ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for JAKMIP2

Gene summary

Gene information	Gene symbol	JAKMIP2
	Gene ID	9832
	Gene name	janus kinase and microtubule interacting protein 2
	Synonyms	JAMIP2\|NECC1
	Cytomap	5q32
	Type of gene	protein-coding
	Description	janus kinase and microtubule-interacting protein 2CTCL tumor antigen HD-CL-04Jak and microtubule interacting protein 2neuroendocrine long coiled-coil protein 1
	Modification date	20180522
	UniProtAcc	Q96AA8
	Context	PubMed: JAKMIP2 [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 JAKMIP2 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 JAKMIP2

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 JAKMIP2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_445178	5	146970924:146971249:146981303:146981374:146991868:146991934	146981303:146981374	ENSG00000176049.11	ENST00000507386.1,ENST00000333010.6
exon_skip_445181	5	146991868:146991934:146997473:146997677:147000228:147000306	146997473:146997677	ENSG00000176049.11	ENST00000265272.5,ENST00000507386.1,ENST00000333010.6
exon_skip_445182	5	146997473:146997677:147000228:147000306:147003183:147003252	147000228:147000306	ENSG00000176049.11	ENST00000265272.5,ENST00000507386.1,ENST00000333010.6
exon_skip_445183	5	147012242:147012341:147015784:147015847:147016527:147016611	147015784:147015847	ENSG00000176049.11	ENST00000265272.5,ENST00000504845.1,ENST00000333010.6
exon_skip_445184	5	147019194:147019323:147020266:147020386:147021270:147021327	147020266:147020386	ENSG00000176049.11	ENST00000265272.5,ENST00000507386.1,ENST00000333010.6
exon_skip_445185	5	147023620:147023761:147024412:147024559:147027938:147028037	147024412:147024559	ENSG00000176049.11	ENST00000265272.5,ENST00000507386.1,ENST00000333010.6
exon_skip_445186	5	147027938:147028037:147029900:147030110:147040510:147041008	147029900:147030110	ENSG00000176049.11	ENST00000265272.5,ENST00000507386.1,ENST00000333010.6
exon_skip_445187	5	147040510:147041008:147051240:147051517:147162018:147162105	147051240:147051517	ENSG00000176049.11	ENST00000265272.5

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for JAKMIP2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_445178	5	146970924:146971249:146981303:146981374:146991868:146991934	146981303:146981374	ENSG00000176049.11	ENST00000507386.1,ENST00000333010.6
exon_skip_445181	5	146991868:146991934:146997473:146997677:147000228:147000306	146997473:146997677	ENSG00000176049.11	ENST00000507386.1,ENST00000265272.5,ENST00000333010.6
exon_skip_445182	5	146997473:146997677:147000228:147000306:147003183:147003252	147000228:147000306	ENSG00000176049.11	ENST00000507386.1,ENST00000265272.5,ENST00000333010.6
exon_skip_445183	5	147012242:147012341:147015784:147015847:147016527:147016611	147015784:147015847	ENSG00000176049.11	ENST00000265272.5,ENST00000333010.6,ENST00000504845.1
exon_skip_445184	5	147019194:147019323:147020266:147020386:147021270:147021327	147020266:147020386	ENSG00000176049.11	ENST00000507386.1,ENST00000265272.5,ENST00000333010.6
exon_skip_445185	5	147023620:147023761:147024412:147024559:147027938:147028037	147024412:147024559	ENSG00000176049.11	ENST00000507386.1,ENST00000265272.5,ENST00000333010.6
exon_skip_445186	5	147027938:147028037:147029900:147030110:147040510:147041008	147029900:147030110	ENSG00000176049.11	ENST00000507386.1,ENST00000265272.5,ENST00000333010.6
exon_skip_445187	5	147040510:147041008:147051240:147051517:147162018:147162105	147051240:147051517	ENSG00000176049.11	ENST00000265272.5

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 JAKMIP2

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
ENST00000265272	147051240	147051517	3UTR-3CDS
ENST00000265272	146997473	146997677	In-frame
ENST00000265272	147000228	147000306	In-frame
ENST00000265272	147015784	147015847	In-frame
ENST00000265272	147020266	147020386	In-frame
ENST00000265272	147024412	147024559	In-frame
ENST00000265272	147029900	147030110	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
ENST00000265272	147051240	147051517	3UTR-3CDS
ENST00000265272	146997473	146997677	In-frame
ENST00000265272	147000228	147000306	In-frame
ENST00000265272	147015784	147015847	In-frame
ENST00000265272	147020266	147020386	In-frame
ENST00000265272	147024412	147024559	In-frame
ENST00000265272	147029900	147030110	In-frame

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Infer the effects of exon skipping event on protein functional features for JAKMIP2

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
ENST00000265272	6018	810	147029900	147030110	1096	1305	209	279
ENST00000265272	6018	810	147024412	147024559	1405	1551	312	361
ENST00000265272	6018	810	147020266	147020386	1750	1869	427	467
ENST00000265272	6018	810	147015784	147015847	2083	2145	538	559
ENST00000265272	6018	810	147000228	147000306	2533	2610	688	714
ENST00000265272	6018	810	146997473	146997677	2611	2814	714	782

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
ENST00000265272	6018	810	147029900	147030110	1096	1305	209	279
ENST00000265272	6018	810	147024412	147024559	1405	1551	312	361
ENST00000265272	6018	810	147020266	147020386	1750	1869	427	467
ENST00000265272	6018	810	147015784	147015847	2083	2145	538	559
ENST00000265272	6018	810	147000228	147000306	2533	2610	688	714
ENST00000265272	6018	810	146997473	146997677	2611	2814	714	782

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
Q96AA8	209	279	1	810	Chain	ID=PRO_0000050762;Note=Janus kinase and microtubule-interacting protein 2
Q96AA8	209	279	207	244	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96AA8	312	361	1	810	Chain	ID=PRO_0000050762;Note=Janus kinase and microtubule-interacting protein 2
Q96AA8	312	361	280	419	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96AA8	312	361	315	315	Natural variant	ID=VAR_035930;Note=In a colorectal cancer sample%3B somatic mutation. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16959974;Dbxref=dbSNP:rs761359853,PMID:16959974
Q96AA8	427	467	1	810	Chain	ID=PRO_0000050762;Note=Janus kinase and microtubule-interacting protein 2
Q96AA8	538	559	539	559	Alternative sequence	ID=VSP_002430;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9628581;Dbxref=PMID:9628581
Q96AA8	538	559	1	810	Chain	ID=PRO_0000050762;Note=Janus kinase and microtubule-interacting protein 2
Q96AA8	538	559	468	597	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96AA8	688	714	1	810	Chain	ID=PRO_0000050762;Note=Janus kinase and microtubule-interacting protein 2
Q96AA8	688	714	664	808	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96AA8	714	782	1	810	Chain	ID=PRO_0000050762;Note=Janus kinase and microtubule-interacting protein 2
Q96AA8	714	782	664	808	Coiled coil	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
Q96AA8	209	279	1	810	Chain	ID=PRO_0000050762;Note=Janus kinase and microtubule-interacting protein 2
Q96AA8	209	279	207	244	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96AA8	312	361	1	810	Chain	ID=PRO_0000050762;Note=Janus kinase and microtubule-interacting protein 2
Q96AA8	312	361	280	419	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96AA8	312	361	315	315	Natural variant	ID=VAR_035930;Note=In a colorectal cancer sample%3B somatic mutation. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16959974;Dbxref=dbSNP:rs761359853,PMID:16959974
Q96AA8	427	467	1	810	Chain	ID=PRO_0000050762;Note=Janus kinase and microtubule-interacting protein 2
Q96AA8	538	559	539	559	Alternative sequence	ID=VSP_002430;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:9628581;Dbxref=PMID:9628581
Q96AA8	538	559	1	810	Chain	ID=PRO_0000050762;Note=Janus kinase and microtubule-interacting protein 2
Q96AA8	538	559	468	597	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96AA8	688	714	1	810	Chain	ID=PRO_0000050762;Note=Janus kinase and microtubule-interacting protein 2
Q96AA8	688	714	664	808	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255
Q96AA8	714	782	1	810	Chain	ID=PRO_0000050762;Note=Janus kinase and microtubule-interacting protein 2
Q96AA8	714	782	664	808	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for JAKMIP2

- 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-VQ-AA6K-01	exon_skip_445181	146997474	146997677	146997615	146997615	Frame_Shift_Del	A	-	p.F735fs
STAD	TCGA-VQ-AA6K-01	exon_skip_445181	146997474	146997677	146997615	146997615	Frame_Shift_Del	A	-	p.G736fs
LIHC	TCGA-DD-A3A0-01	exon_skip_445182	147000229	147000306	147000286	147000286	Frame_Shift_Del	T	-	p.K695fs
LIHC	TCGA-DD-A1EG-01	exon_skip_445183	147015785	147015847	147015816	147015816	Frame_Shift_Del	A	-	p.F549fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_445183	147015785	147015847	147015816	147015816	Frame_Shift_Del	A	-	p.F549fs
COAD	TCGA-G4-6302-01	exon_skip_445181	146997474	146997677	146997590	146997590	Nonsense_Mutation	G	A	p.Q744X
HNSC	TCGA-P3-A5QF-01	exon_skip_445184	147020267	147020386	147020328	147020328	Nonsense_Mutation	G	T	p.S447*
SKCM	TCGA-EE-A3J5-06	exon_skip_445186	147029901	147030110	147029951	147029951	Nonsense_Mutation	G	A	p.R263*
SKCM	TCGA-EE-A3J5-06	exon_skip_445186	147029901	147030110	147029951	147029951	Nonsense_Mutation	G	A	p.R263X
LUAD	TCGA-44-7667-01	exon_skip_445187	147051241	147051517	147051255	147051255	Nonsense_Mutation	G	A	p.Q39*
THCA	TCGA-DJ-A2Q0-01	exon_skip_445187	147051241	147051517	147051354	147051354	Nonsense_Mutation	G	A	p.R6*
THCA	TCGA-DJ-A2Q0-01	exon_skip_445187	147051241	147051517	147051354	147051354	Nonsense_Mutation	G	A	p.R6X
UCEC	TCGA-AP-A059-01	exon_skip_445187	147051241	147051517	147051354	147051354	Nonsense_Mutation	G	A	p.R6*

- 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
LNCAPCLONEFGC_PROSTATE	146997474	146997677	146997484	146997484	Missense_Mutation	T	A	p.Q779L
KMS21BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	146997474	146997677	146997496	146997496	Missense_Mutation	T	A	p.E775V
SNUC4_LARGE_INTESTINE	146997474	146997677	146997496	146997496	Missense_Mutation	T	A	p.E775V
COLO792_SKIN	146997474	146997677	146997668	146997668	Missense_Mutation	C	T	p.E718K
JHUEM7_ENDOMETRIUM	147000229	147000306	147000288	147000288	Missense_Mutation	T	G	p.K695Q
SW480_LARGE_INTESTINE	147020267	147020386	147020271	147020271	Missense_Mutation	T	A	p.D466V
JHUEM7_ENDOMETRIUM	147020267	147020386	147020368	147020368	Missense_Mutation	A	G	p.F434L
ONS76_CENTRAL_NERVOUS_SYSTEM	147024413	147024559	147024460	147024460	Missense_Mutation	G	A	p.R346C
M14_SKIN	147024413	147024559	147024489	147024489	Missense_Mutation	C	T	p.R336K
HMC18_BREAST	147024413	147024559	147024496	147024496	Missense_Mutation	C	A	p.A334S
HEC59_ENDOMETRIUM	147024413	147024559	147024522	147024522	Missense_Mutation	G	T	p.P325H
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	147024413	147024559	147024547	147024547	Missense_Mutation	G	A	p.R317W
MCF7_BREAST	147029901	147030110	147029945	147029945	Missense_Mutation	T	C	p.I265V
NO11_CENTRAL_NERVOUS_SYSTEM	147029901	147030110	147029995	147029995	Missense_Mutation	A	G	p.L248P
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	147029901	147030110	147029995	147029995	Missense_Mutation	A	G	p.L248P
ONS76_CENTRAL_NERVOUS_SYSTEM	147029901	147030110	147030015	147030015	Missense_Mutation	C	A	p.K241N
YD38_UPPER_AERODIGESTIVE_TRACT	147029901	147030110	147030062	147030062	Missense_Mutation	C	T	p.E226K
KU1919_URINARY_TRACT	147029901	147030110	147030070	147030070	Missense_Mutation	A	T	p.L223Q
DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	147051241	147051517	147051312	147051312	Missense_Mutation	G	T	p.Q20K
HT115_LARGE_INTESTINE	147051241	147051517	147051353	147051353	Missense_Mutation	C	T	p.R6Q
HEC151_ENDOMETRIUM	147051241	147051517	147051363	147051363	Missense_Mutation	T	C	p.K3E
ZR7530_BREAST	147024413	147024559	147024454	147024454	Nonsense_Mutation	C	A	p.E348*
BL41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	147000229	147000306	147000229	147000229	Splice_Site	C	A	p.M714I
HEC59_ENDOMETRIUM	147015785	147015847	147015785	147015785	Splice_Site	C	A	p.K559N
SKUT1_SOFT_TISSUE	147015785	147015847	147015786	147015786	Splice_Site	T	-	p.K559fs

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for JAKMIP2

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 JAKMIP2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for JAKMIP2

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RelatedDrugs for JAKMIP2

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 JAKMIP2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
JAKMIP2	C0025202	melanoma	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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