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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:DCLK1-LITAF (FusionGDB2 ID:21618)

Fusion Gene Summary for DCLK1-LITAF

check button Fusion gene summary
Fusion gene informationFusion gene name: DCLK1-LITAF
Fusion gene ID: 21618
HgeneTgene
Gene symbol

DCLK1

LITAF

Gene ID

9201

9516

Gene namedoublecortin like kinase 1lipopolysaccharide induced TNF factor
SynonymsCL1|CLICK1|DCAMKL1|DCDC3A|DCLKPIG7|SIMPLE|TP53I7
Cytomap

13q13.3

16p13.13

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase DCLK1doublecortin domain-containing protein 3Adoublecortin-like and CAM kinase-like 1lipopolysaccharide-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 protein
Modification date2020032020200328
UniProtAcc

O15075

Q99732

Ensembl transtripts involved in fusion geneENST00000255448, ENST00000360631, 
ENST00000379892, ENST00000379893, 
ENST00000460982, 		ENST00000339430, 
ENST00000413364, ENST00000571688, 
ENST00000381810, ENST00000570904, 
ENST00000571459, ENST00000571976, 
ENST00000572255, ENST00000574703, 
ENST00000574763, ENST00000576036, 
Fusion gene scores* DoF score12 X 11 X 3=39613 X 7 X 7=637
# samples 1215
** MAII scorelog2(12/396*10)=-1.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/637*10)=-2.08633087176042
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: DCLK1 [Title/Abstract] AND LITAF [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointDCLK1(36396181)-LITAF(11642150), # 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 DCLK1 (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 LITAF (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/AEC558508DCLK1chr13

36396181

+LITAFchr16

11642150

-


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Fusion Gene ORF analysis for DCLK1-LITAF

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-3UTRENST00000255448ENST00000339430DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000255448ENST00000413364DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000255448ENST00000571688DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000360631ENST00000339430DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000360631ENST00000413364DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000360631ENST00000571688DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000379892ENST00000339430DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000379892ENST00000413364DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000379892ENST00000571688DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000379893ENST00000339430DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000379893ENST00000413364DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000379893ENST00000571688DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000460982ENST00000339430DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000460982ENST00000413364DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-3UTRENST00000460982ENST00000571688DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000255448ENST00000381810DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000255448ENST00000570904DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000255448ENST00000571459DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000255448ENST00000571976DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000255448ENST00000572255DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000255448ENST00000574703DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000255448ENST00000574763DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000255448ENST00000576036DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000360631ENST00000381810DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000360631ENST00000570904DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000360631ENST00000571459DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000360631ENST00000571976DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000360631ENST00000572255DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000360631ENST00000574703DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000360631ENST00000574763DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000360631ENST00000576036DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379892ENST00000381810DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379892ENST00000570904DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379892ENST00000571459DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379892ENST00000571976DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379892ENST00000572255DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379892ENST00000574703DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379892ENST00000574763DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379892ENST00000576036DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379893ENST00000381810DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379893ENST00000570904DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379893ENST00000571459DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379893ENST00000571976DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379893ENST00000572255DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379893ENST00000574703DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379893ENST00000574763DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000379893ENST00000576036DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000460982ENST00000381810DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000460982ENST00000570904DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000460982ENST00000571459DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000460982ENST00000571976DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000460982ENST00000572255DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000460982ENST00000574703DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000460982ENST00000574763DCLK1chr13

36396181

+LITAFchr16

11642150

-
intron-intronENST00000460982ENST00000576036DCLK1chr13

36396181

+LITAFchr16

11642150

-

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 DCLK1-LITAF


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 DCLK1-LITAF


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/:36396181/:11642150)
- 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
DCLK1

O15075

LITAF

Q99732

FUNCTION: Probable kinase that may be involved in a calcium-signaling pathway controlling neuronal migration in the developing brain. May also participate in functions of the mature nervous system.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}.

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 DCLK1-LITAF


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 DCLK1-LITAF


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 DCLK1-LITAF


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 DCLK1-LITAF


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