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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:TUBD1-CLTC (FusionGDB2 ID:94720)

Fusion Gene Summary for TUBD1-CLTC

check button Fusion gene summary
Fusion gene informationFusion gene name: TUBD1-CLTC
Fusion gene ID: 94720
HgeneTgene
Gene symbol

TUBD1

CLTC

Gene ID

51174

1213

Gene nametubulin delta 1clathrin heavy chain
SynonymsTUBDCHC|CHC17|CLH-17|CLTCL2|Hc|MRD56
Cytomap

17q23.1

17q23.1

Type of geneprotein-codingprotein-coding
Descriptiontubulin delta chaindelta-tubulinclathrin heavy chain 1clathrin heavy chain on chromosome 17clathrin, heavy polypeptide (Hc)clathrin, heavy polypeptide-like 2
Modification date2020031320200313
UniProtAcc.

P53675

Ensembl transtripts involved in fusion geneENST00000346141, ENST00000325752, 
ENST00000340993, ENST00000394239, 
ENST00000592426, ENST00000376094, 
ENST00000539018, ENST00000591611, 
ENST00000393043, ENST00000269122, 
ENST00000579456, ENST00000579815, 
Fusion gene scores* DoF score16 X 16 X 8=204818 X 18 X 8=2592
# samples 2222
** MAII scorelog2(22/2048*10)=-3.21864028647534
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(22/2592*10)=-3.55849028935997
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TUBD1 [Title/Abstract] AND CLTC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTUBD1(57970058)-CLTC(57721637), # 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
TgeneCLTC

GO:1900126

negative regulation of hyaluronan biosynthetic process

24251095


check buttonFusion gene breakpoints across TUBD1 (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 CLTC (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
ChimerDB4Non-CancerTCGA-IP-7968-11ATUBD1chr17

57970058

-CLTCchr17

57721637

+


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Fusion Gene ORF analysis for TUBD1-CLTC

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
5UTR-3CDSENST00000346141ENST00000393043TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000346141ENST00000269122TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000346141ENST00000579456TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-intronENST00000346141ENST00000579815TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000325752ENST00000393043TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000325752ENST00000269122TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000325752ENST00000579456TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-intronENST00000325752ENST00000579815TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000340993ENST00000393043TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000340993ENST00000269122TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000340993ENST00000579456TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-intronENST00000340993ENST00000579815TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000394239ENST00000393043TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000394239ENST00000269122TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000394239ENST00000579456TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-intronENST00000394239ENST00000579815TUBD1chr17

57970058

-CLTCchr17

57721637

+
intron-3CDSENST00000592426ENST00000393043TUBD1chr17

57970058

-CLTCchr17

57721637

+
intron-3CDSENST00000592426ENST00000269122TUBD1chr17

57970058

-CLTCchr17

57721637

+
intron-3CDSENST00000592426ENST00000579456TUBD1chr17

57970058

-CLTCchr17

57721637

+
intron-intronENST00000592426ENST00000579815TUBD1chr17

57970058

-CLTCchr17

57721637

+
intron-3CDSENST00000376094ENST00000393043TUBD1chr17

57970058

-CLTCchr17

57721637

+
intron-3CDSENST00000376094ENST00000269122TUBD1chr17

57970058

-CLTCchr17

57721637

+
intron-3CDSENST00000376094ENST00000579456TUBD1chr17

57970058

-CLTCchr17

57721637

+
intron-intronENST00000376094ENST00000579815TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000539018ENST00000393043TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000539018ENST00000269122TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000539018ENST00000579456TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-intronENST00000539018ENST00000579815TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000591611ENST00000393043TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000591611ENST00000269122TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-3CDSENST00000591611ENST00000579456TUBD1chr17

57970058

-CLTCchr17

57721637

+
5UTR-intronENST00000591611ENST00000579815TUBD1chr17

57970058

-CLTCchr17

57721637

+

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 TUBD1-CLTC


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)
TUBD1chr1757970057-CLTCchr1757721636+2.11E-081
TUBD1chr1757970057-CLTCchr1757721636+2.11E-081

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 TUBD1-CLTC


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.CLTC

P53675

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. Two different adapter protein complexes link the clathrin lattice either to the plasma membrane or to the trans-Golgi network (By similarity). {ECO:0000250}.

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 TUBD1-CLTC


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 TUBD1-CLTC


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 TUBD1-CLTC


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 TUBD1-CLTC


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCLTCC4518356MiT family translocation renal cell carcinoma2ORPHANET
TgeneCLTCC4693389MENTAL RETARDATION, AUTOSOMAL DOMINANT 562GENOMICS_ENGLAND;UNIPROT
TgeneCLTCC0079744Diffuse Large B-Cell Lymphoma1CTD_human
TgeneCLTCC0334121Inflammatory Myofibroblastic Tumor1ORPHANET