ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for PBRM1

Gene summary

Gene information	Gene symbol	PBRM1
	Gene ID	55193
	Gene name	polybromo 1
	Synonyms	BAF180\|PB1
	Cytomap	3p21.1
	Type of gene	protein-coding
	Description	protein polybromo-1BRG1-associated factor 180polybromo-1D
	Modification date	20200313
	UniProtAcc	C9J053, C9J409, C9J9L6, C9JCJ2, C9JPI5, C9JQF1, E7EVG2, H0Y5B5, Q86U86,
	Context

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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Gene structures and expression levels for PBRM1

Skipped exons in the ROSMAP, MSBB, and Mayo 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.

ENSG00000163939

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
CB	UP	ENST00000337303.8	PBRM1-202:protein_coding:PBRM1	2.367286e+01	2.996713e+00	4.484263e-03	1.799489e-02
TC	UP	ENST00000337303.8	PBRM1-202:protein_coding:PBRM1	1.438455e+01	1.738935e+00	6.034080e-03	3.853229e-02

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PBRM1

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_118452	chr3	52554783:52554879:52558249:52558413:52561767:52561968	52558249:52558413
exon_skip_121065	chr3	52550747:52550817:52558249:52558413:52561767:52561801	52558249:52558413
exon_skip_141175	chr3	52627273:52627370:52628894:52629035:52634602:52634815	52628894:52629035
exon_skip_150681	chr3	52617262:52617538:52624897:52624941:52627273:52627370	52624897:52624941
exon_skip_170260	chr3	52679634:52679726:52682092:52682233:52685749:52685794	52682092:52682233
exon_skip_1755	chr3	52644704:52644789:52648344:52648442:52651742:52651810	52648344:52648442
exon_skip_177990	chr3	52634602:52634815:52641954:52642045:52644704:52644789	52641954:52642045
exon_skip_187271	chr3	52634602:52634815:52641954:52642045:52643248:52643343	52641954:52642045
exon_skip_19193	chr3	52564050:52564233:52576541:52576698:52579054:52579199	52576541:52576698
exon_skip_192496	chr3	52550747:52550817:52554724:52554879:52558249:52558413	52554724:52554879
exon_skip_205240	chr3	52681704:52681820:52682092:52682233:52685436:52685578	52682092:52682233
exon_skip_215973	chr3	52550747:52550817:52554724:52554879:52561767:52561801	52554724:52554879
exon_skip_226173	chr3	52550747:52550817:52554724:52554879:52561767:52561968	52554724:52554879
exon_skip_229316	chr3	52589070:52589255:52603521:52603732:52609313:52609461	52603521:52603732
exon_skip_267613	chr3	52662204:52662276:52668498:52668645:52678500:52678567	52668498:52668645
exon_skip_278107	chr3	52550747:52550817:52558249:52558413:52561767:52561968	52558249:52558413
exon_skip_279441	chr3	52609313:52609955:52615351:52615456:52617262:52617538	52615351:52615456
exon_skip_281553	chr3	52643248:52643343:52644704:52644789:52648344:52648442	52644704:52644789
exon_skip_284910	chr3	52682092:52682233:52684856:52684914:52685749:52685794	52684856:52684914
exon_skip_293980	chr3	52651764:52651810:52658199:52658315:52662133:52662276	52658199:52658315
exon_skip_35149	chr3	52648344:52648442:52651742:52651810:52658199:52658315	52651742:52651810
exon_skip_62650	chr3	52679583:52679723:52682092:52682233:52685749:52685794	52682092:52682233
exon_skip_6618	chr3	52641954:52642045:52643248:52643343:52644704:52644789	52643248:52643343
exon_skip_70094	chr3	52554783:52554879:52558249:52558413:52561767:52561801	52558249:52558413
exon_skip_78482	chr3	52679634:52679726:52681704:52681820:52682092:52682233	52681704:52681820
exon_skip_95498	chr3	52679574:52679723:52682092:52682233:52685749:52685836	52682092:52682233

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information	Tissue type	Avg(PSIs) in AD	Avg(PSIs) in control	Difference (PSI)	Adj. p-value
exon_skip_150681	MSBB_PG	1.799194e-01	3.136735e-01	-1.337541e-01	1.256157e-03
exon_skip_150681	Mayo_CB	2.497436e-01	3.861667e-01	-1.364231e-01	3.929560e-07

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Open reading frame (ORF) annotation in the exon skipping event for PBRM1

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000296302	52576541	52576698	Frame-shift
ENST00000296302	52603521	52603732	Frame-shift
ENST00000296302	52615351	52615456	Frame-shift
ENST00000296302	52628894	52629035	Frame-shift
ENST00000296302	52641954	52642045	Frame-shift
ENST00000296302	52668498	52668645	Frame-shift
ENST00000296302	52554724	52554879	In-frame
ENST00000296302	52558249	52558413	In-frame
ENST00000296302	52643248	52643343	In-frame
ENST00000296302	52648344	52648442	In-frame
ENST00000296302	52651742	52651810	In-frame
ENST00000296302	52658199	52658315	In-frame

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000296302	52576541	52576698	Frame-shift
ENST00000296302	52615351	52615456	Frame-shift
ENST00000296302	52628894	52629035	Frame-shift
ENST00000296302	52641954	52642045	Frame-shift
ENST00000296302	52668498	52668645	Frame-shift
ENST00000296302	52554724	52554879	In-frame
ENST00000296302	52558249	52558413	In-frame
ENST00000296302	52643248	52643343	In-frame
ENST00000296302	52648344	52648442	In-frame
ENST00000296302	52651742	52651810	In-frame
ENST00000296302	52658199	52658315	In-frame

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000296302	52576541	52576698	Frame-shift
ENST00000296302	52628894	52629035	Frame-shift
ENST00000296302	52641954	52642045	Frame-shift
ENST00000296302	52644704	52644789	Frame-shift
ENST00000296302	52668498	52668645	Frame-shift
ENST00000296302	52554724	52554879	In-frame
ENST00000296302	52558249	52558413	In-frame
ENST00000296302	52643248	52643343	In-frame
ENST00000296302	52648344	52648442	In-frame
ENST00000296302	52651742	52651810	In-frame
ENST00000296302	52658199	52658315	In-frame

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Infer the effects of exon skipping event on protein functional features for PBRM1

p-ENSG00000163939_img4.png
boxplot

Loci of skipped exons in ROSMAP 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
ENST00000296302	5162	1689	52658199	52658315	531	646	176	214
ENST00000296302	5162	1689	52651742	52651810	648	715	215	237
ENST00000296302	5162	1689	52648344	52648442	717	814	238	270
ENST00000296302	5162	1689	52643248	52643343	902	996	300	331
ENST00000296302	5162	1689	52558249	52558413	4291	4454	1429	1484
ENST00000296302	5162	1689	52554724	52554879	4456	4610	1484	1536

Loci of skipped exons in MSBB 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
ENST00000296302	5162	1689	52658199	52658315	531	646	176	214
ENST00000296302	5162	1689	52651742	52651810	648	715	215	237
ENST00000296302	5162	1689	52648344	52648442	717	814	238	270
ENST00000296302	5162	1689	52643248	52643343	902	996	300	331
ENST00000296302	5162	1689	52558249	52558413	4291	4454	1429	1484
ENST00000296302	5162	1689	52554724	52554879	4456	4610	1484	1536

Loci of skipped exons in Mayo 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
ENST00000296302	5162	1689	52658199	52658315	531	646	176	214
ENST00000296302	5162	1689	52651742	52651810	648	715	215	237
ENST00000296302	5162	1689	52648344	52648442	717	814	238	270
ENST00000296302	5162	1689	52643248	52643343	902	996	300	331
ENST00000296302	5162	1689	52558249	52558413	4291	4454	1429	1484
ENST00000296302	5162	1689	52554724	52554879	4456	4610	1484	1536

Lost protein functional features of individual exon skipping events in ROSMAP.

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
Q86U86	176	214	176	178	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KTB
Q86U86	176	214	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	176	214	210	210	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
Q86U86	176	214	200	270	Domain	Note=Bromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
Q86U86	176	214	179	195	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	176	214	206	208	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	176	214	178	178	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q86U86	176	214	202	202	Natural variant	ID=VAR_064660;Note=Found in a endometrial cancer cell line. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=dbSNP:rs765525545,PMID:21248752
Q86U86	176	214	206	206	Natural variant	ID=VAR_064661;Note=Found in hematopoietic and lymphoid cancer cell lines. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	176	214	214	216	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	215	237	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	215	237	200	270	Domain	Note=Bromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
Q86U86	215	237	218	223	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	215	237	230	239	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	215	237	226	226	Natural variant	ID=VAR_064662;Note=Found in hematopoietic and lymphoid cancer cell lines. E->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	215	237	228	228	Natural variant	ID=VAR_064663;Note=Found in a breast cancer cell line. I->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=dbSNP:rs201022657,PMID:21248752
Q86U86	215	237	232	232	Natural variant	ID=VAR_064664;Note=Found in a case of clear cell renal carcinoma%3B somatic mutation. T->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	215	237	233	233	Natural variant	ID=VAR_064665;Note=Found in a renal carcinoma cell line. I->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	215	237	214	216	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	238	270	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	238	270	200	270	Domain	Note=Bromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
Q86U86	238	270	230	239	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	238	270	245	262	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	238	270	268	291	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	238	270	256	256	Natural variant	ID=VAR_064666;Note=Found in an ovary carcinoma cell line. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=dbSNP:rs776146971,PMID:21248752
Q86U86	238	270	242	242	Sequence conflict	Note=Y->C;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q86U86	238	270	251	251	Sequence conflict	Note=D->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q86U86	300	331	300	332	Alternative sequence	ID=VSP_015231;Note=In isoform 3. RTPSNLAAARLTGPSHSKGSLGEERNPTSKYYR->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12487023;Dbxref=PMID:12487023
Q86U86	300	331	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	300	331	316	316	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q86U86	300	331	319	319	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q86U86	1429	1484	857	1689	Alternative sequence	ID=VSP_015232;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12487023;Dbxref=PMID:12487023
Q86U86	1429	1484	1430	1484	Alternative sequence	ID=VSP_015235;Note=In isoform 2%2C isoform 3%2C isoform 4%2C isoform 5%2C isoform 7 and isoform 9. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11078522,ECO:0000303\|PubMed:12487023,ECO:0000303\|PubMed:14
Q86U86	1429	1484	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	1429	1484	1468	1599	Compositional bias	Note=Pro-rich
Q86U86	1429	1484	1379	1447	DNA binding	Note=HMG box;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00267
Q86U86	1429	1484	1453	1453	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:16964243,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692;Dbxref=PMID:16964243,PMID:20068231,PMID:21406692
Q86U86	1484	1536	857	1689	Alternative sequence	ID=VSP_015232;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12487023;Dbxref=PMID:12487023
Q86U86	1484	1536	1430	1484	Alternative sequence	ID=VSP_015235;Note=In isoform 2%2C isoform 3%2C isoform 4%2C isoform 5%2C isoform 7 and isoform 9. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11078522,ECO:0000303\|PubMed:12487023,ECO:0000303\|PubMed:14
Q86U86	1484	1536	1485	1536	Alternative sequence	ID=VSP_015236;Note=In isoform 5%2C isoform 7 and isoform 8. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:12487023,ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:12487023,PMID:14702039,PMID:1548
Q86U86	1484	1536	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	1484	1536	1468	1599	Compositional bias	Note=Pro-rich
Q86U86	1484	1536	1503	1503	Natural variant	ID=VAR_064687;Note=Found in a stomach cancer cell line. G->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	1484	1536	1488	1488	Sequence conflict	Note=G->D;Ontology_term=ECO:0000305;evidence=ECO:0000305

Lost protein functional features of individual exon skipping events in MSBB.

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
Q86U86	176	214	176	178	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KTB
Q86U86	176	214	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	176	214	210	210	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
Q86U86	176	214	200	270	Domain	Note=Bromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
Q86U86	176	214	179	195	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	176	214	206	208	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	176	214	178	178	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q86U86	176	214	202	202	Natural variant	ID=VAR_064660;Note=Found in a endometrial cancer cell line. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=dbSNP:rs765525545,PMID:21248752
Q86U86	176	214	206	206	Natural variant	ID=VAR_064661;Note=Found in hematopoietic and lymphoid cancer cell lines. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	176	214	214	216	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	215	237	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	215	237	200	270	Domain	Note=Bromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
Q86U86	215	237	218	223	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	215	237	230	239	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	215	237	226	226	Natural variant	ID=VAR_064662;Note=Found in hematopoietic and lymphoid cancer cell lines. E->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	215	237	228	228	Natural variant	ID=VAR_064663;Note=Found in a breast cancer cell line. I->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=dbSNP:rs201022657,PMID:21248752
Q86U86	215	237	232	232	Natural variant	ID=VAR_064664;Note=Found in a case of clear cell renal carcinoma%3B somatic mutation. T->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	215	237	233	233	Natural variant	ID=VAR_064665;Note=Found in a renal carcinoma cell line. I->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	215	237	214	216	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	238	270	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	238	270	200	270	Domain	Note=Bromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
Q86U86	238	270	230	239	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	238	270	245	262	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	238	270	268	291	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	238	270	256	256	Natural variant	ID=VAR_064666;Note=Found in an ovary carcinoma cell line. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=dbSNP:rs776146971,PMID:21248752
Q86U86	238	270	242	242	Sequence conflict	Note=Y->C;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q86U86	238	270	251	251	Sequence conflict	Note=D->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q86U86	300	331	300	332	Alternative sequence	ID=VSP_015231;Note=In isoform 3. RTPSNLAAARLTGPSHSKGSLGEERNPTSKYYR->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12487023;Dbxref=PMID:12487023
Q86U86	300	331	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	300	331	316	316	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q86U86	300	331	319	319	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q86U86	1429	1484	857	1689	Alternative sequence	ID=VSP_015232;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12487023;Dbxref=PMID:12487023
Q86U86	1429	1484	1430	1484	Alternative sequence	ID=VSP_015235;Note=In isoform 2%2C isoform 3%2C isoform 4%2C isoform 5%2C isoform 7 and isoform 9. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11078522,ECO:0000303\|PubMed:12487023,ECO:0000303\|PubMed:14
Q86U86	1429	1484	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	1429	1484	1468	1599	Compositional bias	Note=Pro-rich
Q86U86	1429	1484	1379	1447	DNA binding	Note=HMG box;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00267
Q86U86	1429	1484	1453	1453	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:16964243,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692;Dbxref=PMID:16964243,PMID:20068231,PMID:21406692
Q86U86	1484	1536	857	1689	Alternative sequence	ID=VSP_015232;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12487023;Dbxref=PMID:12487023
Q86U86	1484	1536	1430	1484	Alternative sequence	ID=VSP_015235;Note=In isoform 2%2C isoform 3%2C isoform 4%2C isoform 5%2C isoform 7 and isoform 9. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11078522,ECO:0000303\|PubMed:12487023,ECO:0000303\|PubMed:14
Q86U86	1484	1536	1485	1536	Alternative sequence	ID=VSP_015236;Note=In isoform 5%2C isoform 7 and isoform 8. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:12487023,ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:12487023,PMID:14702039,PMID:1548
Q86U86	1484	1536	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	1484	1536	1468	1599	Compositional bias	Note=Pro-rich
Q86U86	1484	1536	1503	1503	Natural variant	ID=VAR_064687;Note=Found in a stomach cancer cell line. G->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	1484	1536	1488	1488	Sequence conflict	Note=G->D;Ontology_term=ECO:0000305;evidence=ECO:0000305

Lost protein functional features of individual exon skipping events in Mayo.

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
Q86U86	176	214	176	178	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2KTB
Q86U86	176	214	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	176	214	210	210	Cross-link	Note=Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2);Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:28112733;Dbxref=PMID:28112733
Q86U86	176	214	200	270	Domain	Note=Bromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
Q86U86	176	214	179	195	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	176	214	206	208	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	176	214	178	178	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:23186163;Dbxref=PMID:23186163
Q86U86	176	214	202	202	Natural variant	ID=VAR_064660;Note=Found in a endometrial cancer cell line. R->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=dbSNP:rs765525545,PMID:21248752
Q86U86	176	214	206	206	Natural variant	ID=VAR_064661;Note=Found in hematopoietic and lymphoid cancer cell lines. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	176	214	214	216	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	215	237	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	215	237	200	270	Domain	Note=Bromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
Q86U86	215	237	218	223	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	215	237	230	239	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	215	237	226	226	Natural variant	ID=VAR_064662;Note=Found in hematopoietic and lymphoid cancer cell lines. E->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	215	237	228	228	Natural variant	ID=VAR_064663;Note=Found in a breast cancer cell line. I->V;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=dbSNP:rs201022657,PMID:21248752
Q86U86	215	237	232	232	Natural variant	ID=VAR_064664;Note=Found in a case of clear cell renal carcinoma%3B somatic mutation. T->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	215	237	233	233	Natural variant	ID=VAR_064665;Note=Found in a renal carcinoma cell line. I->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	215	237	214	216	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	238	270	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	238	270	200	270	Domain	Note=Bromo 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00035
Q86U86	238	270	230	239	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	238	270	245	262	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	238	270	268	291	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3LJW
Q86U86	238	270	256	256	Natural variant	ID=VAR_064666;Note=Found in an ovary carcinoma cell line. A->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=dbSNP:rs776146971,PMID:21248752
Q86U86	238	270	242	242	Sequence conflict	Note=Y->C;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q86U86	238	270	251	251	Sequence conflict	Note=D->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q86U86	300	331	300	332	Alternative sequence	ID=VSP_015231;Note=In isoform 3. RTPSNLAAARLTGPSHSKGSLGEERNPTSKYYR->S;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12487023;Dbxref=PMID:12487023
Q86U86	300	331	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	300	331	316	316	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q86U86	300	331	319	319	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:18669648;Dbxref=PMID:18669648
Q86U86	1429	1484	857	1689	Alternative sequence	ID=VSP_015232;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12487023;Dbxref=PMID:12487023
Q86U86	1429	1484	1430	1484	Alternative sequence	ID=VSP_015235;Note=In isoform 2%2C isoform 3%2C isoform 4%2C isoform 5%2C isoform 7 and isoform 9. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11078522,ECO:0000303\|PubMed:12487023,ECO:0000303\|PubMed:14
Q86U86	1429	1484	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	1429	1484	1468	1599	Compositional bias	Note=Pro-rich
Q86U86	1429	1484	1379	1447	DNA binding	Note=HMG box;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00267
Q86U86	1429	1484	1453	1453	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244\|PubMed:16964243,ECO:0000244\|PubMed:20068231,ECO:0000244\|PubMed:21406692;Dbxref=PMID:16964243,PMID:20068231,PMID:21406692
Q86U86	1484	1536	857	1689	Alternative sequence	ID=VSP_015232;Note=In isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:12487023;Dbxref=PMID:12487023
Q86U86	1484	1536	1430	1484	Alternative sequence	ID=VSP_015235;Note=In isoform 2%2C isoform 3%2C isoform 4%2C isoform 5%2C isoform 7 and isoform 9. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:11078522,ECO:0000303\|PubMed:12487023,ECO:0000303\|PubMed:14
Q86U86	1484	1536	1485	1536	Alternative sequence	ID=VSP_015236;Note=In isoform 5%2C isoform 7 and isoform 8. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:12487023,ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:12487023,PMID:14702039,PMID:1548
Q86U86	1484	1536	1	1689	Chain	ID=PRO_0000211207;Note=Protein polybromo-1
Q86U86	1484	1536	1468	1599	Compositional bias	Note=Pro-rich
Q86U86	1484	1536	1503	1503	Natural variant	ID=VAR_064687;Note=Found in a stomach cancer cell line. G->C;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21248752;Dbxref=PMID:21248752
Q86U86	1484	1536	1488	1488	Sequence conflict	Note=G->D;Ontology_term=ECO:0000305;evidence=ECO:0000305

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3'-UTR located exon skipping events that lost miRNA binding sites in PBRM1

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type

ENST

Exon skip start

Exon skip end

microRNA

Binding site by TargetScan

Binding type by TargetScan

Bdinding site by miRanda

Score of miRanda

Energy by miRanda

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SNVs in the skipped exons for PBRM1

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- 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

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AD stage-associated exon skippint events for PBRM1

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PBRM1

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for PBRM1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	NUP42	exon_skip_278107	4.367930e-01	9.491784e-08
CB	ZNF638	exon_skip_150681	-5.792467e-01	9.861751e-14
CB	RBM6	exon_skip_150681	-4.795685e-01	2.663541e-09
CB	NUP42	exon_skip_150681	6.640777e-01	6.796694e-19
FL	NUP42	exon_skip_150681	4.127834e-01	6.367776e-09
FL	HNRNPL	exon_skip_150681	4.136526e-01	5.875996e-09
FL	NOVA1	exon_skip_150681	4.384204e-01	5.389410e-10
HCC	RBFOX2	exon_skip_226173	-4.310961e-01	2.782792e-13
HCC	RBM6	exon_skip_150681	-4.492257e-01	2.875959e-14
HCC	RBM5	exon_skip_150681	-4.015934e-01	1.859550e-11
HCC	QKI	exon_skip_203036	-4.610792e-01	7.125335e-13
IFG	RBM6	exon_skip_150681	-5.115568e-01	8.954744e-03
IFG	IGF2BP3	exon_skip_150681	-4.382478e-01	2.843290e-02
PCC	RBFOX2	exon_skip_226173	-4.581710e-01	2.085865e-11
PCC	QKI	exon_skip_203036	-4.259097e-01	3.294190e-08
PCC	RALYL	exon_skip_203036	4.239720e-01	3.858120e-08
STG	NUP42	exon_skip_150681	4.021178e-01	1.982887e-04
STG	NOVA1	exon_skip_150681	4.768821e-01	6.769189e-06
TC	RBFOX2	exon_skip_226173	-4.917139e-01	5.948751e-10
TC	RBM24	exon_skip_226173	-4.375866e-01	5.765755e-08
TC	NUP42	exon_skip_150681	5.370626e-01	4.479786e-11
TC	NOVA1	exon_skip_150681	6.300953e-01	9.605642e-16

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RelatedDrugs for PBRM1

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for PBRM1

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 RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for PBRM1

Gene structures and expression levels for PBRM1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PBRM1

Open reading frame (ORF) annotation in the exon skipping event for PBRM1

Infer the effects of exon skipping event on protein functional features for PBRM1

3'-UTR located exon skipping events that lost miRNA binding sites in PBRM1

SNVs in the skipped exons for PBRM1

AD stage-associated exon skippint events for PBRM1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PBRM1

Correlation with RNA binding proteins (RBPs) for PBRM1

RelatedDrugs for PBRM1

RelatedDiseases for PBRM1