ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for NIPA2

Gene summary

Gene information	Gene symbol	NIPA2
	Gene ID	81614
	Gene name	NIPA magnesium transporter 2
	Synonyms	SLC57A2
	Cytomap	15q11.2
	Type of gene	protein-coding
	Description	magnesium transporter NIPA2non imprinted in Prader-Willi/Angelman syndrome 2non-imprinted in Prader-Willi/Angelman syndrome region protein 2
	Modification date	20180523
	UniProtAcc	Q8N8Q9
	Context	PubMed: NIPA2 [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 NIPA2 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 NIPA2

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 NIPA2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_125371	15	23012278:23012439:23014437:23014528:23019799:23019856	23014437:23014528	ENSG00000140157.10	ENST00000398013.3,ENST00000337451.3,ENST00000398014.2
exon_skip_125372	15	23012278:23012439:23014437:23014528:23021197:23021359	23014437:23014528	ENSG00000140157.10	ENST00000359727.4,ENST00000539711.2
exon_skip_125380	15	23014442:23014528:23019799:23019856:23021197:23021359	23019799:23019856	ENSG00000140157.10	ENST00000398013.3,ENST00000337451.3,ENST00000398014.2
exon_skip_125385	15	23014437:23014528:23021197:23021429:23027800:23027922	23021197:23021429	ENSG00000140157.10	ENST00000359727.4
exon_skip_125387	15	23014437:23014528:23021197:23021429:23034146:23034370	23021197:23021429	ENSG00000140157.10	ENST00000539711.2
exon_skip_125394	15	23019818:23019856:23021197:23021429:23033277:23033413	23021197:23021429	ENSG00000140157.10	ENST00000398014.2
exon_skip_125405	15	23021406:23021429:23027800:23027922:23033277:23033413	23027800:23027922	ENSG00000140157.10	ENST00000560205.1,ENST00000337451.3
exon_skip_125407	15	23021406:23021429:23027800:23027922:23034120:23034410	23027800:23027922	ENSG00000140157.10	ENST00000359727.4
exon_skip_125414	15	23021406:23021429:23033277:23033413:23033893:23034006	23033277:23033413	ENSG00000140157.10	ENST00000560762.1,ENST00000559571.1
exon_skip_125416	15	23021406:23021429:23033277:23033413:23034146:23034370	23033277:23033413	ENSG00000140157.10	ENST00000398014.2
exon_skip_125433	15	23027800:23027922:23033277:23033413:23034120:23034410	23033277:23033413	ENSG00000140157.10	ENST00000560205.1
exon_skip_125441	15	23033277:23033413:23033893:23034006:23034146:23034370	23033893:23034006	ENSG00000140157.10	ENST00000560762.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for NIPA2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_125371	15	23012278:23012439:23014437:23014528:23019799:23019856	23014437:23014528	ENSG00000140157.10	ENST00000337451.3,ENST00000398014.2,ENST00000398013.3
exon_skip_125372	15	23012278:23012439:23014437:23014528:23021197:23021359	23014437:23014528	ENSG00000140157.10	ENST00000539711.2,ENST00000359727.4
exon_skip_125380	15	23014442:23014528:23019799:23019856:23021197:23021359	23019799:23019856	ENSG00000140157.10	ENST00000337451.3,ENST00000398014.2,ENST00000398013.3
exon_skip_125385	15	23014437:23014528:23021197:23021429:23027800:23027922	23021197:23021429	ENSG00000140157.10	ENST00000359727.4
exon_skip_125387	15	23014437:23014528:23021197:23021429:23034146:23034370	23021197:23021429	ENSG00000140157.10	ENST00000539711.2
exon_skip_125394	15	23019818:23019856:23021197:23021429:23033277:23033413	23021197:23021429	ENSG00000140157.10	ENST00000398014.2
exon_skip_125405	15	23021406:23021429:23027800:23027922:23033277:23033413	23027800:23027922	ENSG00000140157.10	ENST00000337451.3,ENST00000560205.1
exon_skip_125407	15	23021406:23021429:23027800:23027922:23034120:23034410	23027800:23027922	ENSG00000140157.10	ENST00000359727.4
exon_skip_125414	15	23021406:23021429:23033277:23033413:23033893:23034006	23033277:23033413	ENSG00000140157.10	ENST00000559571.1,ENST00000560762.1
exon_skip_125416	15	23021406:23021429:23033277:23033413:23034146:23034370	23033277:23033413	ENSG00000140157.10	ENST00000398014.2
exon_skip_125433	15	23027800:23027922:23033277:23033413:23034120:23034410	23033277:23033413	ENSG00000140157.10	ENST00000560205.1
exon_skip_125441	15	23033277:23033413:23033893:23034006:23034146:23034370	23033893:23034006	ENSG00000140157.10	ENST00000560762.1

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 NIPA2

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
ENST00000398014	23021197	23021429	3UTR-3CDS
ENST00000337451	23027800	23027922	3UTR-3UTR
ENST00000398014	23033277	23033413	3UTR-3UTR
ENST00000337451	23014437	23014528	Frame-shift
ENST00000398013	23014437	23014528	Frame-shift
ENST00000398014	23014437	23014528	Frame-shift
ENST00000337451	23019799	23019856	In-frame
ENST00000398013	23019799	23019856	In-frame
ENST00000398014	23019799	23019856	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
ENST00000398014	23021197	23021429	3UTR-3CDS
ENST00000337451	23027800	23027922	3UTR-3UTR
ENST00000398014	23033277	23033413	3UTR-3UTR
ENST00000337451	23014437	23014528	Frame-shift
ENST00000398013	23014437	23014528	Frame-shift
ENST00000398014	23014437	23014528	Frame-shift
ENST00000337451	23019799	23019856	In-frame
ENST00000398013	23019799	23019856	In-frame
ENST00000398014	23019799	23019856	In-frame

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Infer the effects of exon skipping event on protein functional features for NIPA2

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
ENST00000337451	3250	360	23019799	23019856	753	809	46	65
ENST00000398013	2297	360	23019799	23019856	468	524	46	65
ENST00000398014	3147	360	23019799	23019856	650	706	46	65

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
ENST00000337451	3250	360	23019799	23019856	753	809	46	65
ENST00000398013	2297	360	23019799	23019856	468	524	46	65
ENST00000398014	3147	360	23019799	23019856	650	706	46	65

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
Q8N8Q9	46	65	47	66	Alternative sequence	ID=VSP_044587;Note=In isoform 2. GQGGHAYLKEWLWWAGLLSM->V;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8N8Q9	46	65	47	66	Alternative sequence	ID=VSP_044587;Note=In isoform 2. GQGGHAYLKEWLWWAGLLSM->V;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8N8Q9	46	65	47	66	Alternative sequence	ID=VSP_044587;Note=In isoform 2. GQGGHAYLKEWLWWAGLLSM->V;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8N8Q9	46	65	1	360	Chain	ID=PRO_0000191743;Note=Magnesium transporter NIPA2
Q8N8Q9	46	65	1	360	Chain	ID=PRO_0000191743;Note=Magnesium transporter NIPA2
Q8N8Q9	46	65	1	360	Chain	ID=PRO_0000191743;Note=Magnesium transporter NIPA2
Q8N8Q9	46	65	31	56	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N8Q9	46	65	31	56	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N8Q9	46	65	31	56	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N8Q9	46	65	57	77	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N8Q9	46	65	57	77	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N8Q9	46	65	57	77	Transmembrane	Note=Helical;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
Q8N8Q9	46	65	47	66	Alternative sequence	ID=VSP_044587;Note=In isoform 2. GQGGHAYLKEWLWWAGLLSM->V;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8N8Q9	46	65	47	66	Alternative sequence	ID=VSP_044587;Note=In isoform 2. GQGGHAYLKEWLWWAGLLSM->V;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8N8Q9	46	65	47	66	Alternative sequence	ID=VSP_044587;Note=In isoform 2. GQGGHAYLKEWLWWAGLLSM->V;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q8N8Q9	46	65	1	360	Chain	ID=PRO_0000191743;Note=Magnesium transporter NIPA2
Q8N8Q9	46	65	1	360	Chain	ID=PRO_0000191743;Note=Magnesium transporter NIPA2
Q8N8Q9	46	65	1	360	Chain	ID=PRO_0000191743;Note=Magnesium transporter NIPA2
Q8N8Q9	46	65	31	56	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N8Q9	46	65	31	56	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N8Q9	46	65	31	56	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N8Q9	46	65	57	77	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N8Q9	46	65	57	77	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8N8Q9	46	65	57	77	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for NIPA2

- 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_125371 exon_skip_125372	23014438	23014528	23014488	23014488	Frame_Shift_Del	A	-	p.F79fs
STAD	TCGA-MX-A5UJ-01	exon_skip_125394 exon_skip_125385 exon_skip_125387	23021198	23021429	23021239	23021239	Frame_Shift_Del	T	-	p.K33fs
UCEC	TCGA-D1-A177-01	exon_skip_125394 exon_skip_125385 exon_skip_125387	23021198	23021429	23021239	23021239	Frame_Shift_Del	T	-	p.K33fs
UCEC	TCGA-D1-A17U-01	exon_skip_125394 exon_skip_125385 exon_skip_125387	23021198	23021429	23021239	23021239	Frame_Shift_Del	T	-	p.K33fs
LIHC	TCGA-DD-A39Y-01	exon_skip_125394 exon_skip_125385 exon_skip_125387	23021198	23021429	23021325	23021325	Frame_Shift_Del	C	-	p.G4fs
COAD	TCGA-CM-4746-01	exon_skip_125394 exon_skip_125385 exon_skip_125387	23021198	23021429	23021237	23021238	Frame_Shift_Ins	-	T	p.G34fs
UCS	TCGA-N7-A4Y0-01	exon_skip_125394 exon_skip_125385 exon_skip_125387	23021198	23021429	23021237	23021238	Frame_Shift_Ins	-	T	p.P34fs
STAD	TCGA-HU-A4GQ-01	exon_skip_125394 exon_skip_125385 exon_skip_125387	23021198	23021429	23021238	23021239	Frame_Shift_Ins	-	T	p.K33fs
UCEC	TCGA-B5-A0K7-01	exon_skip_125394 exon_skip_125385 exon_skip_125387	23021198	23021429	23021238	23021239	Frame_Shift_Ins	-	T	p.K33fs
STAD	TCGA-HU-A4GQ-01	exon_skip_125394 exon_skip_125385 exon_skip_125387	23021198	23021429	23021239	23021240	Frame_Shift_Ins	-	T	p.K33fs
UCS	TCGA-N7-A4Y0-01	exon_skip_125394 exon_skip_125385 exon_skip_125387	23021198	23021429	23021241	23021242	Frame_Shift_Ins	-	T	p.K32fs
BLCA	TCGA-GU-AATP-01		23019800	23019856	23019802	23019802	Nonsense_Mutation	G	C	p.S65*
BLCA	TCGA-CF-A9FF-01		23019800	23019856	23019854	23019854	Nonsense_Mutation	G	A	p.Q48*

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-CM-4746-01
	Cancer type: COAD
	ESID: exon_skip_125387
	Skipped exon start: 23021198
	Skipped exon end: 23021429
	Mutation start: 23021237
	Mutation end: 23021238
	Mutation type: Frame_Shift_Ins
	Reference seq: -
	Mutation seq: T
	AAchange: p.G34fs
exon_skip_125387_COAD_TCGA-CM-4746-01.png
exon_skip_485128_COAD_TCGA-CM-4746-01.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
TUHR14TKB_KIDNEY	23014438	23014528	23014442	23014442	Missense_Mutation	C	T	p.V95I
HTCC3_THYROID	23014438	23014528	23014481	23014481	Missense_Mutation	C	A	p.A82S

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NIPA2

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_125394	15	23019818:23019856:23021197:23021429:23033277:23033413	23021197:23021429	ENST00000398014.2	LGG	rs7170838	chr15:23021238	C/T	5.52e-04
exon_skip_125385	15	23014437:23014528:23021197:23021429:23027800:23027922	23021197:23021429	ENST00000359727.4	LGG	rs7170838	chr15:23021238	C/T	5.52e-04
exon_skip_125387	15	23014437:23014528:23021197:23021429:23034146:23034370	23021197:23021429	ENST00000539711.2	LGG	rs7170838	chr15:23021238	C/T	5.52e-04

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NIPA2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NIPA2

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RelatedDrugs for NIPA2

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 NIPA2

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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Gene summary for NIPA2

Exon skipping events across known transcript of Ensembl for NIPA2 from UCSC genome browser

Gene isoform structures and expression levels for NIPA2

Exon skipping events with PSIs in TCGA for NIPA2

Exon skipping events with PSIs in GTEx for NIPA2

Open reading frame (ORF) annotation in the exon skipping event for NIPA2

Infer the effects of exon skipping event on protein functional features for NIPA2

SNVs in the skipped exons for NIPA2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NIPA2

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NIPA2

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NIPA2

RelatedDrugs for NIPA2

RelatedDiseases for NIPA2