ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for TATDN1

Gene summary

Gene information	Gene symbol	TATDN1
	Gene ID	83940
	Gene name	TatD DNase domain containing 1
	Synonyms	CDA11
	Cytomap	8q24.13
	Type of gene	protein-coding
	Description	putative deoxyribonuclease TATDN1hepatocarcinoma high expression protein
	Modification date	20180526
	UniProtAcc	Q6P1N9
	Context	PubMed: TATDN1 [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

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Exon skipping events across known transcript of Ensembl for TATDN1 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 TATDN1

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 TATDN1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_492231	8	125500870:125500937:125506073:125506200:125507712:125507783	125506073:125506200	ENSG00000147687.12	ENST00000523214.1,ENST00000522927.1,ENST00000522810.1,ENST00000519548.1,ENST00000276692.6
exon_skip_492232	8	125506073:125506200:125507712:125507783:125516080:125516192	125507712:125507783	ENSG00000147687.12	ENST00000523214.1,ENST00000522810.1
exon_skip_492233	8	125506073:125506200:125507712:125507783:125516511:125516588	125507712:125507783	ENSG00000147687.12	ENST00000518485.1,ENST00000517678.1,ENST00000522927.1,ENST00000519548.1,ENST00000276692.6
exon_skip_492241	8	125507758:125507783:125516080:125516192:125516511:125516588	125516080:125516192	ENSG00000147687.12	ENST00000523214.1
exon_skip_492242	8	125507758:125507783:125516080:125516192:125516515:125516588	125516080:125516192	ENSG00000147687.12	ENST00000522810.1
exon_skip_492246	8	125507758:125507783:125516511:125516588:125520714:125520755	125516511:125516588	ENSG00000147687.12	ENST00000517678.1,ENST00000519776.1,ENST00000522927.1,ENST00000523631.1,ENST00000519548.1,ENST00000276692.6
exon_skip_492247	8	125507758:125507783:125516515:125516588:125520714:125520755	125516515:125516588	ENSG00000147687.12	ENST00000521546.1
exon_skip_492249	8	125520858:125520929:125527986:125528029:125528127:125528271	125527986:125528029	ENSG00000147687.12	ENST00000520938.1,ENST00000520321.1,ENST00000523214.1,ENST00000517678.1,ENST00000519776.1,ENST00000523888.1,ENST00000519232.1,ENST00000522310.1,ENST00000521546.1,ENST00000523152.1,ENST00000522810.1,ENST00000521973.1,ENST00000605953.1,ENST00000519548.1,ENS
exon_skip_492259	8	125527986:125528029:125528127:125528271:125531058:125531122	125528127:125528271	ENSG00000147687.12	ENST00000523214.1,ENST00000519776.1,ENST00000523888.1,ENST00000519232.1,ENST00000521546.1,ENST00000522810.1,ENST00000605953.1,ENST00000519548.1,ENST00000276692.6
exon_skip_492269	8	125528164:125528271:125530982:125531122:125535177:125535243	125530982:125531122	ENSG00000147687.12	ENST00000522310.1
exon_skip_492271	8	125528164:125528271:125531058:125531122:125535177:125535243	125531058:125531122	ENSG00000147687.12	ENST00000519776.1,ENST00000523888.1
exon_skip_492272	8	125528164:125528271:125531058:125531122:125551265:125551297	125531058:125531122	ENSG00000147687.12	ENST00000519548.1
exon_skip_492282	8	125531109:125531122:125534391:125534441:125535177:125535243	125534391:125534441	ENSG00000147687.12	ENST00000520938.1,ENST00000518133.1,ENST00000523214.1,ENST00000519232.1,ENST00000521546.1,ENST00000522810.1,ENST00000605953.1,ENST00000276692.6
exon_skip_492283	8	125531058:125531122:125534391:125534441:125551265:125551297	125534391:125534441	ENSG00000147687.12	ENST00000520321.1
exon_skip_492284	8	125531058:125531122:125535177:125535243:125551265:125551297	125535177:125535243	ENSG00000147687.12	ENST00000519776.1,ENST00000522310.1
exon_skip_492286	8	125534391:125534441:125535177:125535243:125550571:125550710	125535177:125535243	ENSG00000147687.12	ENST00000521546.1
exon_skip_492287	8	125534391:125534441:125535177:125535243:125551168:125551278	125535177:125535243	ENSG00000147687.12	ENST00000520938.1,ENST00000519232.1
exon_skip_492288	8	125534391:125534441:125535177:125535243:125551265:125551297	125535177:125535243	ENSG00000147687.12	ENST00000523214.1,ENST00000522280.1,ENST00000522810.1,ENST00000605953.1,ENST00000276692.6

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for TATDN1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_492231	8	125500870:125500937:125506073:125506200:125507712:125507783	125506073:125506200	ENSG00000147687.12	ENST00000522927.1,ENST00000276692.6,ENST00000523214.1,ENST00000519548.1,ENST00000522810.1
exon_skip_492232	8	125506073:125506200:125507712:125507783:125516080:125516192	125507712:125507783	ENSG00000147687.12	ENST00000523214.1,ENST00000522810.1
exon_skip_492233	8	125506073:125506200:125507712:125507783:125516511:125516588	125507712:125507783	ENSG00000147687.12	ENST00000522927.1,ENST00000276692.6,ENST00000519548.1,ENST00000518485.1,ENST00000517678.1
exon_skip_492241	8	125507758:125507783:125516080:125516192:125516511:125516588	125516080:125516192	ENSG00000147687.12	ENST00000523214.1
exon_skip_492242	8	125507758:125507783:125516080:125516192:125516515:125516588	125516080:125516192	ENSG00000147687.12	ENST00000522810.1
exon_skip_492246	8	125507758:125507783:125516511:125516588:125520714:125520755	125516511:125516588	ENSG00000147687.12	ENST00000522927.1,ENST00000276692.6,ENST00000523631.1,ENST00000519548.1,ENST00000517678.1,ENST00000519776.1
exon_skip_492247	8	125507758:125507783:125516515:125516588:125520714:125520755	125516515:125516588	ENSG00000147687.12	ENST00000521546.1
exon_skip_492249	8	125520858:125520929:125527986:125528029:125528127:125528271	125527986:125528029	ENSG00000147687.12	ENST00000276692.6,ENST00000523214.1,ENST00000519548.1,ENST00000522810.1,ENST00000517678.1,ENST00000519776.1,ENST00000521546.1,ENST00000521973.1,ENST00000605953.1,ENST00000520321.1,ENST00000522310.1,ENST00000519232.1,ENST00000520938.1,ENST00000523888.1,ENS
exon_skip_492259	8	125527986:125528029:125528127:125528271:125531058:125531122	125528127:125528271	ENSG00000147687.12	ENST00000276692.6,ENST00000523214.1,ENST00000519548.1,ENST00000522810.1,ENST00000519776.1,ENST00000521546.1,ENST00000605953.1,ENST00000519232.1,ENST00000523888.1
exon_skip_492269	8	125528164:125528271:125530982:125531122:125535177:125535243	125530982:125531122	ENSG00000147687.12	ENST00000522310.1
exon_skip_492271	8	125528164:125528271:125531058:125531122:125535177:125535243	125531058:125531122	ENSG00000147687.12	ENST00000519776.1,ENST00000523888.1
exon_skip_492272	8	125528164:125528271:125531058:125531122:125551265:125551297	125531058:125531122	ENSG00000147687.12	ENST00000519548.1
exon_skip_492282	8	125531109:125531122:125534391:125534441:125535177:125535243	125534391:125534441	ENSG00000147687.12	ENST00000276692.6,ENST00000523214.1,ENST00000522810.1,ENST00000521546.1,ENST00000605953.1,ENST00000519232.1,ENST00000520938.1,ENST00000518133.1
exon_skip_492283	8	125531058:125531122:125534391:125534441:125551265:125551297	125534391:125534441	ENSG00000147687.12	ENST00000520321.1
exon_skip_492284	8	125531058:125531122:125535177:125535243:125551265:125551297	125535177:125535243	ENSG00000147687.12	ENST00000519776.1,ENST00000522310.1
exon_skip_492286	8	125534391:125534441:125535177:125535243:125550571:125550710	125535177:125535243	ENSG00000147687.12	ENST00000521546.1
exon_skip_492287	8	125534391:125534441:125535177:125535243:125551168:125551278	125535177:125535243	ENSG00000147687.12	ENST00000519232.1,ENST00000520938.1
exon_skip_492288	8	125534391:125534441:125535177:125535243:125551265:125551297	125535177:125535243	ENSG00000147687.12	ENST00000276692.6,ENST00000523214.1,ENST00000522810.1,ENST00000605953.1,ENST00000522280.1

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 TATDN1

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
ENST00000276692	125506073	125506200	Frame-shift
ENST00000276692	125507712	125507783	Frame-shift
ENST00000276692	125516511	125516588	Frame-shift
ENST00000276692	125527986	125528029	Frame-shift
ENST00000276692	125534391	125534441	Frame-shift
ENST00000276692	125528127	125528271	In-frame
ENST00000276692	125535177	125535243	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
ENST00000276692	125506073	125506200	Frame-shift
ENST00000276692	125507712	125507783	Frame-shift
ENST00000276692	125516511	125516588	Frame-shift
ENST00000276692	125527986	125528029	Frame-shift
ENST00000276692	125534391	125534441	Frame-shift
ENST00000276692	125528127	125528271	In-frame
ENST00000276692	125535177	125535243	In-frame

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Infer the effects of exon skipping event on protein functional features for TATDN1

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
ENST00000276692	1035	297	125535177	125535243	61	126	7	29
ENST00000276692	1035	297	125528127	125528271	241	384	67	115

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
ENST00000276692	1035	297	125535177	125535243	61	126	7	29
ENST00000276692	1035	297	125528127	125528271	241	384	67	115

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
Q6P1N9	7	29	1	47	Alternative sequence	ID=VSP_030045;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
Q6P1N9	7	29	6	11	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	7	29	1	297	Chain	ID=PRO_0000313590;Note=Putative deoxyribonuclease TATDN1
Q6P1N9	7	29	16	19	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	7	29	27	27	Modified residue	Note=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q6P8M1
Q6P1N9	67	115	70	74	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	67	115	107	116	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	67	115	1	297	Chain	ID=PRO_0000313590;Note=Putative deoxyribonuclease TATDN1
Q6P1N9	67	115	78	82	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	67	115	83	87	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	67	115	89	101	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	67	115	112	112	Metal binding	Note=Divalent metal cation 1;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q6P1N9	67	115	112	112	Metal binding	Note=Divalent metal cation 2;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q6P1N9	67	115	104	106	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO

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
Q6P1N9	7	29	1	47	Alternative sequence	ID=VSP_030045;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
Q6P1N9	7	29	6	11	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	7	29	1	297	Chain	ID=PRO_0000313590;Note=Putative deoxyribonuclease TATDN1
Q6P1N9	7	29	16	19	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	7	29	27	27	Modified residue	Note=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q6P8M1
Q6P1N9	67	115	70	74	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	67	115	107	116	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	67	115	1	297	Chain	ID=PRO_0000313590;Note=Putative deoxyribonuclease TATDN1
Q6P1N9	67	115	78	82	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	67	115	83	87	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	67	115	89	101	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO
Q6P1N9	67	115	112	112	Metal binding	Note=Divalent metal cation 1;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q6P1N9	67	115	112	112	Metal binding	Note=Divalent metal cation 2;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q6P1N9	67	115	104	106	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2XIO

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SNVs in the skipped exons for TATDN1

- 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
LIHC	TCGA-DD-A3A0-01	exon_skip_492246 exon_skip_492247	125516512	125516588	125516548	125516548	Frame_Shift_Del	A	-	p.L186fs
LIHC	TCGA-DD-A3A0-01	exon_skip_492246 exon_skip_492247	125516516	125516588	125516548	125516548	Frame_Shift_Del	A	-	p.L186fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_492249	125527987	125528029	125528025	125528025	Frame_Shift_Del	A	-	p.F117fs
STAD	TCGA-BR-8078-01	exon_skip_492284 exon_skip_492286 exon_skip_492287 exon_skip_492288	125535178	125535243	125535186	125535186	Frame_Shift_Del	T	-	p.K27fs
ESCA	TCGA-IC-A6RE-01	exon_skip_492269	125530983	125531122	125531026	125531027	Frame_Shift_Ins	-	T	p.*62fs
HNSC	TCGA-MT-A7BN-01	exon_skip_492231	125506074	125506200	125506161	125506161	Nonsense_Mutation	G	C	p.S235*
UCEC	TCGA-BS-A0UV-01	exon_skip_492259	125528128	125528271	125528140	125528140	Nonsense_Mutation	C	A	p.E112*
LUSC	TCGA-33-4583-01	exon_skip_492269	125530983	125531122	125531107	125531107	Nonsense_Mutation	C	A	p.G52*
LUSC	TCGA-33-4583-01	exon_skip_492271 exon_skip_492272	125531059	125531122	125531107	125531107	Nonsense_Mutation	C	A	p.G52*
KIRC	TCGA-DV-5575-01	exon_skip_492249	125527987	125528029	125527986	125527986	Splice_Site	C	T	.
LUSC	TCGA-33-4583-01	exon_skip_492271 exon_skip_492272	125531059	125531122	125531058	125531058	Splice_Site	C	A	p.G68_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
CHAGOK1_LUNG	125506074	125506200	125506092	125506092	Missense_Mutation	T	C	p.N258S
HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	125528128	125528271	125528187	125528187	Missense_Mutation	A	C	p.L96W
MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	125535178	125535243	125535198	125535198	Missense_Mutation	C	G	p.R23T
NCIH1869_LUNG	125535178	125535243	125535215	125535215	Missense_Mutation	C	G	p.M17I
SCLC22H_LUNG	125535178	125535243	125535217	125535217	Missense_Mutation	T	C	p.M17V
SCLC21H_LUNG	125535178	125535243	125535217	125535217	Missense_Mutation	T	C	p.M17V
WM35_SKIN	125535178	125535243	125535219	125535219	Missense_Mutation	G	A	p.P16L
HOP62_LUNG	125535178	125535243	125535240	125535240	Missense_Mutation	A	G	p.I9T
NCIH250_LUNG	125527987	125528029	125528021	125528021	Nonsense_Mutation	G	A	p.R119*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TATDN1

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_492259	8	125527986:125528029:125528127:125528271:125531058:125531122	125528127:125528271	ENST00000523214.1,ENST00000519776.1,ENST00000523888.1,ENST00000519232.1,ENST00000521546.1,ENST00000522810.1,ENST00000605953.1,ENST00000519548.1,ENST00000276692.6	BRCA	rs11542673	chr8:125528135	G/A	1.04e-07
exon_skip_492259	8	125527986:125528029:125528127:125528271:125531058:125531122	125528127:125528271	ENST00000523214.1,ENST00000519776.1,ENST00000523888.1,ENST00000519232.1,ENST00000521546.1,ENST00000522810.1,ENST00000605953.1,ENST00000519548.1,ENST00000276692.6	LGG	rs11542673	chr8:125528135	G/A	1.54e-03
exon_skip_492259	8	125527986:125528029:125528127:125528271:125531058:125531122	125528127:125528271	ENST00000523214.1,ENST00000519776.1,ENST00000523888.1,ENST00000519232.1,ENST00000521546.1,ENST00000522810.1,ENST00000605953.1,ENST00000519548.1,ENST00000276692.6	KIRC	rs11542673	chr8:125528135	G/A	2.23e-04
exon_skip_492259	8	125527986:125528029:125528127:125528271:125531058:125531122	125528127:125528271	ENST00000523214.1,ENST00000519776.1,ENST00000523888.1,ENST00000519232.1,ENST00000521546.1,ENST00000522810.1,ENST00000605953.1,ENST00000519548.1,ENST00000276692.6	PRAD	rs11542673	chr8:125528135	G/A	1.65e-04
exon_skip_492259	8	125527986:125528029:125528127:125528271:125531058:125531122	125528127:125528271	ENST00000523214.1,ENST00000519776.1,ENST00000523888.1,ENST00000519232.1,ENST00000521546.1,ENST00000522810.1,ENST00000605953.1,ENST00000519548.1,ENST00000276692.6	STAD	rs11542673	chr8:125528135	G/A	4.18e-04
exon_skip_492259	8	125527986:125528029:125528127:125528271:125531058:125531122	125528127:125528271	ENST00000523214.1,ENST00000519776.1,ENST00000523888.1,ENST00000519232.1,ENST00000521546.1,ENST00000522810.1,ENST00000605953.1,ENST00000519548.1,ENST00000276692.6	THCA	rs11542673	chr8:125528135	G/A	1.70e-10

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TATDN1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TATDN1

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RelatedDrugs for TATDN1

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 TATDN1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
TATDN1	C2239176	Liver carcinoma	1	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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