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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:DDX21-BEX2 (FusionGDB2 ID:21927)

Fusion Gene Summary for DDX21-BEX2

check button Fusion gene summary
Fusion gene informationFusion gene name: DDX21-BEX2
Fusion gene ID: 21927
HgeneTgene
Gene symbol

DDX21

BEX2

Gene ID

54606

84707

Gene nameDEAD-box helicase 56brain expressed X-linked 2
SynonymsDDX21|DDX26|NOH61BEX1|DJ79P11.1
Cytomap

7p13

Xq22.2

Type of geneprotein-codingprotein-coding
Descriptionprobable ATP-dependent RNA helicase DDX5661-kd nucleolar helicaseATP-dependent 61 kDa nucleolar RNA helicaseDEAD (Asp-Glu-Ala-Asp) box helicase 56DEAD (Asp-Glu-Ala-Asp) box polypeptide 56DEAD box protein 21DEAD box protein 56DEAD-box RNA helicasenprotein BEX2brain-expressed X-linked protein 2hBex2
Modification date2020031320200315
UniProtAcc.

Q9BXY8

Ensembl transtripts involved in fusion geneENST00000354185, ENST00000372674, 
ENST00000372677, ENST00000536889, 
Fusion gene scores* DoF score11 X 11 X 2=2423 X 2 X 1=6
# samples 123
** MAII scorelog2(12/242*10)=-1.01197264166608
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/6*10)=2.32192809488736
Context

PubMed: DDX21 [Title/Abstract] AND BEX2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointDDX21(70742402)-BEX2(102564533), # samples:1
Anticipated loss of major functional domain due to fusion event.DDX21-BEX2 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
DDX21-BEX2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
DDX21-BEX2 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
* 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
TgeneBEX2

GO:0042981

regulation of apoptotic process

19711341

TgeneBEX2

GO:0051726

regulation of cell cycle

19711341


check buttonFusion gene breakpoints across DDX21 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across BEX2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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/AAW379411DDX21chr10

70742402

-BEX2chrX

102564533

-


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Fusion Gene ORF analysis for DDX21-BEX2

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
Frame-shiftENST00000354185ENST00000372674DDX21chr10

70742402

-BEX2chrX

102564533

-
Frame-shiftENST00000354185ENST00000372677DDX21chr10

70742402

-BEX2chrX

102564533

-
In-frameENST00000354185ENST00000536889DDX21chr10

70742402

-BEX2chrX

102564533

-

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)
ENST00000354185DDX21chr1070742402-ENST00000536889BEX2chrX102564533-48594607922248718

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
ENST00000354185ENST00000536889DDX21chr1070742402-BEX2chrX102564533-0.0001622360.99983776

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Fusion Genomic Features for DDX21-BEX2


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)

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.
genomic feature

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 DDX21-BEX2


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/chr10:70742402/chrX:102564533)
- 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
.BEX2

Q9BXY8

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Regulator of mitochondrial apoptosis and G1 cell cycle in breast cancer. Protects the breast cancer cells against mitochondrial apoptosis and this effect is mediated through the modulation of BCL2 protein family, which involves the positive regulation of anti-apoptotic member BCL2 and the negative regulation of pro-apoptotic members BAD, BAK1 and PUMA. Required for the normal cell cycle progression during G1 in breast cancer cells through the regulation of CCND1 and CDKN1A. Regulates the level of PP2A regulatory subunit B and PP2A phosphatase activity. {ECO:0000269|PubMed:19711341}.

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
HgeneDDX21chr10:70742402chrX:102564533ENST00000354185-115217_3960784.0DomainHelicase ATP-binding
HgeneDDX21chr10:70742402chrX:102564533ENST00000354185-115429_5730784.0DomainHelicase C-terminal
HgeneDDX21chr10:70742402chrX:102564533ENST00000354185-115186_2140784.0MotifQ motif
HgeneDDX21chr10:70742402chrX:102564533ENST00000354185-115339_3420784.0MotifDEAD box
HgeneDDX21chr10:70742402chrX:102564533ENST00000354185-115230_2370784.0Nucleotide bindingATP
HgeneDDX21chr10:70742402chrX:102564533ENST00000354185-115724_7480784.0RegionNote=3 X 5 AA repeats
HgeneDDX21chr10:70742402chrX:102564533ENST00000354185-115724_7280784.0RepeatNote=1
HgeneDDX21chr10:70742402chrX:102564533ENST00000354185-115734_7380784.0RepeatNote=2
HgeneDDX21chr10:70742402chrX:102564533ENST00000354185-115744_7480784.0RepeatNote=3


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Fusion Gene Sequence for DDX21-BEX2


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.
>21927_21927_1_DDX21-BEX2_DDX21_chr10_70742402_ENST00000354185_BEX2_chrX_102564533_ENST00000536889_length(transcript)=4859nt_BP=4607nt
GGGAAGTGACGAGAGCCGGGTGGACCCAGGGTGGGGAACTACCTCTTCCTCTCCACGCGGTTGAGAAGACCGGTCGGCCTGGGCAACCTG
CGCTGAAGATGCCGGGAAAACTCCGTAGTGACGCTGGTTTGGAATCAGACACCGCAATGAAAAAAGGGGAGACACTGCGAAAGCAAACCG
AGGAGAAAGAGAAAAAAGAGAAGCCAAAATCTGATAAGACTGAAGAGATAGCAGAAGAGGAAGAAACTGTTTTCCCCAAAGCTAAACAAG
TTAAAAAGAAAGCAGAGCCTTCTGAAGTTGACATGAATTCTCCTAAATCCAAAAAGGCAAAAAAGAAAGAGGAGCCATCTCAAAATGACA
TTTCTCCTAAAACCAAAAGTTTGAGAAAGAAAAAGGAGCCCATTGAAAAGAAAGTGGTTTCTTCTAAAACCAAAAAAGTGACAAAAAATG
AGGAGCCTTCTGAGGAAGAAATAGATGCTCCTAAGCCCAAGAAGATGAAGAAAGAAAAGGAAATGAATGGAGAAACTAGAGAGAAAAGCC
CCAAACTGAAGAATGGATTTCCTCATCCTGAACCGGACTGTAACCCCAGTGAAGCTGCCAGTGAAGAAAGTAACAGTGAGATAGAGCAGG
AAATACCTGTGGAACAAAAAGAAGGCGCTTTCTCTAATTTTCCCATATCTGAAGAAACTATTAAACTTCTCAAAGGCCGAGGAGTGACCT
TCCTATTTCCTATACAAGCAAAGACATTCCATCATGTTTACAGCGGGAAGGACTTAATTGCACAGGCACGGACAGGAACTGGGAAGACAT
TCTCCTTTGCCATCCCTTTGATTGAGAAACTTCATGGGGAACTGCAAGACAGGAAGAGAGGCCGTGCCCCTCAGGTACTGGTTCTTGCAC
CTACAAGAGAGTTGGCAAATCAAGTAAGCAAAGACTTCAGTGACATCACAAAAAAGCTGTCAGTGGCTTGTTTTTATGGTGGAACTCCCT
ATGGAGGTCAATTTGAACGCATGAGGAATGGGATTGATATCCTGGTTGGAACACCAGGTCGTATCAAAGACCACATACAGAATGGCAAAC
TAGATCTCACCAAACTTAAGCATGTTGTCCTGGATGAAGTGGACCAGATGTTGGATATGGGATTTGCTGATCAAGTGGAAGAGATTTTAA
GTGTGGCATACAAGAAAGATTCTGAAGACAATCCCCAAACATTGCTTTTTTCTGCAACTTGCCCTCATTGGGTATTTAATGTTGCCAAGA
AATACATGAAATCTACATATGAACAGGTGGACCTGATTGGTAAAAAGACTCAGAAAACGGCAATAACTGTGGAGCATCTGGCTATTAAGT
GCCACTGGACTCAGAGGGCAGCAGTTATTGGGGATGTCATCCGAGTATATAGTGGTCATCAAGGACGCACTATCATCTTTTGTGAAACCA
AGAAAGAAGCCCAGGAGCTGTCCCAGAATTCAGCTATAAAGCAGGATGCTCAGTCCTTGCATGGAGACATTCCACAGAAGCAAAGGGAAA
TCACCCTGAAAGGTTTTAGAAATGGTAGTTTTGGAGTTTTGGTGGCAACCAATGTTGCTGCACGTGGGTTAGACATCCCTGAGGTTGATT
TGGTTATACAAAGCTCTCCACCAAAGGATGTAGAGTCCTACATTCATCGATCCGGGCGGACAGGCAGAGCTGGAAGGACGGGGGTGTGCA
TCTGCTTTTATCAGCACAAGGAAGAATATCAGTTAGTACAAGTGGAGCAAAAAGCGGGAATTAAGTTCAAACGAATAGGTGTTCCTTCTG
CAACAGAAATAATAAAAGCTTCCAGCAAAGATGCCATCAGGCTTTTGGATTCCGTGCCTCCCACTGCCATTAGTCACTTCAAACAATCAG
CTGAGAAGCTGATAGAGGAGAAGGGAGCTGTGGAAGCTCTGGCAGCAGCACTGGCCCATATTTCAGGTGCCACGTCCGTAGACCAGCGCT
CCTTGATCAACTCAAATGTGGGTTTTGTGACCATGATCTTGCAGTGCTCAATTGAAATGCCAAATATTAGTTATGCTTGGAAAGAACTTA
AAGAGCAGCTGGGCGAGGAGATTGATTCCAAAGTGAAGGGAATGGTTTTTCTCAAAGGAAAGCTGGGTGTTTGCTTTGATGTACCTACCG
CATCAGTAACAGAAATACAGAGGCAGTCGAGGCTTCAGGGGACAGCGGGACGGAAACAGAAGATTCAGAGGACAGCGGGAAGGCAGTAGA
GGCCCGAGAGGACAGCGATCAGGAGGTGGCAACAAAAGTAACAGATCCCAAAACAAAGGCCAGAAGCGGAGTTTCAGTAAAGCATTTGGT
CAATAATTAGAAATAGAAGATTTATATAGCAAAAAGAGAATGATGTTTGGCAATATAGAACTGAACATTATTTTTCATGCAAAGTTAAAA
GCACATTGTGCCTCCTTTTGACCACTTGCCAAGTCCCTGTCTCTTTCAGACACAGACAAGCTTCATTTAAATTATTTCATCTGATCATTA
TCATTTATAACTTTATTGTTACTTCTTCATCAGTTTTTCCTTTTGAAAGGTGTATGAATTCATTACATTTTTATTCTAATGTATTATCTG
TAGATTAGAAGATAAAATCAAGCATGTATCTGCCTATACTTTGTGAGTTCACCTGTCTTTATACTCAAAAGTGTCCCTTAATAGTGTCCT
TCCCTGAAATAAATACCTAAGGGAGTGTAACAGTCTCTGGAGGACCACTTTGAGCCTTTGGAAGTTAAGGTTTCCTCAGCCACCTGCCGA
ACAGTTTCTCATGTGGTCCTATTATTTGTCTACTGAGACTTAATACTGAGCAATGTTTTGAAACAAGATTTCAAACTAATCTGGGTTGTA
ATACAGTTTATACCAGTGTATGCTCTAGACTTGGAAGATGTAGTATGTTTGATGTGGATTACCTATACTTATGTTCGTTTTGATACATTT
TTAGCTTCTCATTATAAGGTGATTCATGCTTTAGTGAATTCTTCATAGATAGTATATATAAAAGTACATTTTAATAGAAAGCCAGGGTTT
TAAGGAATTTCACATGTATAAGGTGGCTCCATAGCTTTATTTGTAAGTAGGCTGGATAAATGGTGCTTAAATGGTAATGTACTCCACTTC
TTCCTATTGGAAGATTAACATTATTTACCAAGAAGGACTTAAGGGAGTAGGGGGCGCAGATTAGCATTGCTCAAGAGTATGTAAAAAAAA
AAAAAAAAAAAAAGAACCAAACCACTGGAAATAATCAAATGCAAAAAGGTAACAAATTCATAACTGGAAAGCAAAGAGAAGAACAAGTAT
GATTTGGATGATAAAGCATTGTTTTAATGGTGAAAACTTCACAGATCACTAATGTTTCTAGAGGTTAACTTCAAGTGGGCAAGCTGGGGT
TTTTAGGTAGTCAGTGGCCTAGTTCCTAAAGCCACAGTATAGGATCTGTTAAACTGAATGTCTGTTGAAAGTTTGTTTTAGCTGCTTGGA
GGCTTCCTTTTAAGACAAACTGTATGTGATTAAGTTGTTTTGAGGGAACTGAAGAACCTGATGTAGCCCCTGGCCAGATAACTGCCTGAT
TTCTCAGATATTATTTCTCTGGGAAACATTCTACATAGCACAGGAGCTTAAGAGTGGCATTATCTTCTCGCCTTAATTTCCAGAGATTAT
TTCTGTACTGAGAATCCTGGAACTACTATGCTAGGAAATTTAAAGCTGCATGGTCTGTCTTGTTTTCATTTAATTATTGTGAATACCTAG
AATCTTTCTTGGTCCTGATTTCTCTTGCTTAATCCAGTCTTTATCTCTAACTGCCCCTTATTTGATCACCATGTACTAGGAGCTCTGATA
GCCAGCTCAGCTCCTAATCCTTGAGGCAACATTCTTTTTCTATTTGAACTTCAGTTCTGTCCTTGAATCCCGACTAGATATTTCTTGCCC
TCTGGTCTCAGAATTCTCTTGGCTTTTATTCCTTGATCCACTTGCCAGTTTTATCACTTTACCCTTGTTCCTCATGGCTTCCCATCAAGC
CATGGGTATTAGGTGACAGTGTAATTTATTAGATTCTGGTTTTGCCCAAATACTGGGCATGCTTTAATAATAACTGAACCATTTCATTAT
TTGGATAGGCATGGGTACCTTATCAAGCAGATTAAAAGGATATGGTACCCGTCCTTTAGAAAAGAACAGCTAAAACCTTGTTGTGGATTA
TGGATTTAGCCTAAAGAAAAATAATCTGGCATAAATTAAGAGTAAGAGAGAAGATTAATAGAAATTTCACTTCACATAACTTAAAACATG
GCTATTTCAATAAAGGACTAAAGTTTCTCCTGGATCCCAGAATTCAACCTGTATTTATAAATGTATAATGTATTTAGCTACTTTTTGGTT
TAAATGAACTTGTTGGGTTAGCTTGGTAAATGTTATAATTTTTACTATTTTCTACAAAGAAAATATTTTCTAATTTAAGTTGGAGCTATC
TGTGCAGCAGTTTCTCTACAGTTGTGCATAAATGTTTTTACTATAAAATGAGCTAATGTATAAAATACTGCTGTATACCATAATAAAGAT
AGTAATACTTGATTTTATTGCCTTATGCCCTGAATCCTGATGGTTTCCCTGAAGTTAATAGGGAGACCCCTGCTTCCTAAACTTACACAT
TTGTGGTGTACCTTTGTCGTAAACGTTTTGATGTTACCTATTTCTTGTGGGTCTCCTATTACCAGCTTCTAAATGAATGTTGTTTTTGAC

>21927_21927_1_DDX21-BEX2_DDX21_chr10_70742402_ENST00000354185_BEX2_chrX_102564533_ENST00000536889_length(amino acids)=718AA_BP=
MKMPGKLRSDAGLESDTAMKKGETLRKQTEEKEKKEKPKSDKTEEIAEEEETVFPKAKQVKKKAEPSEVDMNSPKSKKAKKKEEPSQNDI
SPKTKSLRKKKEPIEKKVVSSKTKKVTKNEEPSEEEIDAPKPKKMKKEKEMNGETREKSPKLKNGFPHPEPDCNPSEAASEESNSEIEQE
IPVEQKEGAFSNFPISEETIKLLKGRGVTFLFPIQAKTFHHVYSGKDLIAQARTGTGKTFSFAIPLIEKLHGELQDRKRGRAPQVLVLAP
TRELANQVSKDFSDITKKLSVACFYGGTPYGGQFERMRNGIDILVGTPGRIKDHIQNGKLDLTKLKHVVLDEVDQMLDMGFADQVEEILS
VAYKKDSEDNPQTLLFSATCPHWVFNVAKKYMKSTYEQVDLIGKKTQKTAITVEHLAIKCHWTQRAAVIGDVIRVYSGHQGRTIIFCETK
KEAQELSQNSAIKQDAQSLHGDIPQKQREITLKGFRNGSFGVLVATNVAARGLDIPEVDLVIQSSPPKDVESYIHRSGRTGRAGRTGVCI
CFYQHKEEYQLVQVEQKAGIKFKRIGVPSATEIIKASSKDAIRLLDSVPPTAISHFKQSAEKLIEEKGAVEALAAALAHISGATSVDQRS

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Fusion Gene PPI Analysis for DDX21-BEX2


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 DDX21-BEX2


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 DDX21-BEX2


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