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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:TCOF1-CD74 (FusionGDB2 ID:89852)

Fusion Gene Summary for TCOF1-CD74

check button Fusion gene summary
Fusion gene informationFusion gene name: TCOF1-CD74
Fusion gene ID: 89852
HgeneTgene
Gene symbol

TCOF1

CD74

Gene ID

6949

972

Gene nametreacle ribosome biogenesis factor 1CD74 molecule
SynonymsMFD1|TCS|TCS1|treacleDHLAG|HLADG|II|Ia-GAMMA|p33
Cytomap

5q32-q33.1

5q33.1

Type of geneprotein-codingprotein-coding
Descriptiontreacle proteinTreacher Collins syndrome proteinTreacher Collins-Franceschetti syndrome 1nucleolar trafficking phosphoproteinHLA 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
Modification date2020031320200313
UniProtAcc.

P04233

Ensembl transtripts involved in fusion geneENST00000323668, ENST00000377797, 
ENST00000394269, ENST00000439160, 
ENST00000445265, ENST00000451292, 
ENST00000504761, ENST00000513346, 
ENST00000506063, 		ENST00000009530, 
ENST00000353334, ENST00000377795, 
ENST00000524315, 
Fusion gene scores* DoF score20 X 12 X 3=72031 X 31 X 11=10571
# samples 2139
** MAII scorelog2(21/720*10)=-1.77760757866355
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(39/10571*10)=-4.76049392566144
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TCOF1 [Title/Abstract] AND CD74 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTCOF1(149755117)-CD74(149785884), # 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
TgeneCD74

GO:0001516

prostaglandin biosynthetic process

12782713

TgeneCD74

GO:0001934

positive regulation of protein phosphorylation

24942581

TgeneCD74

GO:0002792

negative regulation of peptide secretion

19849849

TgeneCD74

GO:0033674

positive regulation of kinase activity

24942581

TgeneCD74

GO:0043066

negative regulation of apoptotic process

12782713

TgeneCD74

GO:0043123

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

24942581

TgeneCD74

GO:0043410

positive regulation of MAPK cascade

24942581

TgeneCD74

GO:0043518

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

17045821

TgeneCD74

GO:0045657

positive regulation of monocyte differentiation

24942581

TgeneCD74

GO:0045893

positive regulation of transcription, DNA-templated

24942581

TgeneCD74

GO:0046598

positive regulation of viral entry into host cell

24942581

TgeneCD74

GO:0050731

positive regulation of peptidyl-tyrosine phosphorylation

17045821

TgeneCD74

GO:0070374

positive regulation of ERK1 and ERK2 cascade

17045821|24942581


check buttonFusion gene breakpoints across TCOF1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across CD74 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4GBMTCGA-76-4932-01ATCOF1chr5

149755117

+CD74chr5

149785884

-


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Fusion Gene ORF analysis for TCOF1-CD74

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
In-frameENST00000323668ENST00000009530TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000323668ENST00000353334TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000323668ENST00000377795TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000323668ENST00000524315TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000377797ENST00000009530TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000377797ENST00000353334TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000377797ENST00000377795TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000377797ENST00000524315TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000394269ENST00000009530TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000394269ENST00000353334TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000394269ENST00000377795TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000394269ENST00000524315TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000439160ENST00000009530TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000439160ENST00000353334TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000439160ENST00000377795TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000439160ENST00000524315TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000445265ENST00000009530TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000445265ENST00000353334TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000445265ENST00000377795TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000445265ENST00000524315TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000451292ENST00000009530TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000451292ENST00000353334TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000451292ENST00000377795TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000451292ENST00000524315TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000504761ENST00000009530TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000504761ENST00000353334TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000504761ENST00000377795TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000504761ENST00000524315TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000513346ENST00000009530TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000513346ENST00000353334TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000513346ENST00000377795TCOF1chr5

149755117

+CD74chr5

149785884

-
In-frameENST00000513346ENST00000524315TCOF1chr5

149755117

+CD74chr5

149785884

-
intron-3CDSENST00000506063ENST00000009530TCOF1chr5

149755117

+CD74chr5

149785884

-
intron-3CDSENST00000506063ENST00000353334TCOF1chr5

149755117

+CD74chr5

149785884

-
intron-3CDSENST00000506063ENST00000377795TCOF1chr5

149755117

+CD74chr5

149785884

-
intron-3CDSENST00000506063ENST00000524315TCOF1chr5

149755117

+CD74chr5

149785884

-

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 TCOF1-CD74


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.
genomic feature

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 TCOF1-CD74


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/chr5:149755117/chr5:149785884)
- 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

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: 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}.

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
HgeneTCOF1chr5:149755117chr5:149785884ENST00000323668+1026204_2074911517.3333333333333Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000323668+102689_974911517.3333333333333Compositional biasNote=Poly-Glu
HgeneTCOF1chr5:149755117chr5:149785884ENST00000377797+1127204_2075681584.0Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000377797+112789_975681584.0Compositional biasNote=Poly-Glu
HgeneTCOF1chr5:149755117chr5:149785884ENST00000394269+1118204_207568959.0Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000394269+111889_97568959.0Compositional biasNote=Poly-Glu
HgeneTCOF1chr5:149755117chr5:149785884ENST00000439160+1126204_2075681482.6666666666667Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000439160+112689_975681482.6666666666667Compositional biasNote=Poly-Glu
HgeneTCOF1chr5:149755117chr5:149785884ENST00000445265+1026204_2074911511.0Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000445265+102689_974911511.0Compositional biasNote=Poly-Glu
HgeneTCOF1chr5:149755117chr5:149785884ENST00000504761+1126204_2075681489.0Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000504761+112689_975681489.0Compositional biasNote=Poly-Glu
HgeneTCOF1chr5:149755117chr5:149785884ENST00000323668+10266_384911517.3333333333333DomainLisH
HgeneTCOF1chr5:149755117chr5:149785884ENST00000377797+11276_385681584.0DomainLisH
HgeneTCOF1chr5:149755117chr5:149785884ENST00000394269+11186_38568959.0DomainLisH
HgeneTCOF1chr5:149755117chr5:149785884ENST00000439160+11266_385681482.6666666666667DomainLisH
HgeneTCOF1chr5:149755117chr5:149785884ENST00000445265+10266_384911511.0DomainLisH
HgeneTCOF1chr5:149755117chr5:149785884ENST00000504761+11266_385681489.0DomainLisH
TgeneCD74chr5:149755117chr5:149785884ENST0000000953029210_271126297.0DomainThyroglobulin type-1
TgeneCD74chr5:149755117chr5:149785884ENST0000035333428210_271126233.0DomainThyroglobulin type-1
TgeneCD74chr5:149755117chr5:149785884ENST0000037779526210_271126280.6666666666667DomainThyroglobulin type-1

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTCOF1chr5:149755117chr5:149785884ENST00000323668+10261362_13664911517.3333333333333Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000323668+10261452_14634911517.3333333333333Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000323668+10261475_14824911517.3333333333333Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000323668+1026693_6964911517.3333333333333Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000323668+1026996_10014911517.3333333333333Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000377797+11271362_13665681584.0Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000377797+11271452_14635681584.0Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000377797+11271475_14825681584.0Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000377797+1127693_6965681584.0Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000377797+1127996_10015681584.0Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000394269+11181362_1366568959.0Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000394269+11181452_1463568959.0Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000394269+11181475_1482568959.0Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000394269+1118693_696568959.0Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000394269+1118996_1001568959.0Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000439160+11261362_13665681482.6666666666667Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000439160+11261452_14635681482.6666666666667Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000439160+11261475_14825681482.6666666666667Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000439160+1126693_6965681482.6666666666667Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000439160+1126996_10015681482.6666666666667Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000445265+10261362_13664911511.0Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000445265+10261452_14634911511.0Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000445265+10261475_14824911511.0Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000445265+1026693_6964911511.0Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000445265+1026996_10014911511.0Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000504761+11261362_13665681489.0Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000504761+11261452_14635681489.0Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000504761+11261475_14825681489.0Compositional biasNote=Poly-Lys
HgeneTCOF1chr5:149755117chr5:149785884ENST00000504761+1126693_6965681489.0Compositional biasNote=Poly-Ser
HgeneTCOF1chr5:149755117chr5:149785884ENST00000504761+1126996_10015681489.0Compositional biasNote=Poly-Ser
TgeneCD74chr5:149755117chr5:149785884ENST00000009530291_46126297.0Topological domainCytoplasmic
TgeneCD74chr5:149755117chr5:149785884ENST000000095302973_296126297.0Topological domainExtracellular
TgeneCD74chr5:149755117chr5:149785884ENST00000353334281_46126233.0Topological domainCytoplasmic
TgeneCD74chr5:149755117chr5:149785884ENST000003533342873_296126233.0Topological domainExtracellular
TgeneCD74chr5:149755117chr5:149785884ENST00000377795261_46126280.6666666666667Topological domainCytoplasmic
TgeneCD74chr5:149755117chr5:149785884ENST000003777952673_296126280.6666666666667Topological domainExtracellular
TgeneCD74chr5:149755117chr5:149785884ENST000000095302947_72126297.0TransmembraneHelical%3B Signal-anchor for type II membrane protein
TgeneCD74chr5:149755117chr5:149785884ENST000003533342847_72126233.0TransmembraneHelical%3B Signal-anchor for type II membrane protein
TgeneCD74chr5:149755117chr5:149785884ENST000003777952647_72126280.6666666666667TransmembraneHelical%3B Signal-anchor for type II membrane protein


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Fusion Gene Sequence for TCOF1-CD74


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 TCOF1-CD74


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 TCOF1-CD74


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 TCOF1-CD74


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