ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for ETV6

Gene summary

Gene information	Gene symbol	ETV6
	Gene ID	2120
	Gene name	ETS variant 6
	Synonyms	TEL\|TEL/ABL\|THC5
	Cytomap	12p13.2
	Type of gene	protein-coding
	Description	transcription factor ETV6ETS translocation variant 6ETS-related protein Tel1TEL1 oncogeneets variant gene 6 (TEL oncogene)
	Modification date	20180523
	UniProtAcc	P41212
	Context	PubMed: ETV6 [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
ETV6	GO:0000122	negative regulation of transcription by RNA polymerase II	10514502

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Exon skipping events across known transcript of Ensembl for ETV6 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 ETV6

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 ETV6

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_80253	12	11802944:11803094:11869520:11869677:11905383:11905809	11869520:11869677	ENSG00000139083.6	ENST00000544715.1
exon_skip_80259	12	11905434:11905513:11978577:11978647:11979335:11979364	11978577:11978647	ENSG00000139083.6	ENST00000541426.1
exon_skip_80264	12	11905434:11905513:11992073:11992238:12006360:12006495	11992073:11992238	ENSG00000139083.6	ENST00000396373.4
exon_skip_80272	12	11992073:11992238:12006360:12006495:12022357:12022903	12006360:12006495	ENSG00000139083.6	ENST00000396373.4
exon_skip_80273	12	12006360:12006495:12022357:12022903:12037378:12037521	12022357:12022903	ENSG00000139083.6	ENST00000396373.4
exon_skip_80276	12	12037378:12037521:12038859:12038960:12043874:12048336	12038859:12038960	ENSG00000139083.6	ENST00000396373.4

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for ETV6

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_80253	12	11802944:11803094:11869520:11869677:11905383:11905809	11869520:11869677	ENSG00000139083.6	ENST00000544715.1
exon_skip_80259	12	11905434:11905513:11978577:11978647:11979335:11979364	11978577:11978647	ENSG00000139083.6	ENST00000541426.1
exon_skip_80264	12	11905434:11905513:11992073:11992238:12006360:12006495	11992073:11992238	ENSG00000139083.6	ENST00000396373.4
exon_skip_80272	12	11992073:11992238:12006360:12006495:12022357:12022903	12006360:12006495	ENSG00000139083.6	ENST00000396373.4
exon_skip_80273	12	12006360:12006495:12022357:12022903:12037378:12037521	12022357:12022903	ENSG00000139083.6	ENST00000396373.4
exon_skip_80276	12	12037378:12037521:12038859:12038960:12043874:12048336	12038859:12038960	ENSG00000139083.6	ENST00000396373.4

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 ETV6

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
ENST00000396373	12038859	12038960	Frame-shift
ENST00000396373	11992073	11992238	In-frame
ENST00000396373	12006360	12006495	In-frame
ENST00000396373	12022357	12022903	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
ENST00000396373	12038859	12038960	Frame-shift
ENST00000396373	11992073	11992238	In-frame
ENST00000396373	12006360	12006495	In-frame
ENST00000396373	12022357	12022903	In-frame

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Infer the effects of exon skipping event on protein functional features for ETV6

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
ENST00000396373	6006	452	11992073	11992238	438	602	54	109
ENST00000396373	6006	452	12006360	12006495	603	737	109	154
ENST00000396373	6006	452	12022357	12022903	738	1283	154	336

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
ENST00000396373	6006	452	11992073	11992238	438	602	54	109
ENST00000396373	6006	452	12006360	12006495	603	737	109	154
ENST00000396373	6006	452	12022357	12022903	738	1283	154	336

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
P41212	54	109	1	452	Chain	ID=PRO_0000204121;Note=Transcription factor ETV6
P41212	54	109	40	124	Domain	Note=PNT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00762
P41212	54	109	52	54	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	54	109	58	60	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	54	109	63	76	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	54	109	91	94	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	54	109	99	105	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	54	109	54	55	Site	Note=Breakpoint for translocation to form ETV6-MDS2 in MDS
P41212	54	109	55	56	Site	Note=Breakpoint for translocation to form PAX5-ETV6
P41212	54	109	84	87	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	54	109	107	109	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	109	154	1	452	Chain	ID=PRO_0000204121;Note=Transcription factor ETV6
P41212	109	154	40	124	Domain	Note=PNT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00762
P41212	109	154	110	122	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	109	154	107	109	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	154	336	1	452	Chain	ID=PRO_0000204121;Note=Transcription factor ETV6
P41212	154	336	288	288	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:25755297,ECO:0000244\|PubMed:28112733;Dbxref=PMID:25755297,PMID:28112733
P41212	154	336	302	302	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
P41212	154	336	213	213	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:21406692;Dbxref=PMID:21406692
P41212	154	336	238	238	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P97360
P41212	154	336	257	257	Modified residue	Note=Phosphoserine%3B by MAPK14;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12435397;Dbxref=PMID:12435397
P41212	154	336	302	302	Modified residue	Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
P41212	154	336	323	323	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P97360
P41212	154	336	213	213	Mutagenesis	Note=No effect. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12435397;Dbxref=PMID:12435397
P41212	154	336	238	238	Mutagenesis	Note=No effect. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12435397;Dbxref=PMID:12435397
P41212	154	336	257	257	Mutagenesis	Note=No phosphorylation by MAPK14. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12435397;Dbxref=PMID:12435397
P41212	154	336	214	214	Natural variant	ID=VAR_073322;Note=In THC5%3B abrogates DNA binding%3B alters subcellular location%3B decreases transcriptional repression in a dominant-negative fashion. P->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25581430;Dbxref=dbSNP:rs724159947,PMID:25
P41212	154	336	336	337	Site	Note=Breakpoint for translocation to form ETV6-AML1 in ALL

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
P41212	54	109	1	452	Chain	ID=PRO_0000204121;Note=Transcription factor ETV6
P41212	54	109	40	124	Domain	Note=PNT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00762
P41212	54	109	52	54	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	54	109	58	60	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	54	109	63	76	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	54	109	91	94	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	54	109	99	105	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	54	109	54	55	Site	Note=Breakpoint for translocation to form ETV6-MDS2 in MDS
P41212	54	109	55	56	Site	Note=Breakpoint for translocation to form PAX5-ETV6
P41212	54	109	84	87	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	54	109	107	109	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	109	154	1	452	Chain	ID=PRO_0000204121;Note=Transcription factor ETV6
P41212	109	154	40	124	Domain	Note=PNT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00762
P41212	109	154	110	122	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	109	154	107	109	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1JI7
P41212	154	336	1	452	Chain	ID=PRO_0000204121;Note=Transcription factor ETV6
P41212	154	336	288	288	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:25755297,ECO:0000244\|PubMed:28112733;Dbxref=PMID:25755297,PMID:28112733
P41212	154	336	302	302	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
P41212	154	336	213	213	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:21406692;Dbxref=PMID:21406692
P41212	154	336	238	238	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P97360
P41212	154	336	257	257	Modified residue	Note=Phosphoserine%3B by MAPK14;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12435397;Dbxref=PMID:12435397
P41212	154	336	302	302	Modified residue	Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
P41212	154	336	323	323	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P97360
P41212	154	336	213	213	Mutagenesis	Note=No effect. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12435397;Dbxref=PMID:12435397
P41212	154	336	238	238	Mutagenesis	Note=No effect. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12435397;Dbxref=PMID:12435397
P41212	154	336	257	257	Mutagenesis	Note=No phosphorylation by MAPK14. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12435397;Dbxref=PMID:12435397
P41212	154	336	214	214	Natural variant	ID=VAR_073322;Note=In THC5%3B abrogates DNA binding%3B alters subcellular location%3B decreases transcriptional repression in a dominant-negative fashion. P->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:25581430;Dbxref=dbSNP:rs724159947,PMID:25
P41212	154	336	336	337	Site	Note=Breakpoint for translocation to form ETV6-AML1 in ALL

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SNVs in the skipped exons for ETV6

- 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
HNSC	TCGA-CX-A4AQ-01	exon_skip_80264	11992074	11992238	11992150	11992153	Frame_Shift_Del	GCCA	-	p.RP80fs
LIHC	TCGA-DD-A3A0-01	exon_skip_80272	12006361	12006495	12006380	12006380	Frame_Shift_Del	C	-	p.L117fs
LIHC	TCGA-DD-AACZ-01	exon_skip_80272	12006361	12006495	12006418	12006418	Frame_Shift_Del	T	-	p.L129fs
COAD	TCGA-A6-6780-01	exon_skip_80272	12006361	12006495	12006446	12006447	Frame_Shift_Del	CT	-	p.138_138del
STAD	TCGA-HU-A4GQ-01	exon_skip_80273	12022358	12022903	12022502	12022502	Frame_Shift_Del	C	-	p.S203fs
COAD	TCGA-CK-5916-01	exon_skip_80273	12022358	12022903	12022567	12022567	Nonsense_Mutation	C	T	p.Q225X
LUAD	TCGA-44-7669-01	exon_skip_80273	12022358	12022903	12022774	12022774	Nonsense_Mutation	G	T	p.E294*
BLCA	TCGA-DK-A3WW-01	exon_skip_80273	12022358	12022903	12022357	12022357	Splice_Site	G	T	p.D155_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
HCC1359_LUNG	11992074	11992238	11992190	11992190	Frame_Shift_Del	C	-	p.L97fs
HCC1359_LUNG	11992074	11992238	11992192	11992192	Frame_Shift_Del	C	-	p.L97fs
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12022358	12022903	12022502	12022502	Frame_Shift_Del	C	-	p.S203fs
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12022358	12022903	12022502	12022502	Frame_Shift_Del	C	-	p.S203fs
MHHCALL4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12038860	12038960	12038881	12038893	Frame_Shift_Del	GAGAAAATGTCCA	-	p.EKMSR392fs
TCYIK_CERVIX	11992074	11992238	11992105	11992105	Missense_Mutation	C	G	p.D65E
MDAMB361_BREAST	11992074	11992238	11992136	11992136	Missense_Mutation	G	A	p.E76K
KYSE450_OESOPHAGUS	11992074	11992238	11992159	11992159	Missense_Mutation	C	G	p.D83E
HEC1_ENDOMETRIUM	11992074	11992238	11992220	11992220	Missense_Mutation	T	C	p.Y104H
SBC3_LUNG	12006361	12006495	12006453	12006453	Missense_Mutation	C	T	p.H141Y
SNU1040_LARGE_INTESTINE	12022358	12022903	12022388	12022388	Missense_Mutation	C	A	p.S165Y
A2780_OVARY	12022358	12022903	12022441	12022441	Missense_Mutation	A	G	p.R183G
KYSE140_OESOPHAGUS	12022358	12022903	12022466	12022466	Missense_Mutation	G	A	p.R191Q
MFE319_ENDOMETRIUM	12022358	12022903	12022474	12022474	Missense_Mutation	C	T	p.P194S
SNUC1_LARGE_INTESTINE	12022358	12022903	12022474	12022474	Missense_Mutation	C	G	p.P194A
HEC151_ENDOMETRIUM	12022358	12022903	12022498	12022498	Missense_Mutation	C	T	p.R202W
CP67MEL_SKIN	12022358	12022903	12022534	12022534	Missense_Mutation	C	T	p.P214S
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12022358	12022903	12022535	12022535	Missense_Mutation	C	T	p.P214L
SNU685_ENDOMETRIUM	12022358	12022903	12022556	12022556	Missense_Mutation	C	T	p.P221L
NCIH650_LUNG	12022358	12022903	12022560	12022560	Missense_Mutation	G	T	p.R222S
OV56_OVARY	12022358	12022903	12022562	12022562	Missense_Mutation	C	T	p.P223L
JIYOYEP2003_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12022358	12022903	12022661	12022661	Missense_Mutation	C	T	p.S256F
DU145_PROSTATE	12022358	12022903	12022670	12022670	Missense_Mutation	G	T	p.R259L
HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12022358	12022903	12022751	12022751	Missense_Mutation	A	G	p.D286G
SW756_CERVIX	12022358	12022903	12022819	12022819	Missense_Mutation	C	T	p.R309W
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12022358	12022903	12022835	12022835	Missense_Mutation	A	G	p.Y314C
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12022358	12022903	12022876	12022876	Missense_Mutation	C	T	p.H328Y
HT29_LARGE_INTESTINE	12038860	12038960	12038893	12038893	Missense_Mutation	A	G	p.R396G
P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12038860	12038960	12038902	12038902	Missense_Mutation	C	T	p.R399C
SNU1040_LARGE_INTESTINE	12038860	12038960	12038902	12038902	Missense_Mutation	C	T	p.R399C
KE97_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12038860	12038960	12038912	12038912	Missense_Mutation	A	G	p.Y402C
KMS18_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	12038860	12038960	12038912	12038912	Missense_Mutation	A	G	p.Y402C
VMCUB1_URINARY_TRACT	11992074	11992238	11992093	11992093	Nonsense_Mutation	G	A	p.W61*
NCIH747_LARGE_INTESTINE	12022358	12022903	12022672	12022672	Nonsense_Mutation	C	T	p.Q260*
BICR18_UPPER_AERODIGESTIVE_TRACT	12006361	12006495	12006362	12006362	Splice_Site	T	C	p.G110G
RKN_SOFT_TISSUE	12006361	12006495	12006495	12006495	Splice_Site	G	A	p.D155N
MUGCHOR1_BONE	12022358	12022903	12022359	12022359	Splice_Site	T	A	p.D155E
CL34_LARGE_INTESTINE	12038860	12038960	12038958	12038964	Splice_Site	CAGGTAG	-	p.FR417fs

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ETV6

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 ETV6

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ETV6

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RelatedDrugs for ETV6

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 ETV6

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
ETV6	C0023485	Precursor B-Cell Lymphoblastic Leukemia-Lymphoma	3	CTD_human
ETV6	C0040034	Thrombocytopenia	2	CTD_human;HPO
ETV6	C0236969	Substance-Related Disorders	1	CTD_human
ETV6	C0376545	Hematologic Neoplasms	1	CTD_human
ETV6	C1838656	Macrocytosis, Familial	1	CTD_human
ETV6	C1961102	Precursor Cell Lymphoblastic Leukemia Lymphoma	1	CTD_human
ETV6	C3495559	Juvenile arthritis	1	CTD_human
ETV6	C4015537	THROMBOCYTOPENIA 5	1	UNIPROT

	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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