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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:HLA-DQB1-SRSF3 (FusionGDB2 ID:36545)

Fusion Gene Summary for HLA-DQB1-SRSF3

check button Fusion gene summary
Fusion gene informationFusion gene name: HLA-DQB1-SRSF3
Fusion gene ID: 36545
HgeneTgene
Gene symbol

HLA-DQB1

SRSF3

Gene ID

3120

6428

Gene namemajor histocompatibility complex, class II, DQ beta 2serine and arginine rich splicing factor 3
SynonymsDQB2|HLA-DQB1|HLA-DXBSFRS3|SRp20
Cytomap

6p21.32

6p21.31-p21.2

Type of geneprotein-codingprotein-coding
DescriptionHLA class II histocompatibility antigen, DQ beta 2 chainDV19.1 (major histocompatibility complex, class II, DQ beta 2 (HLA-DXB))HLA class II histocompatibility antigen, DX beta chainMHC class II antigen DQB2serine/arginine-rich splicing factor 3epididymis secretory sperm binding proteinpre-mRNA splicing factor SRp20pre-mRNA-splicing factor SRP20splicing factor, arginine/serine-rich 3splicing factor, arginine/serine-rich, 20-kD
Modification date2020031320200313
UniProtAcc

P01920

.
Ensembl transtripts involved in fusion geneENST00000399082, ENST00000399079, 
ENST00000374943, ENST00000434651, 
ENST00000399084, ENST00000460185, 
ENST00000383121, ENST00000548953, 
ENST00000434886, ENST00000430790, 
ENST00000416192, ENST00000399074, 
ENST00000422950, ENST00000486521, 
ENST00000424530, ENST00000433936, 
ENST00000399088, ENST00000399065, 
ENST00000413089, ENST00000476430, 
ENST00000383247, ENST00000399670, 
ENST00000551970, ENST00000415926, 
ENST00000428219, ENST00000419914, 
ENST00000421888, ENST00000424806, 
ENST00000547498, ENST00000493020, 
ENST00000414518, ENST00000549367, 
ENST00000548083, 
ENST00000373715, 
ENST00000339436, 
Fusion gene scores* DoF score5 X 5 X 2=5011 X 11 X 3=363
# samples 512
** MAII scorelog2(5/50*10)=0log2(12/363*10)=-1.59693514238723
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HLA-DQB1 [Title/Abstract] AND SRSF3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHLA-DQB1(32632574)-SRSF3(36568928), # samples:1
Anticipated loss of major functional domain due to fusion event.HLA-DQB1-SRSF3 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
HLA-DQB1-SRSF3 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
HLA-DQB1-SRSF3 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor 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
TgeneSRSF3

GO:0006406

mRNA export from nucleus

28984244

TgeneSRSF3

GO:0048024

regulation of mRNA splicing, via spliceosome

26876937


check buttonFusion gene breakpoints across HLA-DQB1 (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 SRSF3 (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
ChimerDB4Non-CancerTCGA-BR-8060-11AHLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+


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Fusion Gene ORF analysis for HLA-DQB1-SRSF3

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-3CDSENST00000399082ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000399082ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
Frame-shiftENST00000399079ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
5CDS-intronENST00000399079ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
Frame-shiftENST00000374943ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
5CDS-intronENST00000374943ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
Frame-shiftENST00000434651ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
5CDS-intronENST00000434651ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
Frame-shiftENST00000399084ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
5CDS-intronENST00000399084ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000460185ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000460185ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000383121ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000383121ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000548953ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000548953ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000434886ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000434886ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000430790ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000430790ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000416192ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000416192ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000399074ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000399074ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000422950ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000422950ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000486521ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000486521ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000424530ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000424530ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000433936ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000433936ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000399088ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000399088ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000399065ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000399065ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000413089ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000413089ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000476430ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000476430ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000383247ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000383247ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000399670ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000399670ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000551970ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000551970ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000415926ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000415926ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000428219ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000428219ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000419914ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000419914ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000421888ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000421888ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000424806ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000424806ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000547498ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000547498ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000493020ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000493020ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000414518ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000414518ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000549367ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000549367ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-3CDSENST00000548083ENST00000373715HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+
intron-intronENST00000548083ENST00000339436HLA-DQB1chr6

32632574

-SRSF3chr6

36568928

+

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 HLA-DQB1-SRSF3


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)
HLA-DQB1chr632632574-SRSF3chr636568928+0.55167060.4483294
HLA-DQB1chr632632574-SRSF3chr636568928+0.55167060.4483294

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 HLA-DQB1-SRSF3


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
HLA-DQB1

P01920

.
FUNCTION: Binds peptides derived from antigens that access the endocytic route of antigen presenting cells (APC) and presents them on the cell surface for recognition by the CD4 T-cells. The peptide binding cleft accommodates peptides of 10-30 residues. The peptides presented by MHC class II molecules are generated mostly by degradation of proteins that access the endocytic route, where they are processed by lysosomal proteases and other hydrolases. Exogenous antigens that have been endocytosed by the APC are thus readily available for presentation via MHC II molecules, and for this reason this antigen presentation pathway is usually referred to as exogenous. As membrane proteins on their way to degradation in lysosomes as part of their normal turn-over are also contained in the endosomal/lysosomal compartments, exogenous antigens must compete with those derived from endogenous components. Autophagy is also a source of endogenous peptides, autophagosomes constitutively fuse with MHC class II loading compartments. In addition to APCs, other cells of the gastrointestinal tract, such as epithelial cells, express MHC class II molecules and CD74 and act as APCs, which is an unusual trait of the GI tract. To produce a MHC class II molecule that presents an antigen, three MHC class II molecules (heterodimers of an alpha and a beta chain) associate with a CD74 trimer in the ER to form a heterononamer. Soon after the entry of this complex into the endosomal/lysosomal system where antigen processing occurs, CD74 undergoes a sequential degradation by various proteases, including CTSS and CTSL, leaving a small fragment termed CLIP (class-II-associated invariant chain peptide). The removal of CLIP is facilitated by HLA-DM via direct binding to the alpha-beta-CLIP complex so that CLIP is released. HLA-DM stabilizes MHC class II molecules until primary high affinity antigenic peptides are bound. The MHC II molecule bound to a peptide is then transported to the cell membrane surface. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO. Primary dendritic cells (DCs) also to express HLA-DO. Lysosomal microenvironment has been implicated in the regulation of antigen loading into MHC II molecules, increased acidification produces increased proteolysis and efficient peptide loading.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 HLA-DQB1-SRSF3


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 HLA-DQB1-SRSF3


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 HLA-DQB1-SRSF3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneHLA-DQB1P01920DB00071Insulin porkBiotechApproved
HgeneHLA-DQB1P01920DB00071Insulin porkBiotechApproved

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Related Diseases for HLA-DQB1-SRSF3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHLA-DQB1C0027404Narcolepsy4CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneHLA-DQB1C0030805Bullous pemphigoid2ORPHANET
HgeneHLA-DQB1C0036341Schizophrenia2PSYGENET
HgeneHLA-DQB1C0206085Kleine-Levin Syndrome2GENOMICS_ENGLAND
HgeneHLA-DQB1C0751362Narcolepsy-Cataplexy Syndrome2CTD_human;ORPHANET
HgeneHLA-DQB1C0002994Angioedema1CTD_human
HgeneHLA-DQB1C0004096Asthma1CTD_human
HgeneHLA-DQB1C0011609Drug Eruptions1CTD_human
HgeneHLA-DQB1C0011854Diabetes Mellitus, Insulin-Dependent1CTD_human
HgeneHLA-DQB1C0014848Esophageal Achalasia1CTD_human;ORPHANET
HgeneHLA-DQB1C0017661IGA Glomerulonephritis1CTD_human
HgeneHLA-DQB1C0019193Hepatitis, Toxic1CTD_human
HgeneHLA-DQB1C0020517Hypersensitivity1CTD_human
HgeneHLA-DQB1C0025164Megaesophagus1CTD_human
HgeneHLA-DQB1C0026654Moyamoya Disease1GENOMICS_ENGLAND
HgeneHLA-DQB1C0029295Oropharyngeal Neoplasms1CTD_human
HgeneHLA-DQB1C0036421Systemic Scleroderma1CTD_human
HgeneHLA-DQB1C0042109Urticaria1CTD_human
HgeneHLA-DQB1C0205734Diabetes, Autoimmune1CTD_human
HgeneHLA-DQB1C0342302Brittle diabetes1CTD_human
HgeneHLA-DQB1C0406537Morbilliform Drug Reaction1CTD_human
HgeneHLA-DQB1C0859976Idiopathic achalasia of esophagus1ORPHANET
HgeneHLA-DQB1C0860207Drug-Induced Liver Disease1CTD_human
HgeneHLA-DQB1C1262760Hepatitis, Drug-Induced1CTD_human
HgeneHLA-DQB1C1527304Allergic Reaction1CTD_human
HgeneHLA-DQB1C2349952Oropharyngeal Carcinoma1CTD_human
HgeneHLA-DQB1C3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneHLA-DQB1C3837958Diabetes Mellitus, Ketosis-Prone1CTD_human
HgeneHLA-DQB1C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneHLA-DQB1C4279912Chemically-Induced Liver Toxicity1CTD_human
HgeneHLA-DQB1C4554117Diabetes Mellitus, Sudden-Onset1CTD_human
HgeneHLA-DQB1C4706583Limbic encephalitis with leucine-rich glioma-inactivated 1 antibodies1ORPHANET
TgeneSRSF3C0005586Bipolar Disorder1PSYGENET