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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:LITAF-CNOT10 (FusionGDB2 ID:45669)

Fusion Gene Summary for LITAF-CNOT10

check button Fusion gene summary
Fusion gene informationFusion gene name: LITAF-CNOT10
Fusion gene ID: 45669
HgeneTgene
Gene symbol

LITAF

CNOT10

Gene ID

9516

25904

Gene namelipopolysaccharide induced TNF factorCCR4-NOT transcription complex subunit 10
SynonymsPIG7|SIMPLE|TP53I7-
Cytomap

16p13.13

3p22.3

Type of geneprotein-codingprotein-coding
Descriptionlipopolysaccharide-induced tumor necrosis factor-alpha factorLPS-induced TNF-alpha factorlipopolysaccharide-induced TNF-alpha factorp53-induced gene 7 proteinsmall integral membrane protein of lysosome/late endosometumor protein p53 inducible proteinCCR4-NOT transcription complex subunit 10
Modification date2020032820200313
UniProtAcc

Q99732

Q9H9A5

Ensembl transtripts involved in fusion geneENST00000339430, ENST00000381810, 
ENST00000413364, ENST00000570904, 
ENST00000571459, ENST00000571688, 
ENST00000571976, ENST00000572255, 
ENST00000574703, ENST00000574763, 
ENST00000576036, 
ENST00000328834, 
ENST00000331889, ENST00000454516, 
ENST00000463697, ENST00000538368, 
Fusion gene scores* DoF score11 X 12 X 6=7928 X 7 X 6=336
# samples 178
** MAII scorelog2(17/792*10)=-2.21996568394191
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/336*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LITAF [Title/Abstract] AND CNOT10 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLITAF(11652225)-CNOT10(32812659), # 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

check buttonFusion gene breakpoints across LITAF (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 CNOT10 (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
ChiTaRS5.0N/AEI790451LITAFchr16

11652225

-CNOT10chr3

32812659

-


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Fusion Gene ORF analysis for LITAF-CNOT10

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-intronENST00000339430ENST00000328834LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000339430ENST00000331889LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000339430ENST00000454516LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000339430ENST00000463697LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000339430ENST00000538368LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000381810ENST00000328834LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000381810ENST00000331889LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000381810ENST00000454516LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000381810ENST00000463697LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000381810ENST00000538368LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000413364ENST00000328834LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000413364ENST00000331889LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000413364ENST00000454516LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000413364ENST00000463697LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000413364ENST00000538368LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000570904ENST00000328834LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000570904ENST00000331889LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000570904ENST00000454516LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000570904ENST00000463697LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000570904ENST00000538368LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571459ENST00000328834LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571459ENST00000331889LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571459ENST00000454516LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571459ENST00000463697LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571459ENST00000538368LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571688ENST00000328834LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571688ENST00000331889LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571688ENST00000454516LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571688ENST00000463697LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571688ENST00000538368LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571976ENST00000328834LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571976ENST00000331889LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571976ENST00000454516LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571976ENST00000463697LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000571976ENST00000538368LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000572255ENST00000328834LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000572255ENST00000331889LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000572255ENST00000454516LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000572255ENST00000463697LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000572255ENST00000538368LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000574703ENST00000328834LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000574703ENST00000331889LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000574703ENST00000454516LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000574703ENST00000463697LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000574703ENST00000538368LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000574763ENST00000328834LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000574763ENST00000331889LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000574763ENST00000454516LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000574763ENST00000463697LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000574763ENST00000538368LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000576036ENST00000328834LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000576036ENST00000331889LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000576036ENST00000454516LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000576036ENST00000463697LITAFchr16

11652225

-CNOT10chr3

32812659

-
intron-intronENST00000576036ENST00000538368LITAFchr16

11652225

-CNOT10chr3

32812659

-

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 LITAF-CNOT10


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 LITAF-CNOT10


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/:11652225/:32812659)
- 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
LITAF

Q99732

CNOT10

Q9H9A5

FUNCTION: Plays a role in endosomal protein trafficking and in targeting proteins for lysosomal degradation (PubMed:23166352). Plays a role in targeting endocytosed EGFR and ERGG3 for lysosomal degradation, and thereby helps downregulate downstream signaling cascades (PubMed:23166352). Helps recruit the ESCRT complex components TSG101, HGS and STAM to cytoplasmic membranes (PubMed:23166352). Probably plays a role in regulating protein degradation via its interaction with NEDD4 (PubMed:15776429). May also contribute to the regulation of gene expression in the nucleus (PubMed:10200294, PubMed:15793005). Binds DNA (in vitro) and may play a synergistic role with STAT6 in the nucleus in regulating the expression of various cytokines (PubMed:15793005). May regulate the expression of numerous cytokines, such as TNF, CCL2, CCL5, CXCL1, IL1A and IL10 (PubMed:10200294, PubMed:15793005). {ECO:0000269|PubMed:15793005, ECO:0000269|PubMed:23166352, ECO:0000303|PubMed:15776429, ECO:0000305|PubMed:10200294}.FUNCTION: Component of the CCR4-NOT complex which is one of the major cellular mRNA deadenylases and is linked to various cellular processes including bulk mRNA degradation, miRNA-mediated repression, translational repression during translational initiation and general transcription regulation. Additional complex functions may be a consequence of its influence on mRNA expression. Is not required for association of CNOT7 to the CCR4-NOT complex. {ECO:0000269|PubMed:23221646}.

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 LITAF-CNOT10


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 LITAF-CNOT10


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 LITAF-CNOT10


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 LITAF-CNOT10


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