ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for PAAF1

Gene summary

Gene information	Gene symbol	PAAF1
	Gene ID	80227
	Gene name	proteasomal ATPase associated factor 1
	Synonyms	PAAF\|Rpn14\|WDR71
	Cytomap	11q13.4
	Type of gene	protein-coding
	Description	proteasomal ATPase-associated factor 1WD repeat domain 71WD repeat-containing protein 71
	Modification date	20180525
	UniProtAcc	Q9BRP4
	Context	PubMed: PAAF1 [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 PAAF1 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 PAAF1

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 PAAF1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_63472	11	73588072:73588113:73589823:73589864:73598398:73598502	73589823:73589864	ENSG00000175575.8	ENST00000310571.3
exon_skip_63475	11	73588072:73588113:73589827:73589864:73598398:73598502	73589827:73589864	ENSG00000175575.8	ENST00000542293.1
exon_skip_63478	11	73589827:73589864:73597973:73598144:73598398:73598502	73597973:73598144	ENSG00000175575.8	ENST00000504441.2
exon_skip_63479	11	73589827:73589864:73598075:73598144:73598398:73598502	73598075:73598144	ENSG00000175575.8	ENST00000536003.1
exon_skip_63481	11	73589827:73589864:73598084:73598144:73598398:73598502	73598084:73598144	ENSG00000175575.8	ENST00000544552.1,ENST00000543814.1
exon_skip_63489	11	73598398:73598502:73602156:73602246:73610190:73610289	73602156:73602246	ENSG00000175575.8	ENST00000546039.1,ENST00000543079.1,ENST00000535604.1,ENST00000504441.2,ENST00000544552.1,ENST00000536003.1,ENST00000542293.1,ENST00000536582.1,ENST00000376384.5,ENST00000310571.3,ENST00000541951.1,ENST00000543814.1
exon_skip_63491	11	73610190:73610289:73611314:73611465:73620443:73620557	73611314:73611465	ENSG00000175575.8	ENST00000535604.1,ENST00000544909.1,ENST00000504441.2,ENST00000544552.1,ENST00000536003.1,ENST00000542293.1,ENST00000376384.5,ENST00000310571.3,ENST00000541951.1,ENST00000543814.1
exon_skip_63492	11	73610190:73610289:73611355:73611465:73620443:73620557	73611355:73611465	ENSG00000175575.8	ENST00000546039.1
exon_skip_63493	11	73611412:73611465:73620443:73620638:73625457:73625492	73620443:73620638	ENSG00000175575.8	ENST00000546039.1,ENST00000535604.1,ENST00000544909.1,ENST00000504441.2,ENST00000544552.1,ENST00000536003.1,ENST00000376384.5,ENST00000310571.3,ENST00000541951.1,ENST00000543814.1
exon_skip_63494	11	73611412:73611465:73620443:73620638:73627589:73627661	73620443:73620638	ENSG00000175575.8	ENST00000540659.1
exon_skip_63497	11	73620443:73620638:73625457:73625549:73627589:73627661	73625457:73625549	ENSG00000175575.8	ENST00000546039.1,ENST00000535604.1,ENST00000544909.1,ENST00000544552.1,ENST00000536003.1,ENST00000376384.5,ENST00000310571.3,ENST00000541951.1
exon_skip_63498	11	73627589:73627705:73629994:73630077:73635659:73635742	73629994:73630077	ENSG00000175575.8	ENST00000535604.1,ENST00000544909.1,ENST00000544552.1,ENST00000536003.1,ENST00000376384.5,ENST00000310571.3,ENST00000541951.1
exon_skip_63501	11	73629994:73630077:73635659:73635742:73638329:73638615	73635659:73635742	ENSG00000175575.8	ENST00000535604.1,ENST00000544909.1,ENST00000544552.1,ENST00000536003.1,ENST00000376384.5,ENST00000310571.3,ENST00000541951.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for PAAF1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_63472	11	73588072:73588113:73589823:73589864:73598398:73598502	73589823:73589864	ENSG00000175575.8	ENST00000310571.3
exon_skip_63475	11	73588072:73588113:73589827:73589864:73598398:73598502	73589827:73589864	ENSG00000175575.8	ENST00000542293.1
exon_skip_63478	11	73589827:73589864:73597973:73598144:73598398:73598502	73597973:73598144	ENSG00000175575.8	ENST00000504441.2
exon_skip_63479	11	73589827:73589864:73598075:73598144:73598398:73598502	73598075:73598144	ENSG00000175575.8	ENST00000536003.1
exon_skip_63481	11	73589827:73589864:73598084:73598144:73598398:73598502	73598084:73598144	ENSG00000175575.8	ENST00000543814.1,ENST00000544552.1
exon_skip_63489	11	73598398:73598502:73602156:73602246:73610190:73610289	73602156:73602246	ENSG00000175575.8	ENST00000541951.1,ENST00000310571.3,ENST00000504441.2,ENST00000543814.1,ENST00000535604.1,ENST00000542293.1,ENST00000536003.1,ENST00000544552.1,ENST00000546039.1,ENST00000376384.5,ENST00000543079.1,ENST00000536582.1
exon_skip_63491	11	73610190:73610289:73611314:73611465:73620443:73620557	73611314:73611465	ENSG00000175575.8	ENST00000541951.1,ENST00000310571.3,ENST00000504441.2,ENST00000543814.1,ENST00000535604.1,ENST00000542293.1,ENST00000536003.1,ENST00000544552.1,ENST00000376384.5,ENST00000544909.1
exon_skip_63492	11	73610190:73610289:73611355:73611465:73620443:73620557	73611355:73611465	ENSG00000175575.8	ENST00000546039.1
exon_skip_63493	11	73611412:73611465:73620443:73620638:73625457:73625492	73620443:73620638	ENSG00000175575.8	ENST00000541951.1,ENST00000310571.3,ENST00000504441.2,ENST00000543814.1,ENST00000535604.1,ENST00000536003.1,ENST00000544552.1,ENST00000546039.1,ENST00000376384.5,ENST00000544909.1
exon_skip_63494	11	73611412:73611465:73620443:73620638:73627589:73627661	73620443:73620638	ENSG00000175575.8	ENST00000540659.1
exon_skip_63497	11	73620443:73620638:73625457:73625549:73627589:73627661	73625457:73625549	ENSG00000175575.8	ENST00000541951.1,ENST00000310571.3,ENST00000535604.1,ENST00000536003.1,ENST00000544552.1,ENST00000546039.1,ENST00000376384.5,ENST00000544909.1
exon_skip_63498	11	73627589:73627705:73629994:73630077:73635659:73635742	73629994:73630077	ENSG00000175575.8	ENST00000541951.1,ENST00000310571.3,ENST00000535604.1,ENST00000536003.1,ENST00000544552.1,ENST00000376384.5,ENST00000544909.1
exon_skip_63501	11	73629994:73630077:73635659:73635742:73638329:73638615	73635659:73635742	ENSG00000175575.8	ENST00000541951.1,ENST00000310571.3,ENST00000535604.1,ENST00000536003.1,ENST00000544552.1,ENST00000376384.5,ENST00000544909.1

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 PAAF1

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
ENST00000310571	73589823	73589864	Frame-shift
ENST00000310571	73611314	73611465	Frame-shift
ENST00000310571	73625457	73625549	Frame-shift
ENST00000310571	73629994	73630077	Frame-shift
ENST00000310571	73635659	73635742	Frame-shift
ENST00000310571	73602156	73602246	In-frame
ENST00000310571	73620443	73620638	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
ENST00000310571	73589823	73589864	Frame-shift
ENST00000310571	73611314	73611465	Frame-shift
ENST00000310571	73625457	73625549	Frame-shift
ENST00000310571	73629994	73630077	Frame-shift
ENST00000310571	73635659	73635742	Frame-shift
ENST00000310571	73602156	73602246	In-frame
ENST00000310571	73620443	73620638	In-frame

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Infer the effects of exon skipping event on protein functional features for PAAF1

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
ENST00000310571	1621	392	73602156	73602246	246	335	64	94
ENST00000310571	1621	392	73620443	73620638	586	780	177	242

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
ENST00000310571	1621	392	73602156	73602246	246	335	64	94
ENST00000310571	1621	392	73620443	73620638	586	780	177	242

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

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

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SNVs in the skipped exons for PAAF1

- 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.

PAAF1_CESC_exon_skip_63491_psi_boxplot.png
boxplot

- 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
ESCA	TCGA-VR-A8EO-01	exon_skip_63489	73602157	73602246	73602202	73602202	Frame_Shift_Del	T	-	p.L81fs
LIHC	TCGA-DD-A3A0-01	exon_skip_63493 exon_skip_63494	73620444	73620638	73620621	73620621	Frame_Shift_Del	C	-	p.S238fs
CESC	TCGA-IR-A3LK-01	exon_skip_63491 exon_skip_63492	73611315	73611465	73611423	73611423	Nonsense_Mutation	G	T	p.E164*
CESC	TCGA-IR-A3LK-01	exon_skip_63491 exon_skip_63492	73611356	73611465	73611423	73611423	Nonsense_Mutation	G	T	p.E164*
THYM	TCGA-X7-A8DC-01	exon_skip_63493 exon_skip_63494	73620444	73620638	73620512	73620512	Nonsense_Mutation	C	T	p.R201X
THYM	TCGA-ZC-AAAA-01	exon_skip_63498	73629995	73630077	73630023	73630023	Nonsense_Mutation	G	T	p.G322X

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-IR-A3LK-01
	Cancer type: CESC
	ESID: exon_skip_63492
	Skipped exon start: 73611315
	Skipped exon end: 73611465
	Mutation start: 73611423
	Mutation end: 73611423
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: T
	AAchange: p.E164*
	Sample: TCGA-IR-A3LK-01
	Cancer type: CESC
	ESID: exon_skip_63492
	Skipped exon start: 73611356
	Skipped exon end: 73611465
	Mutation start: 73611423
	Mutation end: 73611423
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: T
	AAchange: p.E164*
exon_skip_129969_CESC_TCGA-IR-A3LK-01.png
exon_skip_131474_CESC_TCGA-IR-A3LK-01.png
exon_skip_435729_CESC_TCGA-IR-A3LK-01.png
exon_skip_457524_CESC_TCGA-IR-A3LK-01.png
exon_skip_63491_CESC_TCGA-IR-A3LK-01.png
exon_skip_71523_CESC_TCGA-IR-A3LK-01.png
exon_skip_7830_CESC_TCGA-IR-A3LK-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
KMH2_THYROID	73620444	73620638	73620600	73620607	Frame_Shift_Del	ACAACTCC	-	p.DNS230fs
SUIT2_PANCREAS	73635660	73635742	73635694	73635694	Frame_Shift_Del	A	-	p.L351fs
NCIH2073_LUNG	73602157	73602246	73602226	73602226	Missense_Mutation	T	C	p.S88P
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	73611315	73611465	73611381	73611381	Missense_Mutation	C	A	p.L150M
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	73611356	73611465	73611381	73611381	Missense_Mutation	C	A	p.L150M
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	73611315	73611465	73611426	73611426	Missense_Mutation	G	T	p.D165Y
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	73611356	73611465	73611426	73611426	Missense_Mutation	G	T	p.D165Y
HCC2450_LUNG	73620444	73620638	73620513	73620513	Missense_Mutation	G	A	p.R201Q
HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	73620444	73620638	73620530	73620530	Missense_Mutation	C	T	p.R207C
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	73620444	73620638	73620603	73620604	Missense_Mutation	AC	CT	p.N231T
MDAMB361_BREAST	73625458	73625549	73625530	73625530	Missense_Mutation	G	C	p.G267A
HS683_CENTRAL_NERVOUS_SYSTEM	73629995	73630077	73630039	73630039	Missense_Mutation	C	T	p.S327F
L363_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	73635660	73635742	73635662	73635662	Missense_Mutation	G	A	p.D341N
LNCAPCLONEFGC_PROSTATE	73635660	73635742	73635686	73635686	Nonsense_Mutation	C	T	p.Q349*
SNU1040_LARGE_INTESTINE	73589828	73589864	73589863	73589863	Splice_Site	A	G	p.P29P
SNU1040_LARGE_INTESTINE	73589824	73589864	73589863	73589863	Splice_Site	A	G	p.P29P

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PAAF1

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_63491	11	73610190:73610289:73611314:73611465:73620443:73620557	73611314:73611465	ENST00000535604.1,ENST00000544909.1,ENST00000504441.2,ENST00000544552.1,ENST00000536003.1,ENST00000542293.1,ENST00000376384.5,ENST00000310571.3,ENST00000541951.1,ENST00000543814.1	LUAD	rs2067912	chr11:73611349	C/G	4.62e-04
exon_skip_63491	11	73610190:73610289:73611314:73611465:73620443:73620557	73611314:73611465	ENST00000535604.1,ENST00000544909.1,ENST00000504441.2,ENST00000544552.1,ENST00000536003.1,ENST00000542293.1,ENST00000376384.5,ENST00000310571.3,ENST00000541951.1,ENST00000543814.1	LUAD	rs2067912	chr11:73611349	C/G	5.73e-04
exon_skip_63493	11	73611412:73611465:73620443:73620638:73625457:73625492	73620443:73620638	ENST00000546039.1,ENST00000535604.1,ENST00000544909.1,ENST00000504441.2,ENST00000544552.1,ENST00000536003.1,ENST00000376384.5,ENST00000310571.3,ENST00000541951.1,ENST00000543814.1	BRCA	rs3741138	chr11:73620537	C/G	6.08e-04
exon_skip_63493	11	73611412:73611465:73620443:73620638:73625457:73625492	73620443:73620638	ENST00000546039.1,ENST00000535604.1,ENST00000544909.1,ENST00000504441.2,ENST00000544552.1,ENST00000536003.1,ENST00000376384.5,ENST00000310571.3,ENST00000541951.1,ENST00000543814.1	BRCA	rs3741138	chr11:73620537	C/G	8.73e-04
exon_skip_63493	11	73611412:73611465:73620443:73620638:73625457:73625492	73620443:73620638	ENST00000546039.1,ENST00000535604.1,ENST00000544909.1,ENST00000504441.2,ENST00000544552.1,ENST00000536003.1,ENST00000376384.5,ENST00000310571.3,ENST00000541951.1,ENST00000543814.1	LGG	rs3741138	chr11:73620537	C/G	2.87e-04
exon_skip_63493	11	73611412:73611465:73620443:73620638:73625457:73625492	73620443:73620638	ENST00000546039.1,ENST00000535604.1,ENST00000544909.1,ENST00000504441.2,ENST00000544552.1,ENST00000536003.1,ENST00000376384.5,ENST00000310571.3,ENST00000541951.1,ENST00000543814.1	LGG	rs3741138	chr11:73620537	C/G	3.53e-04
exon_skip_63494	11	73611412:73611465:73620443:73620638:73627589:73627661	73620443:73620638	ENST00000540659.1	BRCA	rs3741138	chr11:73620537	C/G	6.08e-04
exon_skip_63494	11	73611412:73611465:73620443:73620638:73627589:73627661	73620443:73620638	ENST00000540659.1	BRCA	rs3741138	chr11:73620537	C/G	8.73e-04
exon_skip_63494	11	73611412:73611465:73620443:73620638:73627589:73627661	73620443:73620638	ENST00000540659.1	LGG	rs3741138	chr11:73620537	C/G	2.87e-04
exon_skip_63494	11	73611412:73611465:73620443:73620638:73627589:73627661	73620443:73620638	ENST00000540659.1	LGG	rs3741138	chr11:73620537	C/G	3.53e-04

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PAAF1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PAAF1

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RelatedDrugs for PAAF1

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 PAAF1

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 PAAF1

Exon skipping events across known transcript of Ensembl for PAAF1 from UCSC genome browser

Gene isoform structures and expression levels for PAAF1

Exon skipping events with PSIs in TCGA for PAAF1

Exon skipping events with PSIs in GTEx for PAAF1

Open reading frame (ORF) annotation in the exon skipping event for PAAF1

Infer the effects of exon skipping event on protein functional features for PAAF1

SNVs in the skipped exons for PAAF1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PAAF1

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PAAF1

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PAAF1

RelatedDrugs for PAAF1

RelatedDiseases for PAAF1