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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:DCAF4-IFT140 (FusionGDB2 ID:21499)

Fusion Gene Summary for DCAF4-IFT140

check button Fusion gene summary
Fusion gene informationFusion gene name: DCAF4-IFT140
Fusion gene ID: 21499
HgeneTgene
Gene symbol

DCAF4

IFT140

Gene ID

26094

9742

Gene nameDDB1 and CUL4 associated factor 4intraflagellar transport 140
SynonymsWDR21|WDR21AMZSDS|RP80|SRTD9|WDTC2|c305C8.4|c380F5.1|gs114
Cytomap

14q24.2

16p13.3

Type of geneprotein-codingprotein-coding
DescriptionDDB1- and CUL4-associated factor 4WD repeat domain 21AWD repeat-containing protein 21Aintraflagellar transport protein 140 homologWD and tetratricopeptide repeats protein 2intraflagellar transport 140 homolog
Modification date2020031320200320
UniProtAcc

Q8WV16

Q96RY7

Ensembl transtripts involved in fusion geneENST00000510612, ENST00000353777, 
ENST00000358377, ENST00000509153, 
ENST00000555042, ENST00000553457, 
ENST00000394234, 		ENST00000361339, 
ENST00000426508, ENST00000439987, 
Fusion gene scores* DoF score3 X 4 X 3=3612 X 12 X 7=1008
# samples 414
** MAII scorelog2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(14/1008*10)=-2.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: DCAF4 [Title/Abstract] AND IFT140 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointDCAF4(73404778)-IFT140(1576797), # samples:2
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 DCAF4 (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 IFT140 (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
ChimerDB4OVTCGA-29-A5NZ-01ADCAF4chr14

73404774

+IFT140chr16

1576801

-
ChimerDB4OVTCGA-29-A5NZ-01ADCAF4chr14

73404778

-IFT140chr16

1576797

-
ChimerDB4OVTCGA-29-A5NZDCAF4chr14

73404778

+IFT140chr16

1576797

-


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Fusion Gene ORF analysis for DCAF4-IFT140

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
3UTR-5UTRENST00000510612ENST00000361339DCAF4chr14

73404774

+IFT140chr16

1576801

-
3UTR-5UTRENST00000510612ENST00000361339DCAF4chr14

73404778

+IFT140chr16

1576797

-
3UTR-5UTRENST00000510612ENST00000426508DCAF4chr14

73404774

+IFT140chr16

1576801

-
3UTR-5UTRENST00000510612ENST00000426508DCAF4chr14

73404778

+IFT140chr16

1576797

-
3UTR-intronENST00000510612ENST00000439987DCAF4chr14

73404774

+IFT140chr16

1576801

-
3UTR-intronENST00000510612ENST00000439987DCAF4chr14

73404778

+IFT140chr16

1576797

-
5CDS-5UTRENST00000353777ENST00000361339DCAF4chr14

73404774

+IFT140chr16

1576801

-
5CDS-5UTRENST00000353777ENST00000361339DCAF4chr14

73404778

+IFT140chr16

1576797

-
5CDS-5UTRENST00000353777ENST00000426508DCAF4chr14

73404774

+IFT140chr16

1576801

-
5CDS-5UTRENST00000353777ENST00000426508DCAF4chr14

73404778

+IFT140chr16

1576797

-
5CDS-5UTRENST00000358377ENST00000361339DCAF4chr14

73404774

+IFT140chr16

1576801

-
5CDS-5UTRENST00000358377ENST00000361339DCAF4chr14

73404778

+IFT140chr16

1576797

-
5CDS-5UTRENST00000358377ENST00000426508DCAF4chr14

73404774

+IFT140chr16

1576801

-
5CDS-5UTRENST00000358377ENST00000426508DCAF4chr14

73404778

+IFT140chr16

1576797

-
5CDS-5UTRENST00000509153ENST00000361339DCAF4chr14

73404774

+IFT140chr16

1576801

-
5CDS-5UTRENST00000509153ENST00000361339DCAF4chr14

73404778

+IFT140chr16

1576797

-
5CDS-5UTRENST00000509153ENST00000426508DCAF4chr14

73404774

+IFT140chr16

1576801

-
5CDS-5UTRENST00000509153ENST00000426508DCAF4chr14

73404778

+IFT140chr16

1576797

-
5CDS-5UTRENST00000555042ENST00000361339DCAF4chr14

73404774

+IFT140chr16

1576801

-
5CDS-5UTRENST00000555042ENST00000361339DCAF4chr14

73404778

+IFT140chr16

1576797

-
5CDS-5UTRENST00000555042ENST00000426508DCAF4chr14

73404774

+IFT140chr16

1576801

-
5CDS-5UTRENST00000555042ENST00000426508DCAF4chr14

73404778

+IFT140chr16

1576797

-
5CDS-intronENST00000353777ENST00000439987DCAF4chr14

73404774

+IFT140chr16

1576801

-
5CDS-intronENST00000353777ENST00000439987DCAF4chr14

73404778

+IFT140chr16

1576797

-
5CDS-intronENST00000358377ENST00000439987DCAF4chr14

73404774

+IFT140chr16

1576801

-
5CDS-intronENST00000358377ENST00000439987DCAF4chr14

73404778

+IFT140chr16

1576797

-
5CDS-intronENST00000509153ENST00000439987DCAF4chr14

73404774

+IFT140chr16

1576801

-
5CDS-intronENST00000509153ENST00000439987DCAF4chr14

73404778

+IFT140chr16

1576797

-
5CDS-intronENST00000555042ENST00000439987DCAF4chr14

73404774

+IFT140chr16

1576801

-
5CDS-intronENST00000555042ENST00000439987DCAF4chr14

73404778

+IFT140chr16

1576797

-
5UTR-5UTRENST00000553457ENST00000361339DCAF4chr14

73404774

+IFT140chr16

1576801

-
5UTR-5UTRENST00000553457ENST00000361339DCAF4chr14

73404778

+IFT140chr16

1576797

-
5UTR-5UTRENST00000553457ENST00000426508DCAF4chr14

73404774

+IFT140chr16

1576801

-
5UTR-5UTRENST00000553457ENST00000426508DCAF4chr14

73404778

+IFT140chr16

1576797

-
5UTR-intronENST00000553457ENST00000439987DCAF4chr14

73404774

+IFT140chr16

1576801

-
5UTR-intronENST00000553457ENST00000439987DCAF4chr14

73404778

+IFT140chr16

1576797

-
intron-5UTRENST00000394234ENST00000361339DCAF4chr14

73404774

+IFT140chr16

1576801

-
intron-5UTRENST00000394234ENST00000361339DCAF4chr14

73404778

+IFT140chr16

1576797

-
intron-5UTRENST00000394234ENST00000426508DCAF4chr14

73404774

+IFT140chr16

1576801

-
intron-5UTRENST00000394234ENST00000426508DCAF4chr14

73404778

+IFT140chr16

1576797

-
intron-intronENST00000394234ENST00000439987DCAF4chr14

73404774

+IFT140chr16

1576801

-
intron-intronENST00000394234ENST00000439987DCAF4chr14

73404778

+IFT140chr16

1576797

-

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 DCAF4-IFT140


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 DCAF4-IFT140


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/:73404778/:1576797)
- 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
DCAF4

Q8WV16

IFT140

Q96RY7

FUNCTION: May function as a substrate receptor for CUL4-DDB1 E3 ubiquitin-protein ligase complex. {ECO:0000269|PubMed:16949367, ECO:0000269|PubMed:16964240}.FUNCTION: Component of the IFT complex A (IFT-A), a complex required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs) (PubMed:20889716, PubMed:22503633). Plays a pivotal role in proper development and function of ciliated cells through its role in ciliogenesis and/or cilium maintenance (PubMed:22503633). Required for the development and maintenance of the outer segments of rod and cone photoreceptor cells. Plays a role in maintenance and the delivery of opsin to the outer segment of photoreceptor cells (By similarity). {ECO:0000250|UniProtKB:E9PY46, ECO:0000269|PubMed:20889716, ECO:0000269|PubMed:22503633, ECO:0000269|PubMed:28724397}.

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 DCAF4-IFT140


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 DCAF4-IFT140


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 DCAF4-IFT140


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 DCAF4-IFT140


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