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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:BRD1-SLC3A2 (FusionGDB2 ID:10229)

Fusion Gene Summary for BRD1-SLC3A2

check button Fusion gene summary
Fusion gene informationFusion gene name: BRD1-SLC3A2
Fusion gene ID: 10229
HgeneTgene
Gene symbol

BRD1

SLC3A2

Gene ID

23774

6520

Gene namebromodomain containing 1solute carrier family 3 member 2
SynonymsBRL|BRPF1|BRPF24F2|4F2HC|4T2HC|CD98|CD98HC|MDU1|NACAE
Cytomap

22q13.33

11q12.3

Type of geneprotein-codingprotein-coding
Descriptionbromodomain-containing protein 1BR140-like proteinbromodomain and PHD finger-containing protein 24F2 cell-surface antigen heavy chainCD98 heavy chainantigen defined by monoclonal antibody 4F2, heavy chainantigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43lymphocyte activation antigen 4F2 large subunitmonoclonal antibody 44D7
Modification date2020032720200313
UniProtAcc

O95696

.
Ensembl transtripts involved in fusion geneENST00000216267, ENST00000404034, 
ENST00000404760, ENST00000457780, 
ENST00000542442, ENST00000342989, 
ENST00000459821, 		ENST00000377892, 
ENST00000377890, ENST00000377891, 
ENST00000377889, ENST00000535296, 
ENST00000338663, ENST00000538682, 
ENST00000536981, 
Fusion gene scores* DoF score7 X 7 X 6=29410 X 11 X 7=770
# samples 813
** MAII scorelog2(8/294*10)=-1.877744249949
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/770*10)=-2.56634682255381
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BRD1 [Title/Abstract] AND SLC3A2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBRD1(50219378)-SLC3A2(62652649), # samples:2
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
HgeneBRD1

GO:0043966

histone H3 acetylation

16387653


check buttonFusion gene breakpoints across BRD1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across SLC3A2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4SKCMTCGA-FS-A1ZK-06ABRD1chr22

50219378

-SLC3A2chr11

62652649

+
ChimerDB4SKCMTCGA-FS-A1ZK-06ABRD1chr22

50219378

-SLC3A2chr11

62652649

+


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Fusion Gene ORF analysis for BRD1-SLC3A2

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-3CDSENST00000216267ENST00000377892BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000216267ENST00000377890BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000216267ENST00000377891BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000216267ENST00000377889BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000216267ENST00000535296BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000216267ENST00000338663BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3UTRENST00000216267ENST00000538682BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-5UTRENST00000216267ENST00000536981BRD1chr22

50219378

-SLC3A2chr11

62652649

+
5UTR-3CDSENST00000404034ENST00000377892BRD1chr22

50219378

-SLC3A2chr11

62652649

+
5UTR-3CDSENST00000404034ENST00000377890BRD1chr22

50219378

-SLC3A2chr11

62652649

+
5UTR-3CDSENST00000404034ENST00000377891BRD1chr22

50219378

-SLC3A2chr11

62652649

+
5UTR-3CDSENST00000404034ENST00000377889BRD1chr22

50219378

-SLC3A2chr11

62652649

+
5UTR-3CDSENST00000404034ENST00000535296BRD1chr22

50219378

-SLC3A2chr11

62652649

+
5UTR-3CDSENST00000404034ENST00000338663BRD1chr22

50219378

-SLC3A2chr11

62652649

+
5UTR-3UTRENST00000404034ENST00000538682BRD1chr22

50219378

-SLC3A2chr11

62652649

+
5UTR-5UTRENST00000404034ENST00000536981BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000404760ENST00000377892BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000404760ENST00000377890BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000404760ENST00000377891BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000404760ENST00000377889BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000404760ENST00000535296BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000404760ENST00000338663BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3UTRENST00000404760ENST00000538682BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-5UTRENST00000404760ENST00000536981BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000457780ENST00000377892BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000457780ENST00000377890BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000457780ENST00000377891BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000457780ENST00000377889BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000457780ENST00000535296BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000457780ENST00000338663BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3UTRENST00000457780ENST00000538682BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-5UTRENST00000457780ENST00000536981BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000542442ENST00000377892BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000542442ENST00000377890BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000542442ENST00000377891BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000542442ENST00000377889BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000542442ENST00000535296BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000542442ENST00000338663BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3UTRENST00000542442ENST00000538682BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-5UTRENST00000542442ENST00000536981BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000342989ENST00000377892BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000342989ENST00000377890BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000342989ENST00000377891BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000342989ENST00000377889BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000342989ENST00000535296BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000342989ENST00000338663BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3UTRENST00000342989ENST00000538682BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-5UTRENST00000342989ENST00000536981BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000459821ENST00000377892BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000459821ENST00000377890BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000459821ENST00000377891BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000459821ENST00000377889BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000459821ENST00000535296BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3CDSENST00000459821ENST00000338663BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-3UTRENST00000459821ENST00000538682BRD1chr22

50219378

-SLC3A2chr11

62652649

+
intron-5UTRENST00000459821ENST00000536981BRD1chr22

50219378

-SLC3A2chr11

62652649

+

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

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Fusion Genomic Features for BRD1-SLC3A2


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)
BRD1chr2250219377-SLC3A2chr1162652648+0.04120020.95879984
BRD1chr2250219377-SLC3A2chr1162652648+0.04120020.95879984

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for BRD1-SLC3A2


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
BRD1

O95696

.
FUNCTION: Scaffold subunit of various histone acetyltransferase (HAT) complexes, such as the MOZ/MORF and HBO1 complexes, that acts as a regulator of hematopoiesis (PubMed:16387653, PubMed:21753189, PubMed:21880731). Plays a key role in HBO1 complex by directing KAT7/HBO1 specificity towards histone H3 'Lys-14' acetylation (H3K14ac), thereby promoting erythroid differentiation (PubMed:21753189). {ECO:0000269|PubMed:16387653, ECO:0000269|PubMed:21753189, ECO:0000269|PubMed:21880731}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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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Fusion Gene Sequence for BRD1-SLC3A2


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.

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Fusion Gene PPI Analysis for BRD1-SLC3A2


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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Related Drugs for BRD1-SLC3A2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for BRD1-SLC3A2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBRD1C0036341Schizophrenia5PSYGENET
HgeneBRD1C0005586Bipolar Disorder4PSYGENET
HgeneBRD1C0010606Adenoid Cystic Carcinoma1CTD_human
TgeneSLC3A2C0024121Lung Neoplasms1CTD_human
TgeneSLC3A2C0242379Malignant neoplasm of lung1CTD_human