FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:CD74-LY6E (FusionGDB2 ID:14638)

Fusion Gene Summary for CD74-LY6E

check button Fusion gene summary
Fusion gene informationFusion gene name: CD74-LY6E
Fusion gene ID: 14638
HgeneTgene
Gene symbol

CD74

LY6E

Gene ID

972

4061

Gene nameCD74 moleculelymphocyte antigen 6 family member E
SynonymsDHLAG|HLADG|II|Ia-GAMMA|p33RIG-E|RIGE|SCA-2|SCA2|TSA-1
Cytomap

5q33.1

8q24.3

Type of geneprotein-codingprotein-coding
DescriptionHLA class II histocompatibility antigen gamma chainCD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated)CD74 molecule, major histocompatibility complex, class II invariant chainHLA-DR antigens-associated lymphocyte antigen 6Ely-6Elymphocyte antigen 6 complex, locus Eretinoic acid induced gene Eretinoic acid-induced gene E proteinstem cell antigen 2thymic shared antigen 1
Modification date2020031320200313
UniProtAcc

P04233

Q16553

Ensembl transtripts involved in fusion geneENST00000009530, ENST00000353334, 
ENST00000377795, ENST00000524315, 
ENST00000292494, ENST00000429120, 
ENST00000517503, ENST00000519546, 
ENST00000519611, ENST00000521182, 
ENST00000521699, ENST00000522528, 
ENST00000522971, ENST00000519615, 
ENST00000520466, ENST00000520531, 
ENST00000521003, ENST00000522024, 
ENST00000523847, 
Fusion gene scores* DoF score43 X 51 X 20=438604 X 5 X 2=40
# samples 595
** MAII scorelog2(59/43860*10)=-6.21604704731175
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/40*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: CD74 [Title/Abstract] AND LY6E [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCD74(149786800)-LY6E(144103189), # 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
HgeneCD74

GO:0001516

prostaglandin biosynthetic process

12782713

HgeneCD74

GO:0001934

positive regulation of protein phosphorylation

24942581

HgeneCD74

GO:0002792

negative regulation of peptide secretion

19849849

HgeneCD74

GO:0033674

positive regulation of kinase activity

24942581

HgeneCD74

GO:0043066

negative regulation of apoptotic process

12782713

HgeneCD74

GO:0043123

positive regulation of I-kappaB kinase/NF-kappaB signaling

24942581

HgeneCD74

GO:0043410

positive regulation of MAPK cascade

24942581

HgeneCD74

GO:0043518

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

17045821

HgeneCD74

GO:0045657

positive regulation of monocyte differentiation

24942581

HgeneCD74

GO:0045893

positive regulation of transcription, DNA-templated

24942581

HgeneCD74

GO:0046598

positive regulation of viral entry into host cell

24942581

HgeneCD74

GO:0050731

positive regulation of peptidyl-tyrosine phosphorylation

17045821

HgeneCD74

GO:0070374

positive regulation of ERK1 and ERK2 cascade

17045821|24942581


check buttonFusion gene breakpoints across CD74 (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 LY6E (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
ChimerDB4UCECTCGA-B5-A11P-01BCD74chr5

149786800

-LY6Echr8

144103189

+


Top

Fusion Gene ORF analysis for CD74-LY6E

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-3UTRENST00000009530ENST00000292494CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000009530ENST00000429120CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000009530ENST00000517503CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000009530ENST00000519546CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000009530ENST00000519611CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000009530ENST00000521182CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000009530ENST00000521699CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000009530ENST00000522528CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000009530ENST00000522971CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000353334ENST00000292494CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000353334ENST00000429120CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000353334ENST00000517503CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000353334ENST00000519546CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000353334ENST00000519611CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000353334ENST00000521182CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000353334ENST00000521699CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000353334ENST00000522528CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000353334ENST00000522971CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000377795ENST00000292494CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000377795ENST00000429120CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000377795ENST00000517503CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000377795ENST00000519546CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000377795ENST00000519611CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000377795ENST00000521182CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000377795ENST00000521699CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000377795ENST00000522528CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000377795ENST00000522971CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000524315ENST00000292494CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000524315ENST00000429120CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000524315ENST00000517503CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000524315ENST00000519546CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000524315ENST00000519611CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000524315ENST00000521182CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000524315ENST00000521699CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000524315ENST00000522528CD74chr5

149786800

-LY6Echr8

144103189

+
intron-3UTRENST00000524315ENST00000522971CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000009530ENST00000519615CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000009530ENST00000520466CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000009530ENST00000520531CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000009530ENST00000521003CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000009530ENST00000522024CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000009530ENST00000523847CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000353334ENST00000519615CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000353334ENST00000520466CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000353334ENST00000520531CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000353334ENST00000521003CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000353334ENST00000522024CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000353334ENST00000523847CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000377795ENST00000519615CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000377795ENST00000520466CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000377795ENST00000520531CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000377795ENST00000521003CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000377795ENST00000522024CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000377795ENST00000523847CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000524315ENST00000519615CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000524315ENST00000520466CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000524315ENST00000520531CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000524315ENST00000521003CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000524315ENST00000522024CD74chr5

149786800

-LY6Echr8

144103189

+
intron-intronENST00000524315ENST00000523847CD74chr5

149786800

-LY6Echr8

144103189

+

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

Top

Fusion Genomic Features for CD74-LY6E


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.

Top

Fusion Protein Features for CD74-LY6E


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/:149786800/:144103189)
- 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
CD74

P04233

LY6E

Q16553

FUNCTION: Plays a critical role in MHC class II antigen processing by stabilizing peptide-free class II alpha/beta heterodimers in a complex soon after their synthesis and directing transport of the complex from the endoplasmic reticulum to the endosomal/lysosomal system where the antigen processing and binding of antigenic peptides to MHC class II takes place. Serves as cell surface receptor for the cytokine MIF.; FUNCTION: [Class-II-associated invariant chain peptide]: Binds to the peptide-binding site of MHC class II alpha/beta heterodimers forming an alpha-beta-CLIP complex, thereby preventing the loading of antigenic peptides to the MHC class II complex until its release by HLA-DM in the endosome. {ECO:0000269|PubMed:1448172}.; FUNCTION: [Isoform p41]: Stabilizes the conformation of mature CTSL by binding to its active site and serving as a chaperone to help maintain a pool of mature enzyme in endocytic compartments and extracellular space of antigen-presenting cells (APCs). Has antiviral activity by stymieing the endosomal entry of Ebola virus and coronaviruses, including SARS-CoV-2 (PubMed:32855215). Disrupts cathepsin-mediated Ebola virus glycoprotein processing, which prevents viral fusion and entry. This antiviral activity is specific to p41 isoform (PubMed:32855215). {ECO:0000250|UniProtKB:P04441, ECO:0000269|PubMed:32855215}.FUNCTION: GPI-anchored cell surface protein that regulates T-lymphocytes proliferation, differentiation, and activation. Regulates the T-cell receptor (TCR) signaling by interacting with component CD3Z/CD247 at the plasma membrane, leading to CD3Z/CD247 phosphorylation modulation (By similarity). Restricts the entry of human coronaviruses, including SARS-CoV, MERS-CoV and SARS-CoV-2, by interfering with spike protein-mediated membrane fusion (PubMed:32641482). Plays also an essential role in placenta formation by acting as the main receptor for syncytin-A (SynA). Therefore, participates in the normal fusion of syncytiotrophoblast layer I (SynT-I) and in the proper morphogenesis of both fetal and maternal vasculatures within the placenta. May also act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity (By similarity). {ECO:0000250|UniProtKB:Q64253, ECO:0000269|PubMed:32641482}.; FUNCTION: (Microbial infection) Promotes entry, likely through an enhanced virus-cell fusion process, of various viruses including HIV-1, West Nile virus, dengue virus and Zika virus (PubMed:28130445). In contrast, the paramyxovirus PIV5, which enters at the plasma membrane, does not require LY6E (PubMed:28130445, PubMed:29610346). Mechanistically, adopts a microtubule-like organization upon viral infection and enhances viral uncoating after endosomal escape (PubMed:28130445, PubMed:30190477). {ECO:0000269|PubMed:28130445, ECO:0000269|PubMed:29610346, ECO:0000269|PubMed:30190477}.

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


Top

Fusion Gene Sequence for CD74-LY6E


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.

Top

Fusion Gene PPI Analysis for CD74-LY6E


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


Top

Related Drugs for CD74-LY6E


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

Top

Related Diseases for CD74-LY6E


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