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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:CD44-BPIFC (FusionGDB2 ID:14549)

Fusion Gene Summary for CD44-BPIFC

check button Fusion gene summary
Fusion gene informationFusion gene name: CD44-BPIFC
Fusion gene ID: 14549
HgeneTgene
Gene symbol

CD44

BPIFC

Gene ID

960

254240

Gene nameCD44 molecule (Indian blood group)BPI fold containing family C
SynonymsCDW44|CSPG8|ECMR-III|HCELL|HUTCH-I|IN|LHR|MC56|MDU2|MDU3|MIC4|Pgp1BPIL2
Cytomap

11p13

22q12.3

Type of geneprotein-codingprotein-coding
DescriptionCD44 antigenGP90 lymphocyte homing/adhesion receptorHermes antigenIndian blood group antigencell surface glycoprotein CD44chondroitin sulfate proteoglycan 8epicanextracellular matrix receptor IIIhematopoietic cell E- and L-selectin ligandheparan BPI fold-containing family C proteinBPI-like 2bactericidal/permeability-increasing protein-like 2
Modification date2020032920200313
UniProtAcc

P16070

Q8NFQ6

Ensembl transtripts involved in fusion geneENST00000263398, ENST00000526025, 
ENST00000449691, ENST00000360158, 
ENST00000415148, ENST00000437706, 
ENST00000433354, ENST00000428726, 
ENST00000526669, ENST00000433892, 
ENST00000278386, ENST00000434472, 
ENST00000352818, ENST00000528922, 
ENST00000300399, ENST00000397452, 
ENST00000534972, ENST00000432451, 
ENST00000397450, 
Fusion gene scores* DoF score24 X 25 X 12=72004 X 4 X 3=48
# samples 364
** MAII scorelog2(36/7200*10)=-4.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CD44 [Title/Abstract] AND BPIFC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCD44(35211612)-BPIFC(32810412), # samples:1
Anticipated loss of major functional domain due to fusion event.CD44-BPIFC seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
CD44-BPIFC seems lost the major protein functional domain in Hgene partner, which is a cell metabolism 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
HgeneCD44

GO:0007155

cell adhesion

19703720

HgeneCD44

GO:0016477

cell migration

22726066

HgeneCD44

GO:0030214

hyaluronan catabolic process

17170110

HgeneCD44

GO:0033138

positive regulation of peptidyl-serine phosphorylation

17045821

HgeneCD44

GO:0042110

T cell activation

7528188

HgeneCD44

GO:0043518

negative regulation of DNA damage response, signal transduction by p53 class mediator

17045821

HgeneCD44

GO:0044344

cellular response to fibroblast growth factor stimulus

19577615

HgeneCD44

GO:0050731

positive regulation of peptidyl-tyrosine phosphorylation

17045821

HgeneCD44

GO:0070374

positive regulation of ERK1 and ERK2 cascade

17045821

HgeneCD44

GO:1902166

negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator

17045821


check buttonFusion gene breakpoints across CD44 (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 BPIFC (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
ChimerDB4ESCATCGA-IG-A3Y9CD44chr11

35211612

+BPIFCchr22

32810412

-


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Fusion Gene ORF analysis for CD44-BPIFC

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-shiftENST00000263398ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000263398ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000263398ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000263398ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
5CDS-intronENST00000263398ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000526025ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000526025ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000526025ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000526025ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-intronENST00000526025ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000449691ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000449691ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000449691ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000449691ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
5CDS-intronENST00000449691ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000360158ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000360158ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000360158ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000360158ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
5CDS-intronENST00000360158ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000415148ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000415148ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000415148ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000415148ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
5CDS-intronENST00000415148ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000437706ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000437706ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000437706ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000437706ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
5CDS-intronENST00000437706ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000433354ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000433354ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000433354ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000433354ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
5CDS-intronENST00000433354ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000428726ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000428726ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000428726ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000428726ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
5CDS-intronENST00000428726ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000526669ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000526669ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000526669ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000526669ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-intronENST00000526669ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000433892ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000433892ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000433892ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000433892ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
5CDS-intronENST00000433892ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000278386ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000278386ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000278386ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000278386ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-intronENST00000278386ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000434472ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000434472ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000434472ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000434472ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
5CDS-intronENST00000434472ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000352818ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000352818ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000352818ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
Frame-shiftENST00000352818ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
5CDS-intronENST00000352818ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000528922ENST00000300399CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000528922ENST00000397452CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000528922ENST00000534972CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-3CDSENST00000528922ENST00000432451CD44chr11

35211612

+BPIFCchr22

32810412

-
intron-intronENST00000528922ENST00000397450CD44chr11

35211612

+BPIFCchr22

32810412

-

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 CD44-BPIFC


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.

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 CD44-BPIFC


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
CD44

P16070

BPIFC

Q8NFQ6

FUNCTION: Cell-surface receptor that plays a role in cell-cell interactions, cell adhesion and migration, helping them to sense and respond to changes in the tissue microenvironment (PubMed:16541107, PubMed:19703720, PubMed:22726066). Participates thereby in a wide variety of cellular functions including the activation, recirculation and homing of T-lymphocytes, hematopoiesis, inflammation and response to bacterial infection (PubMed:7528188). Engages, through its ectodomain, extracellular matrix components such as hyaluronan/HA, collagen, growth factors, cytokines or proteases and serves as a platform for signal transduction by assembling, via its cytoplasmic domain, protein complexes containing receptor kinases and membrane proteases (PubMed:18757307, PubMed:23589287). Such effectors include PKN2, the RhoGTPases RAC1 and RHOA, Rho-kinases and phospholipase C that coordinate signaling pathways promoting calcium mobilization and actin-mediated cytoskeleton reorganization essential for cell migration and adhesion (PubMed:15123640). {ECO:0000269|PubMed:15123640, ECO:0000269|PubMed:16541107, ECO:0000269|PubMed:18757307, ECO:0000269|PubMed:19703720, ECO:0000269|PubMed:22726066, ECO:0000269|PubMed:23589287, ECO:0000269|PubMed:7528188}.

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 CD44-BPIFC


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 CD44-BPIFC


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 CD44-BPIFC


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneCD44P16070DB08818Hyaluronic acidSmall moleculeApproved|Vet_approved
HgeneCD44P16070DB08818Hyaluronic acidSmall moleculeApproved|Vet_approved
HgeneCD44P16070DB08818Hyaluronic acidSmall moleculeApproved|Vet_approved
HgeneCD44P16070DB08818Hyaluronic acidSmall moleculeApproved|Vet_approved
HgeneCD44P16070DB08818Hyaluronic acidSmall moleculeApproved|Vet_approved

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Related Diseases for CD44-BPIFC


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCD44C0023487Acute Promyelocytic Leukemia2CTD_human
HgeneCD44C0009405Hereditary Nonpolyposis Colorectal Neoplasms1CTD_human
HgeneCD44C0011616Contact Dermatitis1CTD_human
HgeneCD44C0017661IGA Glomerulonephritis1CTD_human
HgeneCD44C0022660Kidney Failure, Acute1CTD_human
HgeneCD44C0023467Leukemia, Myelocytic, Acute1CTD_human
HgeneCD44C0024623Malignant neoplasm of stomach1CTD_human
HgeneCD44C0024668Mammary Neoplasms, Experimental1CTD_human
HgeneCD44C0026998Acute Myeloid Leukemia, M11CTD_human
HgeneCD44C0027627Neoplasm Metastasis1CTD_human
HgeneCD44C0027746Nerve Degeneration1CTD_human
HgeneCD44C0030297Pancreatic Neoplasm1CTD_human
HgeneCD44C0032580Adenomatous Polyposis Coli1CTD_human
HgeneCD44C0037274Dermatologic disorders1CTD_human
HgeneCD44C0038356Stomach Neoplasms1CTD_human
HgeneCD44C0042900Vitiligo1CTD_human
HgeneCD44C0162351Contact hypersensitivity1CTD_human
HgeneCD44C0274861Arsenic Poisoning, Inorganic1CTD_human
HgeneCD44C0274862Nervous System, Organic Arsenic Poisoning1CTD_human
HgeneCD44C0311375Arsenic Poisoning1CTD_human
HgeneCD44C0346647Malignant neoplasm of pancreas1CTD_human
HgeneCD44C0751851Arsenic Encephalopathy1CTD_human
HgeneCD44C0751852Arsenic Induced Polyneuropathy1CTD_human
HgeneCD44C1333990Hereditary Nonpolyposis Colorectal Cancer1CTD_human
HgeneCD44C1565662Acute Kidney Insufficiency1CTD_human
HgeneCD44C1708349Hereditary Diffuse Gastric Cancer1CTD_human
HgeneCD44C1879321Acute Myeloid Leukemia (AML-M2)1CTD_human
HgeneCD44C2609414Acute kidney injury1CTD_human
HgeneCD44C2713442Polyposis, Adenomatous Intestinal1CTD_human
HgeneCD44C2713443Familial Intestinal Polyposis1CTD_human
HgeneCD44C4552100Lynch Syndrome1CTD_human