD	TCGA-HC-A6AS-01	exon_skip_62580	68822643	68822820	68822730	68822730	Nonsense_Mutation	C	A	p.Y113X
SKCM	TCGA-XV-A9W2-01	exon_skip_62610	68840095	68840176	68840132	68840132	Nonsense_Mutation	C	T	p.Q367*
HNSC	TCGA-CV-7423-01	exon_skip_62575	68822189	68822265	68822187	68822187	Splice_Site	A	G	p.Y59_splice

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

Depth of coverage in three exons

Mutation description

- 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
C8166_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	68839391	68839491	68839462	68839462	Frame_Shift_Del	G	-	p.M344fs
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	68822189	68822265	68822220	68822220	Missense_Mutation	G	A	p.S69N
SNU1041_UPPER_AERODIGESTIVE_TRACT	68822189	68822265	68822238	68822238	Missense_Mutation	G	A	p.R75Q
SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	68822189	68822265	68822238	68822238	Missense_Mutation	G	A	p.R75Q
ZR751_BREAST	68822189	68822265	68822250	68822250	Missense_Mutation	C	T	p.S79L
MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	68822643	68822820	68822720	68822720	Missense_Mutation	A	G	p.D110G
MFE319_ENDOMETRIUM	68825046	68825162	68825089	68825089	Missense_Mutation	T	C	p.L158P
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	68831363	68831435	68831365	68831365	Missense_Mutation	T	C	p.V219A
SNU620_STOMACH	68834971	68835073	68835002	68835002	Missense_Mutation	C	G	p.T253S
MEWO_SKIN	68834971	68835073	68835037	68835037	Missense_Mutation	C	T	p.L265F
KM12_LARGE_INTESTINE	68839391	68839491	68839463	68839463	Missense_Mutation	G	A	p.V345M
SKLMS1_SOFT_TISSUE	68839391	68839491	68839466	68839466	Missense_Mutation	G	C	p.G346R
NCIH1573_LUNG	68840095	68840176	68840147	68840147	Missense_Mutation	G	T	p.D372Y
HT1197_URINARY_TRACT	68840095	68840176	68840174	68840174	Missense_Mutation	G	C	p.E381Q
LC2AD_LUNG	68848868	68848967	68848873	68848873	Missense_Mutation	C	T	p.P532L
NCIH1339_LUNG	68848868	68848967	68848959	68848959	Missense_Mutation	A	G	p.S561G
JHUEM2_ENDOMETRIUM	68851413	68851484	68851462	68851462	Missense_Mutation	G	A	p.R580H
NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	68851413	68851484	68851465	68851465	Missense_Mutation	C	T	p.A581V
T3M10_LUNG	68852678	68852754	68852706	68852706	Missense_Mutation	G	T	p.G597V
GRANTA519_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	68852678	68852754	68852726	68852726	Missense_Mutation	G	T	p.V604F
RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	68853991	68854072	68854018	68854018	Missense_Mutation	G	C	p.W677C
HT55_LARGE_INTESTINE	68853991	68854072	68854047	68854047	Missense_Mutation	A	T	p.N687I
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	68854580	68854674	68854605	68854605	Missense_Mutation	G	A	p.R704H
VMRCRCZ_KIDNEY	68854580	68854674	68854605	68854605	Missense_Mutation	G	T	p.R704L
SNU1040_LARGE_INTESTINE	68854580	68854674	68854626	68854626	Missense_Mutation	C	T	p.A711V
SNU175_LARGE_INTESTINE	68822189	68822265	68822237	68822237	Nonsense_Mutation	C	T	p.R75*
RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	68834971	68835073	68834972	68834972	Splice_Site	A	G	p.Q243R
KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	68854580	68854674	68854673	68854673	Splice_Site	A	C	p.R727R

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TPCN2

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

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TPCN2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TPCN2

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RelatedDrugs for TPCN2

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 TPCN2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	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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