ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for PRDM16

Gene summary

Gene information	Gene symbol	PRDM16
	Gene ID	63976
	Gene name	PR/SET domain 16
	Synonyms	CMD1LL\|KMT8F\|LVNC8\|MEL1\|PFM13
	Cytomap	1p36.32
	Type of gene	protein-coding
	Description	PR domain zinc finger protein 16MDS1/EVI1-like gene 1PR domain 16PR domain containing 16transcription factor MEL1
	Modification date	20180522
	UniProtAcc	Q9HAZ2
	Context	PubMed: PRDM16 [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
PRDM16	GO:0000122	negative regulation of transcription by RNA polymerase II	19049980
PRDM16	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	14656887
PRDM16	GO:0045892	negative regulation of transcription, DNA-templated	12816872
PRDM16	GO:0045893	positive regulation of transcription, DNA-templated	25578880

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Exon skipping events across known transcript of Ensembl for PRDM16 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 PRDM16

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 PRDM16

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_531	1	2985774:2985860:3102688:3103038:3160650:3160701	3102688:3103038	ENSG00000142611.12	ENST00000270722.5,ENST00000378391.2,ENST00000514189.1,ENST00000441472.2,ENST00000442529.2,ENST00000378398.3
exon_skip_532	1	3160695:3160701:3301712:3301850:3313054:3313157	3301712:3301850	ENSG00000142611.12	ENST00000511072.1,ENST00000514189.1
exon_skip_533	1	3160695:3160701:3301715:3301850:3313054:3313157	3301715:3301850	ENSG00000142611.12	ENST00000270722.5,ENST00000378391.2,ENST00000512462.1,ENST00000441472.2,ENST00000442529.2
exon_skip_535	1	3347435:3347672:3348529:3348704:3350240:3350489	3348529:3348704	ENSG00000142611.12	ENST00000270722.5,ENST00000509860.1,ENST00000512462.1,ENST00000441472.2,ENST00000378398.3
exon_skip_536	1	3347435:3347672:3348529:3348704:3350297:3351985	3348529:3348704	ENSG00000142611.12	ENST00000378391.2,ENST00000442529.2

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for PRDM16

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_531	1	2985774:2985860:3102688:3103038:3160650:3160701	3102688:3103038	ENSG00000142611.12	ENST00000378398.3,ENST00000441472.2,ENST00000442529.2,ENST00000378391.2,ENST00000514189.1,ENST00000270722.5
exon_skip_532	1	3160695:3160701:3301712:3301850:3313054:3313157	3301712:3301850	ENSG00000142611.12	ENST00000511072.1,ENST00000514189.1
exon_skip_533	1	3160695:3160701:3301715:3301850:3313054:3313157	3301715:3301850	ENSG00000142611.12	ENST00000441472.2,ENST00000442529.2,ENST00000378391.2,ENST00000270722.5,ENST00000512462.1
exon_skip_535	1	3347435:3347672:3348529:3348704:3350240:3350489	3348529:3348704	ENSG00000142611.12	ENST00000378398.3,ENST00000441472.2,ENST00000270722.5,ENST00000512462.1,ENST00000509860.1
exon_skip_536	1	3347435:3347672:3348529:3348704:3350297:3351985	3348529:3348704	ENSG00000142611.12	ENST00000442529.2,ENST00000378391.2

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 PRDM16

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
ENST00000270722	3102688	3103038	Frame-shift
ENST00000270722	3348529	3348704	Frame-shift
ENST00000270722	3301715	3301850	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
ENST00000270722	3102688	3103038	Frame-shift
ENST00000270722	3348529	3348704	Frame-shift
ENST00000270722	3301715	3301850	In-frame

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Infer the effects of exon skipping event on protein functional features for PRDM16

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
ENST00000270722	8707	1276	3301715	3301850	488	622	146	191

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
ENST00000270722	8707	1276	3301715	3301850	488	622	146	191

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
Q9HAZ2	146	191	1	184	Alternative sequence	ID=VSP_038063;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9HAZ2	146	191	191	191	Alternative sequence	ID=VSP_038064;Note=In isoform 3. Q->QV;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
Q9HAZ2	146	191	161	163	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N1I
Q9HAZ2	146	191	183	188	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N1I
Q9HAZ2	146	191	191	198	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N1I
Q9HAZ2	146	191	1	1276	Chain	ID=PRO_0000047773;Note=PR domain zinc finger protein 16
Q9HAZ2	146	191	82	211	Domain	Note=SET;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00190
Q9HAZ2	146	191	167	170	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N1I
Q9HAZ2	146	191	178	180	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N1I
Q9HAZ2	146	191	153	155	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N1I

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
Q9HAZ2	146	191	1	184	Alternative sequence	ID=VSP_038063;Note=In isoform 4. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9HAZ2	146	191	191	191	Alternative sequence	ID=VSP_038064;Note=In isoform 3. Q->QV;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.2
Q9HAZ2	146	191	161	163	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N1I
Q9HAZ2	146	191	183	188	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N1I
Q9HAZ2	146	191	191	198	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N1I
Q9HAZ2	146	191	1	1276	Chain	ID=PRO_0000047773;Note=PR domain zinc finger protein 16
Q9HAZ2	146	191	82	211	Domain	Note=SET;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00190
Q9HAZ2	146	191	167	170	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N1I
Q9HAZ2	146	191	178	180	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N1I
Q9HAZ2	146	191	153	155	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2N1I

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SNVs in the skipped exons for PRDM16

- 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_531	3102689	3103038	3102721	3102721	Frame_Shift_Del	C	-	p.P24fs
LIHC	TCGA-DD-A1EG-01	exon_skip_531	3102689	3103038	3102939	3102939	Frame_Shift_Del	G	-	p.L96fs
BLCA	TCGA-DK-A3WW-01	exon_skip_535 exon_skip_536	3348530	3348704	3348546	3348546	Nonsense_Mutation	G	T	p.E1180*

- 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
MDAPCA2B_PROSTATE	3102689	3103038	3102984	3102984	Frame_Shift_Del	C	-	p.G111fs
HEC1A_ENDOMETRIUM	3301716	3301850	3301765	3301766	Frame_Shift_Ins	-	G	p.AG163fs
HEC1A_ENDOMETRIUM	3301713	3301850	3301765	3301766	Frame_Shift_Ins	-	G	p.AG163fs
SNU349_KIDNEY	3102689	3103038	3102694	3102694	Missense_Mutation	G	A	p.G15S
HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	3102689	3103038	3102712	3102712	Missense_Mutation	A	G	p.M21V
L428_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	3102689	3103038	3102727	3102727	Missense_Mutation	C	T	p.R26W
SW684_SOFT_TISSUE	3102689	3103038	3102729	3102730	Missense_Mutation	GG	AA	p.D27N
KM12_LARGE_INTESTINE	3102689	3103038	3102752	3102752	Missense_Mutation	C	T	p.A34V
KGN_OVARY	3102689	3103038	3102760	3102760	Missense_Mutation	G	A	p.E37K
OCIM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	3102689	3103038	3102778	3102778	Missense_Mutation	A	G	p.M43V
NCIH508_LARGE_INTESTINE	3102689	3103038	3102833	3102833	Missense_Mutation	C	T	p.T61I
MFE319_ENDOMETRIUM	3102689	3103038	3102863	3102863	Missense_Mutation	C	T	p.P71L
UPCISCC152_UPPER_AERODIGESTIVE_TRACT	3102689	3103038	3102911	3102911	Missense_Mutation	G	A	p.R87Q
SCC90_UPPER_AERODIGESTIVE_TRACT	3102689	3103038	3102911	3102911	Missense_Mutation	G	A	p.R87Q
SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	3102689	3103038	3102915	3102915	Missense_Mutation	G	T	p.E88D
TTC466_BONE	3102689	3103038	3102921	3102922	Missense_Mutation	CA	AT	p.I91F
YD15_SALIVARY_GLAND	3102689	3103038	3102928	3102928	Missense_Mutation	G	A	p.G93R
CP66MEL_SKIN	3102689	3103038	3103010	3103010	Missense_Mutation	C	T	p.A120V
HEC6_ENDOMETRIUM	3301716	3301850	3301765	3301765	Missense_Mutation	C	T	p.A163V
HEC6_ENDOMETRIUM	3301713	3301850	3301765	3301765	Missense_Mutation	C	T	p.A163V
NO10_CENTRAL_NERVOUS_SYSTEM	3301716	3301850	3301765	3301765	Missense_Mutation	C	T	p.A163V
NO10_CENTRAL_NERVOUS_SYSTEM	3301713	3301850	3301765	3301765	Missense_Mutation	C	T	p.A163V
HEC251_ENDOMETRIUM	3301716	3301850	3301789	3301789	Missense_Mutation	A	G	p.Y171C
HEC251_ENDOMETRIUM	3301713	3301850	3301789	3301789	Missense_Mutation	A	G	p.Y171C
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	3301716	3301850	3301810	3301810	Missense_Mutation	G	T	p.C178F
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	3301713	3301850	3301810	3301810	Missense_Mutation	G	T	p.C178F
BCPAP_THYROID	3301716	3301850	3301838	3301838	Missense_Mutation	G	C	p.Q187H
BCPAP_THYROID	3301713	3301850	3301838	3301838	Missense_Mutation	G	C	p.Q187H
MON_SOFT_TISSUE	3301716	3301850	3301842	3301842	Missense_Mutation	A	G	p.S189G
MON_SOFT_TISSUE	3301713	3301850	3301842	3301842	Missense_Mutation	A	G	p.S189G
BICR18_UPPER_AERODIGESTIVE_TRACT	3348530	3348704	3348574	3348574	Missense_Mutation	T	C	p.M1189T
PK45H_PANCREAS	3348530	3348704	3348631	3348631	Missense_Mutation	T	C	p.V1208A
AN3CA_ENDOMETRIUM	3348530	3348704	3348661	3348661	Missense_Mutation	C	A	p.S1218Y
22RV1_PROSTATE	3348530	3348704	3348678	3348678	Missense_Mutation	A	G	p.T1224A
CW2_LARGE_INTESTINE	3348530	3348704	3348685	3348685	Missense_Mutation	G	A	p.C1226Y

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PRDM16

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 PRDM16

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PRDM16

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RelatedDrugs for PRDM16

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 PRDM16

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
PRDM16	C0149931	Migraine Disorders	1	CTD_human
PRDM16	C3809288	LEFT VENTRICULAR NONCOMPACTION 8	1	ORPHANET;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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