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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:JAK2-RCL1 (FusionGDB2 ID:40677)

Fusion Gene Summary for JAK2-RCL1

check button Fusion gene summary
Fusion gene informationFusion gene name: JAK2-RCL1
Fusion gene ID: 40677
HgeneTgene
Gene symbol

JAK2

RCL1

Gene ID

3717

10171

Gene nameJanus kinase 2RNA terminal phosphate cyclase like 1
SynonymsJTK10|THCYT3RNAC|RPCL1
Cytomap

9p24.1

9p24.1

Type of geneprotein-codingprotein-coding
Descriptiontyrosine-protein kinase JAK2JAK-2Janus kinase 2 (a protein tyrosine kinase)RNA 3'-terminal phosphate cyclase-like proteinRNA cyclase homolog
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000539801, ENST00000381652, 
ENST00000544510, ENST00000487310, 
ENST00000381750, ENST00000381730, 
ENST00000381728, ENST00000448872, 
ENST00000381732, ENST00000445485, 
Fusion gene scores* DoF score13 X 10 X 8=10407 X 8 X 6=336
# samples 119
** MAII scorelog2(11/1040*10)=-3.24100809950379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/336*10)=-1.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: JAK2 [Title/Abstract] AND RCL1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointJAK2(5090911)-RCL1(4834141), # samples:3
Anticipated loss of major functional domain due to fusion event.JAK2-RCL1 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
JAK2-RCL1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
JAK2-RCL1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
JAK2-RCL1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
JAK2-RCL1 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneJAK2

GO:0010811

positive regulation of cell-substrate adhesion

10925297

HgeneJAK2

GO:0019221

cytokine-mediated signaling pathway

8609418

HgeneJAK2

GO:0033209

tumor necrosis factor-mediated signaling pathway

8609418

HgeneJAK2

GO:0034612

response to tumor necrosis factor

8609418

HgeneJAK2

GO:0035409

histone H3-Y41 phosphorylation

19783980

HgeneJAK2

GO:0035722

interleukin-12-mediated signaling pathway

7528775

HgeneJAK2

GO:0046677

response to antibiotic

16280321

HgeneJAK2

GO:0050727

regulation of inflammatory response

10925297

HgeneJAK2

GO:0060396

growth hormone receptor signaling pathway

10925297

HgeneJAK2

GO:0070671

response to interleukin-12

7528775


check buttonFusion gene breakpoints across JAK2 (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 RCL1 (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
ChimerDB4CESCTCGA-PN-A8MA-01AJAK2chr9

5090911

+RCL1chr9

4834141

+
ChimerDB4CESCTCGA-PN-A8MA-01AJAK2chr9

5090911

+RCL1chr9

4834141

+
ChimerDB4CESCTCGA-PN-A8MA-01AJAK2chr9

5090911

-RCL1chr9

4834141

+


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Fusion Gene ORF analysis for JAK2-RCL1

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-shiftENST00000539801ENST00000381750JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000539801ENST00000381730JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000539801ENST00000381728JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000539801ENST00000448872JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000539801ENST00000381732JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000539801ENST00000445485JAK2chr9

5090911

+RCL1chr9

4834141

+
Frame-shiftENST00000381652ENST00000381750JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000381652ENST00000381730JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000381652ENST00000381728JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000381652ENST00000448872JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000381652ENST00000381732JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000381652ENST00000445485JAK2chr9

5090911

+RCL1chr9

4834141

+
Frame-shiftENST00000544510ENST00000381750JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000544510ENST00000381730JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000544510ENST00000381728JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000544510ENST00000448872JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000544510ENST00000381732JAK2chr9

5090911

+RCL1chr9

4834141

+
5CDS-intronENST00000544510ENST00000445485JAK2chr9

5090911

+RCL1chr9

4834141

+
intron-3CDSENST00000487310ENST00000381750JAK2chr9

5090911

+RCL1chr9

4834141

+
intron-intronENST00000487310ENST00000381730JAK2chr9

5090911

+RCL1chr9

4834141

+
intron-intronENST00000487310ENST00000381728JAK2chr9

5090911

+RCL1chr9

4834141

+
intron-intronENST00000487310ENST00000448872JAK2chr9

5090911

+RCL1chr9

4834141

+
intron-intronENST00000487310ENST00000381732JAK2chr9

5090911

+RCL1chr9

4834141

+
intron-intronENST00000487310ENST00000445485JAK2chr9

5090911

+RCL1chr9

4834141

+

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 JAK2-RCL1


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)
JAK2chr95090911+RCL1chr94834140+0.3695010.630499
JAK2chr95090911+RCL1chr94834140+0.3695010.630499

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 JAK2-RCL1


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
..
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.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 JAK2-RCL1


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 JAK2-RCL1


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 JAK2-RCL1


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 JAK2-RCL1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneJAK2C0032463Polycythemia Vera12CTD_human;ORPHANET;UNIPROT
HgeneJAK2C0040028Thrombocythemia, Essential10CTD_human;ORPHANET
HgeneJAK2C0001815Primary Myelofibrosis9CGI;CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneJAK2C3489628Thrombocytosis, Autosomal Dominant8CTD_human
HgeneJAK2C0019154Hepatic Vein Thrombosis3CTD_human;ORPHANET
HgeneJAK2C0856761Budd-Chiari Syndrome3CTD_human;ORPHANET
HgeneJAK2C0009324Ulcerative Colitis2CTD_human
HgeneJAK2C0027022Myeloproliferative disease2CTD_human
HgeneJAK2C0151744Myocardial Ischemia2CTD_human
HgeneJAK2C0836924Thrombocytosis2CTD_human
HgeneJAK2C3281125THROMBOCYTHEMIA 32UNIPROT
HgeneJAK2C0000786Spontaneous abortion1CTD_human
HgeneJAK2C0000822Abortion, Tubal1CTD_human
HgeneJAK2C0006663Calcinosis1CTD_human
HgeneJAK2C0007873Uterine Cervical Neoplasm1CTD_human
HgeneJAK2C0018824Heart valve disease1CTD_human
HgeneJAK2C0019207Hepatoma, Morris1CTD_human
HgeneJAK2C0019208Hepatoma, Novikoff1CTD_human
HgeneJAK2C0021368Inflammation1CTD_human
HgeneJAK2C0023418leukemia1CTD_human
HgeneJAK2C0023467Leukemia, Myelocytic, Acute1CGI;CTD_human;UNIPROT
HgeneJAK2C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneJAK2C0023904Liver Neoplasms, Experimental1CTD_human
HgeneJAK2C0025472Mesenteric Vascular Occlusion1CTD_human
HgeneJAK2C0026998Acute Myeloid Leukemia, M11CTD_human
HgeneJAK2C0032461Polycythemia1CTD_human
HgeneJAK2C0032962Pregnancy Complications1CTD_human
HgeneJAK2C0033578Prostatic Neoplasms1CTD_human
HgeneJAK2C0040038Thromboembolism1CTD_human
HgeneJAK2C0042487Venous Thrombosis1CTD_human
HgeneJAK2C0086404Experimental Hepatoma1CTD_human
HgeneJAK2C0149871Deep Vein Thrombosis1CTD_human
HgeneJAK2C0263628Tumoral calcinosis1CTD_human
HgeneJAK2C0376358Malignant neoplasm of prostate1CTD_human
HgeneJAK2C0400966Non-alcoholic Fatty Liver Disease1CTD_human
HgeneJAK2C0521174Microcalcification1CTD_human
HgeneJAK2C1527405Erythrocytosis1CTD_human
HgeneJAK2C1879321Acute Myeloid Leukemia (AML-M2)1CTD_human
HgeneJAK2C3241937Nonalcoholic Steatohepatitis1CTD_human
HgeneJAK2C3495676Anorectal Malformations1GENOMICS_ENGLAND
HgeneJAK2C3830362Early Pregnancy Loss1CTD_human
HgeneJAK2C4048328cervical cancer1CTD_human
HgeneJAK2C4303761Familial thrombocytosis1ORPHANET
HgeneJAK2C4552766Miscarriage1CTD_human
TgeneRCL1C0152013Adenocarcinoma of lung (disorder)1CTD_human