ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for AGR2

Gene summary

Gene information	Gene symbol	AGR2
	Gene ID	10551
	Gene name	anterior gradient 2, protein disulphide isomerase family member
	Synonyms	AG-2\|AG2\|GOB-4\|HAG-2\|HEL-S-116\|HPC8\|PDIA17\|XAG-2
	Cytomap	7p21.1
	Type of gene	protein-coding
	Description	anterior gradient protein 2 homologanterior gradient homolog 2epididymis secretory protein Li 116protein disulfide isomerase family A, member 17secreted cement gland homologsecreted cement gland protein XAG-2 homolog
	Modification date	20180523
	UniProtAcc	O95994
	Context	PubMed: AGR2 [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
AGR2	GO:1903896	positive regulation of IRE1-mediated unfolded protein response	23220234
AGR2	GO:1903899	positive regulation of PERK-mediated unfolded protein response	23220234

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Exon skipping events across known transcript of Ensembl for AGR2 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 AGR2

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 AGR2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENSG00000106541.7	ENST00000450569.1
exon_skip_473896	7	16832265:16832581:16834559:16834643:16837254:16837318	16834559:16834643	ENSG00000106541.7	ENST00000419304.2,ENST00000419572.2
exon_skip_473909	7	16834561:16834643:16837254:16837318:16839367:16839441	16837254:16837318	ENSG00000106541.7	ENST00000401412.1,ENST00000419304.2,ENST00000450569.1,ENST00000419572.2
exon_skip_473926	7	16839367:16839441:16840774:16840827:16840943:16841007	16840774:16840827	ENSG00000106541.7	ENST00000489523.1,ENST00000401412.1,ENST00000412973.1,ENST00000419304.2,ENST00000419572.2
exon_skip_473932	7	16840943:16841007:16841281:16841427:16844558:16844619	16841281:16841427	ENSG00000106541.7	ENST00000489523.1
exon_skip_473933	7	16840943:16841007:16841281:16841427:16844576:16844611	16841281:16841427	ENSG00000106541.7	ENST00000401412.1
exon_skip_473939	7	16841283:16841427:16851288:16851379:16872879:16872932	16851288:16851379	ENSG00000106541.7	ENST00000412973.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for AGR2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENSG00000106541.7	ENST00000450569.1
exon_skip_473896	7	16832265:16832581:16834559:16834643:16837254:16837318	16834559:16834643	ENSG00000106541.7	ENST00000419304.2,ENST00000419572.2
exon_skip_473909	7	16834561:16834643:16837254:16837318:16839367:16839441	16837254:16837318	ENSG00000106541.7	ENST00000419304.2,ENST00000450569.1,ENST00000419572.2,ENST00000401412.1
exon_skip_473926	7	16839367:16839441:16840774:16840827:16840943:16841007	16840774:16840827	ENSG00000106541.7	ENST00000419304.2,ENST00000419572.2,ENST00000401412.1,ENST00000412973.1,ENST00000489523.1
exon_skip_473932	7	16840943:16841007:16841281:16841427:16844558:16844619	16841281:16841427	ENSG00000106541.7	ENST00000489523.1
exon_skip_473933	7	16840943:16841007:16841281:16841427:16844576:16844611	16841281:16841427	ENSG00000106541.7	ENST00000401412.1
exon_skip_473939	7	16841283:16841427:16851288:16851379:16872879:16872932	16851288:16851379	ENSG00000106541.7	ENST00000412973.1

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 AGR2

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
ENST00000419304	16837254	16837318	Frame-shift
ENST00000419304	16840774	16840827	Frame-shift
ENST00000419304	16834559	16834643	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
ENST00000419304	16837254	16837318	Frame-shift
ENST00000419304	16840774	16840827	Frame-shift
ENST00000419304	16834559	16834643	In-frame

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Infer the effects of exon skipping event on protein functional features for AGR2

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
ENST00000419304	1795	175	16834559	16834643	548	631	131	159

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
ENST00000419304	1795	175	16834559	16834643	548	631	131	159

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
O95994	131	159	127	132	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LNS
O95994	131	159	21	175	Chain	ID=PRO_0000001037;Note=Anterior gradient protein 2 homolog
O95994	131	159	157	167	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LNS
O95994	131	159	133	135	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LNS
O95994	131	159	146	150	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LNS
O95994	131	159	154	156	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LNS

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
O95994	131	159	127	132	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LNS
O95994	131	159	21	175	Chain	ID=PRO_0000001037;Note=Anterior gradient protein 2 homolog
O95994	131	159	157	167	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LNS
O95994	131	159	133	135	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LNS
O95994	131	159	146	150	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LNS
O95994	131	159	154	156	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2LNS

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SNVs in the skipped exons for AGR2

- 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-G3-A3CJ-01	exon_skip_473909	16837255	16837318	16837265	16837265	Frame_Shift_Del	A	-	p.I128fs
KIRP	TCGA-B1-5398-01	exon_skip_473909	16837255	16837318	16837319	16837319	Splice_Site	C	A	.
KIRP	TCGA-B1-5398-01	exon_skip_473909	16837255	16837318	16837319	16837319	Splice_Site	C	A	p.Y111_splice
UCEC	TCGA-BS-A0UF-01	exon_skip_473926	16840775	16840827	16840828	16840828	Splice_Site	C	A	e3-1

- 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
MELJUSO_SKIN	16841282	16841427	16841308	16841309	Frame_Shift_Ins	-	GTCGA	p.P38fs
RERFLCAD2_LUNG	16834475	16834643	16834620	16834620	Missense_Mutation	C	T	p.D140N
RERFLCAD2_LUNG	16834560	16834643	16834620	16834620	Missense_Mutation	C	T	p.D140N
NCIH250_LUNG	16837255	16837318	16837264	16837264	Missense_Mutation	T	C	p.M129V

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for AGR2

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_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	COAD	rs4719480	chr7:16834551	A/C	4.61e-13
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	COAD	rs4719480	chr7:16834551	A/C	4.61e-13
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	BRCA	rs4719480	chr7:16834551	A/C	2.50e-06
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	BRCA	rs4719480	chr7:16834551	A/C	2.91e-06
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	LUAD	rs4719480	chr7:16834551	A/C	1.02e-08
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	LUAD	rs4719480	chr7:16834551	A/C	1.02e-08
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	LUAD	rs6842	chr7:16834597	C/T	4.06e-06
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	LUAD	rs6842	chr7:16834597	C/T	4.09e-06
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	LUAD	rs4719480	chr7:16834551	A/C	2.38e-03
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	LUSC	rs4719480	chr7:16834551	A/C	3.09e-03
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	LUSC	rs4719480	chr7:16834551	A/C	3.10e-03
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	PAAD	rs4719480	chr7:16834551	A/C	1.08e-04
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	PRAD	rs4719480	chr7:16834551	A/C	1.47e-10
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	PRAD	rs4719480	chr7:16834551	A/C	1.50e-10
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	PRAD	rs4719480	chr7:16834551	A/C	3.24e-04
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	PRAD	rs4719480	chr7:16834551	A/C	3.27e-04
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	PRAD	rs6842	chr7:16834597	C/T	3.97e-04
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	PRAD	rs6842	chr7:16834597	C/T	3.97e-04
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	STAD	rs4719480	chr7:16834551	A/C	1.51e-03
exon_skip_473895	7	16832265:16832581:16834474:16834643:16837254:16837318	16834474:16834643	ENST00000450569.1	STAD	rs4719480	chr7:16834551	A/C	1.53e-03
exon_skip_473896	7	16832265:16832581:16834559:16834643:16837254:16837318	16834559:16834643	ENST00000419304.2,ENST00000419572.2	LUAD	rs6842	chr7:16834597	C/T	4.06e-06
exon_skip_473896	7	16832265:16832581:16834559:16834643:16837254:16837318	16834559:16834643	ENST00000419304.2,ENST00000419572.2	LUAD	rs6842	chr7:16834597	C/T	4.09e-06
exon_skip_473896	7	16832265:16832581:16834559:16834643:16837254:16837318	16834559:16834643	ENST00000419304.2,ENST00000419572.2	PRAD	rs6842	chr7:16834597	C/T	3.97e-04
exon_skip_473896	7	16832265:16832581:16834559:16834643:16837254:16837318	16834559:16834643	ENST00000419304.2,ENST00000419572.2	PRAD	rs6842	chr7:16834597	C/T	3.97e-04

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for AGR2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for AGR2

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RelatedDrugs for AGR2

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 AGR2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
AGR2	C0033578	Prostatic Neoplasms	2	CTD_human
AGR2	C1458155	Mammary Neoplasms	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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