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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for BNC2

check button Gene summary
Gene informationGene symbol

BNC2

Gene ID

54796

Gene namebasonuclin 2
SynonymsBSN2
Cytomap

9p22.3-p22.2

Type of geneprotein-coding
Descriptionzinc finger protein basonuclin-2
Modification date20180519
UniProtAcc

Q6ZN30

ContextPubMed: BNC2 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID

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Exon skipping events across known transcript of Ensembl for BNC2 from UCSC genome browser

check buttonSkipped 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.
all structure

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Gene isoform structures and expression levels for BNC2

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for BNC2

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_502747916418540:16419641:16435035:16435097:16435552:1643637016435035:16435097ENSG00000173068.13ENST00000418777.1
exon_skip_502748916418986:16419647:16421259:16421293:16429297:1642999716421259:16421293ENSG00000173068.13ENST00000484726.1
exon_skip_502749916418986:16419647:16421259:16421293:16431400:1643148516421259:16421293ENSG00000173068.13ENST00000411752.1
exon_skip_502760916418986:16419647:16435552:16437522:16552527:1655276316435552:16437522ENSG00000173068.13ENST00000545497.1,ENST00000380667.2,ENST00000380672.4
exon_skip_502762916421259:16421293:16429297:16429997:16435552:1643637016429297:16429997ENSG00000173068.13ENST00000484726.1
exon_skip_502770916431400:16431485:16435035:16435097:16435552:1643637016435035:16435097ENSG00000173068.13ENST00000411752.1
exon_skip_502771916552597:16552763:16582980:16583083:16727794:1672799516582980:16583083ENSG00000173068.13ENST00000603713.1,ENST00000418777.1,ENST00000484726.1,ENST00000380672.4,ENST00000603313.1,ENST00000486514.1,ENST00000380666.2
exon_skip_502773916582980:16583083:16727794:16727995:16738357:1673848316727794:16727995ENSG00000173068.13ENST00000484726.1,ENST00000380672.4,ENST00000380666.2
exon_skip_502774916582980:16583083:16727794:16727995:16870643:1687070416727794:16727995ENSG00000173068.13ENST00000486514.1
exon_skip_502777916582980:16583083:16738357:16738483:16870643:1687070416738357:16738483ENSG00000173068.13ENST00000380667.2
exon_skip_502779916727794:16727995:16738357:16738483:16870643:1687070416738357:16738483ENSG00000173068.13ENST00000484726.1,ENST00000380666.2

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for BNC2

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_502747916418540:16419641:16435035:16435097:16435552:1643637016435035:16435097ENSG00000173068.13ENST00000418777.1
exon_skip_502748916418986:16419647:16421259:16421293:16429297:1642999716421259:16421293ENSG00000173068.13ENST00000484726.1
exon_skip_502749916418986:16419647:16421259:16421293:16431400:1643148516421259:16421293ENSG00000173068.13ENST00000411752.1
exon_skip_502760916418986:16419647:16435552:16437522:16552527:1655276316435552:16437522ENSG00000173068.13ENST00000380672.4,ENST00000380667.2,ENST00000545497.1
exon_skip_502762916421259:16421293:16429297:16429997:16435552:1643637016429297:16429997ENSG00000173068.13ENST00000484726.1
exon_skip_502764916421259:16421293:16431400:16431485:16435035:1643509716431400:16431485ENSG00000173068.13ENST00000411752.1
exon_skip_502770916431400:16431485:16435035:16435097:16435552:1643637016435035:16435097ENSG00000173068.13ENST00000411752.1
exon_skip_502771916552597:16552763:16582980:16583083:16727794:1672799516582980:16583083ENSG00000173068.13ENST00000380672.4,ENST00000484726.1,ENST00000418777.1,ENST00000380666.2,ENST00000603713.1,ENST00000486514.1,ENST00000603313.1
exon_skip_502773916582980:16583083:16727794:16727995:16738357:1673848316727794:16727995ENSG00000173068.13ENST00000380672.4,ENST00000484726.1,ENST00000380666.2
exon_skip_502774916582980:16583083:16727794:16727995:16870643:1687070416727794:16727995ENSG00000173068.13ENST00000486514.1
exon_skip_502777916582980:16583083:16738357:16738483:16870643:1687070416738357:16738483ENSG00000173068.13ENST00000380667.2
exon_skip_502779916727794:16727995:16738357:16738483:16870643:1687070416738357:16738483ENSG00000173068.13ENST00000484726.1,ENST00000380666.2

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for BNC2

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003806721643555216437522Frame-shift
ENST000003806721658298016583083Frame-shift
ENST000003806721672779416727995In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003806721643555216437522Frame-shift
ENST000003806721658298016583083Frame-shift
ENST000003806721672779416727995In-frame

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Infer the effects of exon skipping event on protein functional features for BNC2

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000380672128611099167277941672799518838843110

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000380672128611099167277941672799518838843110

check button 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 featureDescription of feature
Q6ZN304311011099ChainID=PRO_0000046934;Note=Zinc finger protein basonuclin-2


check button 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 featureDescription of feature
Q6ZN304311011099ChainID=PRO_0000046934;Note=Zinc finger protein basonuclin-2


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SNVs in the skipped exons for BNC2

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-DD-A3A1-01exon_skip_502760
16435553164375221643611816436118Frame_Shift_DelA-p.S692fs
COADTCGA-A6-6781-01exon_skip_502760
16435553164375221643637516436375Frame_Shift_DelG-p.P606fs
COADTCGA-AA-3663-01exon_skip_502760
16435553164375221643637516436375Frame_Shift_DelG-p.P606fs
LIHCTCGA-DD-A1EG-01exon_skip_502760
16435553164375221643637516436375Frame_Shift_DelG-p.P608fs
PRADTCGA-J4-A67K-01exon_skip_502760
16435553164375221643637516436375Frame_Shift_DelG-p.P606fs
PRADTCGA-J4-A67K-01exon_skip_502760
16435553164375221643637516436375Frame_Shift_DelG-p.P608fs
STADTCGA-BR-4292-01exon_skip_502760
16435553164375221643637516436375Frame_Shift_DelG-p.P606fs
LIHCTCGA-DD-A39Y-01exon_skip_502760
16435553164375221643641316436413Frame_Shift_DelG-p.P593fs
LIHCTCGA-G3-A3CJ-01exon_skip_502760
16435553164375221643665516436655Frame_Shift_DelC-p.A513fs
LIHCTCGA-DD-A3A0-01exon_skip_502760
16435553164375221643717316437173Frame_Shift_DelG-p.P340fs
COADTCGA-F4-6570-01exon_skip_502760
16435553164375221643720316437203Frame_Shift_DelG-p.P330fs
CESCTCGA-C5-A3HE-01exon_skip_502774
exon_skip_502773
16727795167279951672794916727952Frame_Shift_DelTCTC-p.R58fs
LIHCTCGA-DD-A1EG-01exon_skip_502779
exon_skip_502777
16738358167384831673838916738389Frame_Shift_DelG-p.P33fs
LIHCTCGA-BC-A10S-01exon_skip_502760
16435553164375221643574416435745Frame_Shift_Ins-Cp.T816fs
DLBCTCGA-FA-8693-01exon_skip_502760
16435553164375221643637416436375Frame_Shift_Ins-Gp.P606fs
BLCATCGA-BT-A0YX-01exon_skip_502760
16435553164375221643586616435866Nonsense_MutationCAp.E776*
UCECTCGA-AP-A056-01exon_skip_502760
16435553164375221643604316436043Nonsense_MutationCAp.E717*
STADTCGA-CG-4466-01exon_skip_502760
16435553164375221643658616436586Nonsense_MutationGAp.R536*
STADTCGA-CG-4466-01exon_skip_502760
16435553164375221643658616436586Nonsense_MutationGAp.R536X
UCECTCGA-BS-A0UV-01exon_skip_502760
16435553164375221643674216436742Nonsense_MutationGAp.R484*
SKCMTCGA-EB-A5SE-01exon_skip_502760
16435553164375221643678416436784Nonsense_MutationGAp.R470*
SKCMTCGA-W3-AA1Q-06exon_skip_502760
16435553164375221643678416436784Nonsense_MutationGAp.R470*
STADTCGA-BR-4368-01exon_skip_502760
16435553164375221643681216436812Nonsense_MutationGTp.Y460*
STADTCGA-BR-4368-01exon_skip_502760
16435553164375221643681216436812Nonsense_MutationGTp.Y460X
BLCATCGA-BL-A13I-01exon_skip_502760
16435553164375221643745616437456Nonsense_MutationGAp.Q246*
HNSCTCGA-D6-6516-01exon_skip_502760
16435553164375221643749416437494Nonsense_MutationCTp.W233*
LUSCTCGA-34-5236-01exon_skip_502771
16582981165830831658300816583008Nonsense_MutationGAp.Q136*
LGGTCGA-S9-A7IX-01exon_skip_502774
exon_skip_502773
16727795167279951672791616727916Nonsense_MutationACp.L70*
BRCATCGA-A8-A07C-01exon_skip_502779
exon_skip_502777
16738358167384831673836016738360Nonsense_MutationCAp.E43*
LIHCTCGA-G3-AAUZ-01exon_skip_502779
exon_skip_502777
16738358167384831673842016738420Nonsense_MutationCAp.E23X

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
HCC38_MATCHED_NORMAL_TISSUE16429298164299971642994616429946Frame_Shift_DelC-p.E897fs
SNU1_STOMACH16435553164375221643637516436375Frame_Shift_DelG-p.P608fs
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16435553164375221643637516436375Frame_Shift_DelG-p.P608fs
LCLC103H_LUNG16435553164375221643720116437201Frame_Shift_DelC-p.V331fs
HEC108_ENDOMETRIUM16435553164375221643655716436558Frame_Shift_Ins-Gp.P545fs
GB1_CENTRAL_NERVOUS_SYSTEM16429298164299971642998016429980Missense_MutationTCp.N886S
HCC2998_LARGE_INTESTINE16435553164375221643561516435615Missense_MutationCAp.E859D
TOV112D_OVARY16435553164375221643569316435693Missense_MutationTGp.K833N
HEC108_ENDOMETRIUM16435553164375221643580816435808Missense_MutationTCp.N795S
TT2609C02_THYROID16435553164375221643596316435963Missense_MutationGTp.H743Q
EN_ENDOMETRIUM16435553164375221643597016435970Missense_MutationTCp.D741G
GSU_STOMACH16435553164375221643597116435971Missense_MutationCTp.D741N
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16435553164375221643597316435973Missense_MutationCTp.G740E
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16435553164375221643603416436034Missense_MutationGAp.R720W
KP2_PANCREAS16435553164375221643606516436065Missense_MutationGTp.D709E
TGBC11TKB_STOMACH16435553164375221643607316436073Missense_MutationTCp.R707G
639V_URINARY_TRACT16435553164375221643609116436091Missense_MutationAGp.S701P
SNU1040_LARGE_INTESTINE16435553164375221643610016436100Missense_MutationGAp.R698W
LK2_LUNG16435553164375221643623216436232Missense_MutationCGp.D654H
MDAMB175VII_BREAST16435553164375221643627416436274Missense_MutationCGp.V640L
SNU182_LIVER16435553164375221643630916436309Missense_MutationGTp.A628E
NCIH1573_LUNG16435553164375221643633916436339Missense_MutationATp.M618K
SNU601_STOMACH16435553164375221643638216436382Missense_MutationGTp.H604N
NCIH1618_LUNG16435553164375221643639016436390Missense_MutationAGp.I601T
NCIH1341_LUNG16435553164375221643639316436393Missense_MutationGTp.T600N
HEC265_ENDOMETRIUM16435553164375221643642416436424Missense_MutationGAp.P590S
GP2D_LARGE_INTESTINE16435553164375221643642716436427Missense_MutationGTp.L589I
GP5D_LARGE_INTESTINE16435553164375221643642716436427Missense_MutationGTp.L589I
SKLU1_LUNG16435553164375221643651016436510Missense_MutationGCp.S561C
AU565_BREAST16435553164375221643651716436517Missense_MutationCAp.V559L
M1203273_SKIN16435553164375221643653116436531Missense_MutationAGp.L554P
LNCAPCLONEFGC_PROSTATE16435553164375221643655816436558Missense_MutationGAp.P545L
HEC1_ENDOMETRIUM16435553164375221643658016436580Missense_MutationGAp.P538S
HEC1B_ENDOMETRIUM16435553164375221643658016436580Missense_MutationGAp.P538S
HEC251_ENDOMETRIUM16435553164375221643665816436658Missense_MutationGAp.R512W
MHHPREB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16435553164375221643667516436675Missense_MutationCAp.R506L
CW2_LARGE_INTESTINE16435553164375221643672316436723Missense_MutationCTp.S490N
NCIH630_LARGE_INTESTINE16435553164375221643680716436807Missense_MutationGAp.A462V
HCC2998_LARGE_INTESTINE16435553164375221643682916436829Missense_MutationTCp.T455A
NCIH2110_LUNG16435553164375221643684716436847Missense_MutationTCp.T449A
JHUEM7_ENDOMETRIUM16435553164375221643691016436910Missense_MutationGAp.R428W
SNU1040_LARGE_INTESTINE16435553164375221643691916436919Missense_MutationGAp.R425W
HEC251_ENDOMETRIUM16435553164375221643697116436971Missense_MutationACp.N407K
OCIAML3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16435553164375221643697116436971Missense_MutationATp.N407K
SW684_SOFT_TISSUE16435553164375221643707416437074Missense_MutationGAp.P373L
OC316_OVARY16435553164375221643712916437129Missense_MutationGAp.P355S
OC314_OVARY16435553164375221643712916437129Missense_MutationGAp.P355S
CORL279_LUNG16435553164375221643717416437174Missense_MutationGAp.P340S
BB49EBV_MATCHED_NORMAL_TISSUE16435553164375221643723316437233Missense_MutationGTp.A320E
HEC251_ENDOMETRIUM16435553164375221643725516437255Missense_MutationCTp.E313K
MFE319_ENDOMETRIUM16435553164375221643738416437384Missense_MutationCTp.A270T
DU145_PROSTATE16435553164375221643740716437407Missense_MutationGAp.A262V
MRKNU1_BREAST16435553164375221643743716437437Missense_MutationCAp.G252V
NCIH650_LUNG16435553164375221643749316437493Missense_MutationCAp.W233C
SW948_LARGE_INTESTINE16582981165830831658301616583016Missense_MutationGAp.T133I
HPAC_PANCREAS16727795167279951672782916727829Missense_MutationGCp.A99G
SNU668_STOMACH16727795167279951672783916727839Missense_MutationATp.W96R
BICR18_UPPER_AERODIGESTIVE_TRACT16727795167279951672786616727866Missense_MutationTCp.T87A
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16727795167279951672786616727866Missense_MutationTCp.T87A
GMEL_SKIN16727795167279951672786616727866Missense_MutationTCp.T87A
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16727795167279951672786616727866Missense_MutationTCp.T87A
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16727795167279951672786616727866Missense_MutationTCp.T87A
BICR18_UPPER_AERODIGESTIVE_TRACT16727795167279951672796016727960Missense_MutationCGp.E55D
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16727795167279951672796016727960Missense_MutationCGp.E55D
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16727795167279951672796016727960Missense_MutationCGp.E55D
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16727795167279951672796016727960Missense_MutationCGp.E55D
HCC2218_BREAST16727795167279951672796416727964Missense_MutationCAp.R54I
HCC2218_MATCHED_NORMAL_TISSUE16727795167279951672796416727964Missense_MutationCAp.R54I
NCIBL209_MATCHED_NORMAL_TISSUE16727795167279951672796416727964Missense_MutationCAp.R54I
ONS76_CENTRAL_NERVOUS_SYSTEM16738358167384831673836816738368Missense_MutationGAp.S40F
ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16738358167384831673844116738441Missense_MutationTCp.K16E
COLO678_LARGE_INTESTINE16738358167384831673846216738462Missense_MutationGAp.P9S
BICR18_UPPER_AERODIGESTIVE_TRACT16429298164299971642999616429996Splice_SiteAGp.Y881H
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16429298164299971642999616429996Splice_SiteAGp.Y881H
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16429298164299971642999616429996Splice_SiteAGp.Y881H
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE16429298164299971642999616429996Splice_SiteAGp.Y881H
AN3CA_ENDOMETRIUM16582981165830831658298216582982Splice_SiteAGp.H144H

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for BNC2

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BNC2


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for BNC2


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RelatedDrugs for BNC2

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for BNC2

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
BNC2C0008925Cleft Palate1CTD_human
BNC2C0376634Craniofacial Abnormalities1CTD_human
BNC2C0919267ovarian neoplasm1CTD_human