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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-TMEM43 (FusionGDB2 ID:HG960TG79188)

Fusion Gene Summary for CD44-TMEM43

check button Fusion gene summary
Fusion gene informationFusion gene name: CD44-TMEM43
Fusion gene ID: hg960tg79188
HgeneTgene
Gene symbol

CD44

TMEM43

Gene ID

960

79188

Gene nameCD44 molecule (Indian blood group)transmembrane protein 43
SynonymsCDW44|CSPG8|ECMR-III|HCELL|HUTCH-I|IN|LHR|MC56|MDU2|MDU3|MIC4|Pgp1ARVC5|ARVD5|EDMD7|LUMA
Cytomap('CD44')('TMEM43')

11p13

3p25.1

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 transmembrane protein 43
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000415148, ENST00000428726, 
ENST00000433354, ENST00000433892, 
ENST00000434472, ENST00000449691, 
ENST00000263398, ENST00000278386, 
ENST00000352818, ENST00000360158, 
ENST00000437706, ENST00000526025, 
ENST00000526669, ENST00000528922, 
Fusion gene scores* DoF score24 X 25 X 12=72003 X 3 X 3=27
# samples 363
** MAII scorelog2(36/7200*10)=-4.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CD44 [Title/Abstract] AND TMEM43 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCD44(35232876)-TMEM43(14184588), # samples:1
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
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

TgeneTMEM43

GO:0071763

nuclear membrane organization

18230648



check button Fusion gene information
* 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
ChimerDB4STADTCGA-FP-8209-01ACD44chr11

35232876

+TMEM43chr3

14184588

+


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Fusion Gene ORF analysis for CD44-TMEM43

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
5CDS-3UTRENST00000415148ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
5CDS-3UTRENST00000428726ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
5CDS-3UTRENST00000433354ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
5CDS-3UTRENST00000433892ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
5CDS-3UTRENST00000434472ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
5CDS-3UTRENST00000449691ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
intron-3UTRENST00000263398ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
intron-3UTRENST00000278386ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
intron-3UTRENST00000352818ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
intron-3UTRENST00000360158ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
intron-3UTRENST00000437706ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
intron-3UTRENST00000526025ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
intron-3UTRENST00000526669ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+
intron-3UTRENST00000528922ENST00000306077CD44chr11

35232876

+TMEM43chr3

14184588

+

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-TMEM43


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)


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Fusion Protein Features for CD44-TMEM43


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/:35232876/:14184588)
- 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
..
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: 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}.

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-TMEM43


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-TMEM43


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-TMEM43


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 CD44-TMEM43


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
TgeneC1858379ARRHYTHMOGENIC RIGHT VENTRICULAR DYSPLASIA, FAMILIAL, 5 (disorder)3CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC3553060EMERY-DREIFUSS MUSCULAR DYSTROPHY 7, AUTOSOMAL DOMINANT3GENOMICS_ENGLAND;UNIPROT
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0085298Sudden Cardiac Death1CTD_human
TgeneC0410190Autosomal Dominant Emery-Dreifuss Muscular Dystrophy (disorder)1CTD_human;ORPHANET
TgeneC1720824Sudden Cardiac Arrest1CTD_human