Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:BRAF-AFF3 (FusionGDB2 ID:HG673TG3899)

Fusion Gene Summary for BRAF-AFF3

check button Fusion gene summary
Fusion gene informationFusion gene name: BRAF-AFF3
Fusion gene ID: hg673tg3899
HgeneTgene
Gene symbol

BRAF

AFF3

Gene ID

673

3899

Gene nameB-Raf proto-oncogene, serine/threonine kinaseAF4/FMR2 family member 3
SynonymsB-RAF1|B-raf|BRAF1|NS7|RAFB1LAF4|MLLT2-like
Cytomap('BRAF')('AFF3')

7q34

2q11.2

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase B-raf94 kDa B-raf proteinB-Raf proto-oncogene serine/threonine-protein kinase (p94)B-Raf serine/threonine-proteinmurine sarcoma viral (v-raf) oncogene homolog B1proto-oncogene B-Rafv-raf murine sarcoma viral oncogene AF4/FMR2 family member 3MLLT2-related proteinlymphoid nuclear protein 4lymphoid nuclear protein related to AF4protein LAF-4
Modification date2020032920200313
UniProtAcc

P15056

P51826

Ensembl transtripts involved in fusion geneENST00000288602, 
Fusion gene scores* DoF score28 X 21 X 11=646814 X 19 X 6=1596
# samples 3216
** MAII scorelog2(32/6468*10)=-4.3371758685863
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1596*10)=-3.31831684133498
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BRAF [Title/Abstract] AND AFF3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBRAF(140434287)-AFF3(100321956), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneBRAF

GO:0000186

activation of MAPKK activity

29433126

HgeneBRAF

GO:0006468

protein phosphorylation

17563371

HgeneBRAF

GO:0010828

positive regulation of glucose transmembrane transport

23010278

HgeneBRAF

GO:0033138

positive regulation of peptidyl-serine phosphorylation

19667065

HgeneBRAF

GO:0043066

negative regulation of apoptotic process

19667065

HgeneBRAF

GO:0070374

positive regulation of ERK1 and ERK2 cascade

22065586

HgeneBRAF

GO:0071277

cellular response to calcium ion

18567582

HgeneBRAF

GO:0090150

establishment of protein localization to membrane

23010278



check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS5.0N/ABC038966BRAFchr7

140434287

-AFF3chr2

100321956

+


Top

Fusion Gene ORF analysis for BRAF-AFF3

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
intron-intronENST00000288602ENST00000317233BRAFchr7

140434287

-AFF3chr2

100321956

+
intron-intronENST00000288602ENST00000356421BRAFchr7

140434287

-AFF3chr2

100321956

+
intron-intronENST00000288602ENST00000409236BRAFchr7

140434287

-AFF3chr2

100321956

+
intron-intronENST00000288602ENST00000409579BRAFchr7

140434287

-AFF3chr2

100321956

+
intron-intronENST00000288602ENST00000483600BRAFchr7

140434287

-AFF3chr2

100321956

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

Top

Fusion Genomic Features for BRAF-AFF3


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


Top

Fusion Protein Features for BRAF-AFF3


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:140434287/:100321956)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

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

P15056

AFF3

P51826

FUNCTION: Protein kinase involved in the transduction of mitogenic signals from the cell membrane to the nucleus (Probable). Phosphorylates MAP2K1, and thereby activates the MAP kinase signal transduction pathway (PubMed:21441910, PubMed:29433126). May play a role in the postsynaptic responses of hippocampal neurons (PubMed:1508179). {ECO:0000269|PubMed:1508179, ECO:0000269|PubMed:21441910, ECO:0000269|PubMed:29433126, ECO:0000305}.FUNCTION: Putative transcription activator that may function in lymphoid development and oncogenesis. Binds, in vitro, to double-stranded DNA.

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


Top

Fusion Gene Sequence for BRAF-AFF3


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

Top

Fusion Gene PPI Analysis for BRAF-AFF3


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


Top

Related Drugs for BRAF-AFF3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneBRAFP15056DB08881VemurafenibInhibitorSmall moleculeApproved
HgeneBRAFP15056DB08881VemurafenibInhibitorSmall moleculeApproved
HgeneBRAFP15056DB08881VemurafenibInhibitorSmall moleculeApproved
HgeneBRAFP15056DB08896RegorafenibInhibitorSmall moleculeApproved
HgeneBRAFP15056DB08896RegorafenibInhibitorSmall moleculeApproved
HgeneBRAFP15056DB08896RegorafenibInhibitorSmall moleculeApproved
HgeneBRAFP15056DB14840RipretinibInhibitorSmall moleculeApproved
HgeneBRAFP15056DB14840RipretinibInhibitorSmall moleculeApproved
HgeneBRAFP15056DB14840RipretinibInhibitorSmall moleculeApproved
HgeneBRAFP15056DB00398SorafenibInhibitorSmall moleculeApproved|Investigational
HgeneBRAFP15056DB00398SorafenibInhibitorSmall moleculeApproved|Investigational
HgeneBRAFP15056DB00398SorafenibInhibitorSmall moleculeApproved|Investigational
HgeneBRAFP15056DB08912DabrafenibAntagonist|InhibitorSmall moleculeApproved|Investigational
HgeneBRAFP15056DB08912DabrafenibAntagonist|InhibitorSmall moleculeApproved|Investigational
HgeneBRAFP15056DB08912DabrafenibAntagonist|InhibitorSmall moleculeApproved|Investigational
HgeneBRAFP15056DB11718EncorafenibInhibitorSmall moleculeApproved|Investigational
HgeneBRAFP15056DB11718EncorafenibInhibitorSmall moleculeApproved|Investigational
HgeneBRAFP15056DB11718EncorafenibInhibitorSmall moleculeApproved|Investigational
HgeneBRAFP15056DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
HgeneBRAFP15056DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
HgeneBRAFP15056DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational

Top

Related Diseases for BRAF-AFF3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBRAFC0025202melanoma24CGI;CTD_human;UNIPROT
HgeneBRAFC1275081Cardio-facio-cutaneous syndrome14CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneBRAFC0009402Colorectal Carcinoma8CTD_human;UNIPROT
HgeneBRAFC0028326Noonan Syndrome8CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneBRAFC0238463Papillary thyroid carcinoma8CTD_human;ORPHANET
HgeneBRAFC0040136Thyroid Neoplasm6CGI;CTD_human
HgeneBRAFC0151468Thyroid Gland Follicular Adenoma6CTD_human
HgeneBRAFC0175704LEOPARD Syndrome6CLINGEN;GENOMICS_ENGLAND
HgeneBRAFC0549473Thyroid carcinoma6CGI;CTD_human
HgeneBRAFC3150970NOONAN SYNDROME 75CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneBRAFC0009404Colorectal Neoplasms4CTD_human
HgeneBRAFC3150971LEOPARD SYNDROME 34CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneBRAFC1519086Pilomyxoid astrocytoma3ORPHANET
HgeneBRAFC0004565Melanoma, B162CTD_human
HgeneBRAFC0009075Melanoma, Cloudman S912CTD_human
HgeneBRAFC0018598Melanoma, Harding-Passey2CTD_human
HgeneBRAFC0023443Hairy Cell Leukemia2CGI;ORPHANET
HgeneBRAFC0025205Melanoma, Experimental2CTD_human
HgeneBRAFC0033578Prostatic Neoplasms2CTD_human
HgeneBRAFC0152013Adenocarcinoma of lung (disorder)2CGI;CTD_human
HgeneBRAFC0376358Malignant neoplasm of prostate2CTD_human
HgeneBRAFC0587248Costello syndrome (disorder)2CLINGEN;CTD_human
HgeneBRAFC3501843Nonmedullary Thyroid Carcinoma2CTD_human
HgeneBRAFC3501844Familial Nonmedullary Thyroid Cancer2CTD_human
HgeneBRAFC0002448Ameloblastoma1CTD_human
HgeneBRAFC0004114Astrocytoma1CTD_human
HgeneBRAFC0010276Craniopharyngioma1CTD_human;ORPHANET
HgeneBRAFC0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
HgeneBRAFC0017638Glioma1CGI;CTD_human
HgeneBRAFC0019621Histiocytosis, Langerhans-Cell1CGI;ORPHANET
HgeneBRAFC0022665Kidney Neoplasm1CTD_human
HgeneBRAFC0023903Liver neoplasms1CTD_human
HgeneBRAFC0024232Lymphatic Metastasis1CTD_human
HgeneBRAFC0024694Mandibular Neoplasms1CTD_human
HgeneBRAFC0027659Neoplasms, Experimental1CTD_human
HgeneBRAFC0027962Melanocytic nevus1GENOMICS_ENGLAND
HgeneBRAFC0036920Sezary Syndrome1CTD_human
HgeneBRAFC0041409Turner Syndrome, Male1CTD_human
HgeneBRAFC0079773Lymphoma, T-Cell, Cutaneous1CTD_human
HgeneBRAFC0205768Subependymal Giant Cell Astrocytoma1CTD_human
HgeneBRAFC0206686Adrenocortical carcinoma1CTD_human
HgeneBRAFC0206754Neuroendocrine Tumors1CTD_human
HgeneBRAFC0259783mixed gliomas1CTD_human
HgeneBRAFC0278875Adult Craniopharyngioma1CTD_human
HgeneBRAFC0280783Juvenile Pilocytic Astrocytoma1CTD_human
HgeneBRAFC0280785Diffuse Astrocytoma1CTD_human
HgeneBRAFC0334579Anaplastic astrocytoma1CGI;CTD_human
HgeneBRAFC0334580Protoplasmic astrocytoma1CTD_human
HgeneBRAFC0334581Gemistocytic astrocytoma1CTD_human
HgeneBRAFC0334582Fibrillary Astrocytoma1CTD_human
HgeneBRAFC0334583Pilocytic Astrocytoma1CGI;CTD_human
HgeneBRAFC0338070Childhood Cerebral Astrocytoma1CTD_human
HgeneBRAFC0345904Malignant neoplasm of liver1CTD_human
HgeneBRAFC0376407Granulomatous Slack Skin1CTD_human
HgeneBRAFC0406803Syringocystadenoma Papilliferum1GENOMICS_ENGLAND
HgeneBRAFC0431128Papillary craniopharyngioma1CTD_human
HgeneBRAFC0431129Adamantinous Craniopharyngioma1CTD_human
HgeneBRAFC0547065Mixed oligoastrocytoma1CTD_human
HgeneBRAFC0555198Malignant Glioma1CTD_human
HgeneBRAFC0596263Carcinogenesis1CTD_human
HgeneBRAFC0684249Carcinoma of lung1CGI;UNIPROT
HgeneBRAFC0740457Malignant neoplasm of kidney1CTD_human
HgeneBRAFC0750935Cerebral Astrocytoma1CTD_human
HgeneBRAFC0750936Intracranial Astrocytoma1CTD_human
HgeneBRAFC0751061Craniopharyngioma, Child1CTD_human
HgeneBRAFC0920269Microsatellite Instability1CTD_human
HgeneBRAFC1527404Female Pseudo-Turner Syndrome1CTD_human
HgeneBRAFC1704230Grade I Astrocytoma1CTD_human
HgeneBRAFC1721098Replication Error Phenotype1CTD_human
HgeneBRAFC2239176Liver carcinoma1CTD_human
HgeneBRAFC4551484Leopard Syndrome 11GENOMICS_ENGLAND
HgeneBRAFC4551602Noonan Syndrome 11CTD_human
HgeneBRAFC4721532Lymphoma, Non-Hodgkin, Familial1UNIPROT
HgeneBRAFC4733333familial non-medullary thyroid cancer1GENOMICS_ENGLAND
TgeneC0003873Rheumatoid Arthritis2CTD_human
TgeneC0013146Drug abuse1CTD_human
TgeneC0013170Drug habituation1CTD_human
TgeneC0013222Drug Use Disorders1CTD_human
TgeneC0029231Organic Mental Disorders, Substance-Induced1CTD_human
TgeneC0036572Seizures1GENOMICS_ENGLAND
TgeneC0038580Substance Dependence1CTD_human
TgeneC0038586Substance Use Disorders1CTD_human
TgeneC0236969Substance-Related Disorders1CTD_human
TgeneC0740858Substance abuse problem1CTD_human
TgeneC1510472Drug Dependence1CTD_human
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneC4316881Prescription Drug Abuse1CTD_human