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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 4349

FusionGeneSummary for BPTF_SMG1

check button Fusion gene summary
Fusion gene informationFusion gene name: BPTF_SMG1
Fusion gene ID: 4349
HgeneTgene
Gene symbol

BPTF

SMG1

Gene ID

2186

23049

Gene namebromodomain PHD finger transcription factorSMG1, nonsense mediated mRNA decay associated PI3K related kinase
SynonymsFAC1|FALZ|NEDDFL|NURF30161E3.4|ATX|LIP
Cytomap

17q24.2

16p12.3

Type of geneprotein-codingprotein-coding
Descriptionnucleosome-remodeling factor subunit BPTFbromodomain and PHD domain transcription factorbromodomain and PHD finger-containing transcription factorfetal Alz-50 clone 1 proteinfetal Alz-50 reactive clone 1fetal Alzheimer antigennucleosome remodeling fserine/threonine-protein kinase SMG1PI-3-kinase-related kinase SMG-1SMG1 phosphatidylinositol 3-kinase-related kinaselambda-interacting proteinlambda/iota protein kinase C-interacting proteinsmg-1 homolog, phosphatidylinositol 3-kinase-related kinase
Modification date2018051920180523
UniProtAcc

Q12830

Q96Q15

Ensembl transtripts involved in fusion geneENST00000335221, ENST00000321892, 
ENST00000306378, ENST00000424123, 
ENST00000577770, 		ENST00000389467, 
ENST00000446231, ENST00000565224, 
ENST00000567737, 
Fusion gene scores* DoF score20 X 16 X 10=32007 X 8 X 4=224
# samples 258
** MAII scorelog2(25/3200*10)=-3.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/224*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BPTF [Title/Abstract] AND SMG1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneBPTF

GO:0000122

negative regulation of transcription by RNA polymerase II

10727212

HgeneBPTF

GO:0006338

chromatin remodeling

14609955

TgeneSMG1

GO:0000184

nuclear-transcribed mRNA catabolic process, nonsense-mediated decay

11544179

TgeneSMG1

GO:0018105

peptidyl-serine phosphorylation

11544179|15175154

TgeneSMG1

GO:0046777

protein autophosphorylation

11331269|11544179

TgeneSMG1

GO:0046854

phosphatidylinositol phosphorylation

11331269

TgeneSMG1

GO:2001020

regulation of response to DNA damage stimulus

15175154


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1DB219627BPTFchr17

65944305

+SMG1chr16

18826827

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
In-frameENST00000335221ENST00000389467BPTFchr17

65944305

+SMG1chr16

18826827

-
In-frameENST00000335221ENST00000446231BPTFchr17

65944305

+SMG1chr16

18826827

-
5CDS-intronENST00000335221ENST00000565224BPTFchr17

65944305

+SMG1chr16

18826827

-
5CDS-intronENST00000335221ENST00000567737BPTFchr17

65944305

+SMG1chr16

18826827

-
In-frameENST00000321892ENST00000389467BPTFchr17

65944305

+SMG1chr16

18826827

-
In-frameENST00000321892ENST00000446231BPTFchr17

65944305

+SMG1chr16

18826827

-
5CDS-intronENST00000321892ENST00000565224BPTFchr17

65944305

+SMG1chr16

18826827

-
5CDS-intronENST00000321892ENST00000567737BPTFchr17

65944305

+SMG1chr16

18826827

-
In-frameENST00000306378ENST00000389467BPTFchr17

65944305

+SMG1chr16

18826827

-
In-frameENST00000306378ENST00000446231BPTFchr17

65944305

+SMG1chr16

18826827

-
5CDS-intronENST00000306378ENST00000565224BPTFchr17

65944305

+SMG1chr16

18826827

-
5CDS-intronENST00000306378ENST00000567737BPTFchr17

65944305

+SMG1chr16

18826827

-
In-frameENST00000424123ENST00000389467BPTFchr17

65944305

+SMG1chr16

18826827

-
In-frameENST00000424123ENST00000446231BPTFchr17

65944305

+SMG1chr16

18826827

-
5CDS-intronENST00000424123ENST00000565224BPTFchr17

65944305

+SMG1chr16

18826827

-
5CDS-intronENST00000424123ENST00000567737BPTFchr17

65944305

+SMG1chr16

18826827

-
intron-3CDSENST00000577770ENST00000389467BPTFchr17

65944305

+SMG1chr16

18826827

-
intron-3CDSENST00000577770ENST00000446231BPTFchr17

65944305

+SMG1chr16

18826827

-
intron-intronENST00000577770ENST00000565224BPTFchr17

65944305

+SMG1chr16

18826827

-
intron-intronENST00000577770ENST00000567737BPTFchr17

65944305

+SMG1chr16

18826827

-

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FusionProtFeatures for BPTF_SMG1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
BPTF

Q12830

SMG1

Q96Q15

Histone-binding component of NURF (nucleosome-remodelingfactor), a complex which catalyzes ATP-dependent nucleosomesliding and facilitates transcription of chromatin. Specificallyrecognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which marktranscription start sites of virtually all active genes. May alsoregulate transcription through direct binding to DNA ortranscription factors. Serine/threonine protein kinase involved in both mRNAsurveillance and genotoxic stress response pathways. Recognizesthe substrate consensus sequence [ST]-Q. Plays a central role innonsense-mediated decay (NMD) of mRNAs containing premature stopcodons by phosphorylating UPF1/RENT1. Recruited by release factorsto stalled ribosomes together with SMG8 and SMG9 (forming theSMG1C protein kinase complex), and UPF1 to form the transient SURF(SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURFcomplex associates with the exon junction complex (EJC) throughUPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillancecomplex which is believed to activate NMD. Also acts as agenotoxic stress-activated protein kinase that displays somefunctional overlap with ATM. Can phosphorylate p53/TP53 and isrequired for optimal p53/TP53 activation after cellular exposureto genotoxic stress. Its depletion leads to spontaneous DNA damageand increased sensitivity to ionizing radiation (IR). May activatePRKCI but not PRKCZ. {ECO:0000269|PubMed:11331269,ECO:0000269|PubMed:11544179, ECO:0000269|PubMed:15175154,ECO:0000269|PubMed:16452507}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

.

* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for BPTF_SMG1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.
>In-frame_BPTF_ENST00000335221_chr17_65944305_+_SMG1_ENST00000389467_chr16_18826827_-_0aa

>In-frame_BPTF_ENST00000335221_chr17_65944305_+_SMG1_ENST00000446231_chr16_18826827_-_0aa

>In-frame_BPTF_ENST00000321892_chr17_65944305_+_SMG1_ENST00000389467_chr16_18826827_-_0aa

>In-frame_BPTF_ENST00000321892_chr17_65944305_+_SMG1_ENST00000446231_chr16_18826827_-_0aa

>In-frame_BPTF_ENST00000306378_chr17_65944305_+_SMG1_ENST00000389467_chr16_18826827_-_0aa

>In-frame_BPTF_ENST00000306378_chr17_65944305_+_SMG1_ENST00000446231_chr16_18826827_-_0aa

>In-frame_BPTF_ENST00000424123_chr17_65944305_+_SMG1_ENST00000389467_chr16_18826827_-_0aa

>In-frame_BPTF_ENST00000424123_chr17_65944305_+_SMG1_ENST00000446231_chr16_18826827_-_0aa


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_BPTF_ENST00000335221_chr17_65944305_+_SMG1_ENST00000389467_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000335221_chr17_65944305_+_SMG1_ENST00000446231_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000321892_chr17_65944305_+_SMG1_ENST00000389467_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000321892_chr17_65944305_+_SMG1_ENST00000446231_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000306378_chr17_65944305_+_SMG1_ENST00000389467_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000306378_chr17_65944305_+_SMG1_ENST00000446231_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000424123_chr17_65944305_+_SMG1_ENST00000389467_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000424123_chr17_65944305_+_SMG1_ENST00000446231_chr16_18826827_-_0nt


* Fusion transcript sequences (Full-length transcript).
>In-frame_BPTF_ENST00000335221_chr17_65944305_+_SMG1_ENST00000389467_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000335221_chr17_65944305_+_SMG1_ENST00000446231_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000321892_chr17_65944305_+_SMG1_ENST00000389467_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000321892_chr17_65944305_+_SMG1_ENST00000446231_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000306378_chr17_65944305_+_SMG1_ENST00000389467_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000306378_chr17_65944305_+_SMG1_ENST00000446231_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000424123_chr17_65944305_+_SMG1_ENST00000389467_chr16_18826827_-_0nt

>In-frame_BPTF_ENST00000424123_chr17_65944305_+_SMG1_ENST00000446231_chr16_18826827_-_0nt


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FusionGenePPI for BPTF_SMG1


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for BPTF_SMG1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for BPTF_SMG1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBPTFC0005695Bladder Neoplasm1CTD_human