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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 40931

FusionGeneSummary for USB1_CX3CL1

check button Fusion gene summary
Fusion gene informationFusion gene name: USB1_CX3CL1
Fusion gene ID: 40931
HgeneTgene
Gene symbol

USB1

CX3CL1

Gene ID

79650

6376

Gene nameU6 snRNA biogenesis phosphodiesterase 1C-X3-C motif chemokine ligand 1
SynonymsC16orf57|HVSL1|Mpn1|PN|hUsb1ABCD-3|C3Xkine|CXC3|CXC3C|NTN|NTT|SCYD1|fractalkine|neurotactin
Cytomap

16q21

16q21

Type of geneprotein-codingprotein-coding
DescriptionU6 snRNA phosphodiesteraseHVSL motif containing 1U six biogenesis 1U6 snRNA biogenesis 1UPF0406 protein C16orf57mutated in poikiloderma with neutropenia protein 1putative U6 snRNA phosphodiesterasefractalkineC-X3-C motif chemokine 1CX3C membrane-anchored chemokinechemokine (C-X3-C motif) ligand 1small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)small inducible cytokine subfamily D (Cys-X3-Cys), member-1smal
Modification date2018052620180523
UniProtAcc

Q9BQ65

P78423

Ensembl transtripts involved in fusion geneENST00000561743, ENST00000219281, 
ENST00000539737, ENST00000423271, 
ENST00000565662, ENST00000563149, 
ENST00000006053, ENST00000563383, 
ENST00000564948, ENST00000565912, 
Fusion gene scores* DoF score3 X 3 X 3=271 X 1 X 1=1
# samples 51
** MAII scorelog2(5/27*10)=0.888968687611256
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(1/1*10)=3.32192809488736
Context

PubMed: USB1 [Title/Abstract] AND CX3CL1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
TgeneCX3CL1

GO:0006935

chemotaxis

21829356

TgeneCX3CL1

GO:0030336

negative regulation of cell migration

25435433

TgeneCX3CL1

GO:0051041

positive regulation of calcium-independent cell-cell adhesion

12714508


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGALDPCPGTCGA-QR-A6GW-01AUSB1chr16

58048230

+CX3CL1chr16

57413546

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
Frame-shitENST00000561743ENST00000006053USB1chr16

58048230

+CX3CL1chr16

57413546

+
Frame-shitENST00000561743ENST00000563383USB1chr16

58048230

+CX3CL1chr16

57413546

+
5CDS-intronENST00000561743ENST00000564948USB1chr16

58048230

+CX3CL1chr16

57413546

+
5CDS-5UTRENST00000561743ENST00000565912USB1chr16

58048230

+CX3CL1chr16

57413546

+
Frame-shitENST00000219281ENST00000006053USB1chr16

58048230

+CX3CL1chr16

57413546

+
Frame-shitENST00000219281ENST00000563383USB1chr16

58048230

+CX3CL1chr16

57413546

+
5CDS-intronENST00000219281ENST00000564948USB1chr16

58048230

+CX3CL1chr16

57413546

+
5CDS-5UTRENST00000219281ENST00000565912USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-3CDSENST00000539737ENST00000006053USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-3CDSENST00000539737ENST00000563383USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-intronENST00000539737ENST00000564948USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-5UTRENST00000539737ENST00000565912USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-3CDSENST00000423271ENST00000006053USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-3CDSENST00000423271ENST00000563383USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-intronENST00000423271ENST00000564948USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-5UTRENST00000423271ENST00000565912USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-3CDSENST00000565662ENST00000006053USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-3CDSENST00000565662ENST00000563383USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-intronENST00000565662ENST00000564948USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-5UTRENST00000565662ENST00000565912USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-3CDSENST00000563149ENST00000006053USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-3CDSENST00000563149ENST00000563383USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-intronENST00000563149ENST00000564948USB1chr16

58048230

+CX3CL1chr16

57413546

+
intron-5UTRENST00000563149ENST00000565912USB1chr16

58048230

+CX3CL1chr16

57413546

+

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FusionProtFeatures for USB1_CX3CL1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
USB1

Q9BQ65

CX3CL1

P78423

Phosphodiesterase responsible for the U6 snRNA 3' endprocessing. Acts as an exoribonuclease (RNase) responsible fortrimming the poly(U) tract of the last nucleotides in the pre-U6snRNA molecule, leading to the formation of mature U6 snRNA 3'end-terminated with a 2',3'-cyclic phosphate. {ECO:0000255|HAMAP-Rule:MF_03040, ECO:0000269|PubMed:22899009,ECO:0000269|PubMed:23190533}. Acts as a ligand for both CX3CR1 and integrins. Binds toCX3CR1 (PubMed:23125415, PubMed:9931005, PubMed:21829356). Bindsto integrins ITGAV:ITGB3 and ITGA4:ITGB1. Can activate integrinsin both a CX3CR1-dependent and CX3CR1-independent manner. In thepresence of CX3CR1, activates integrins by binding to theclassical ligand-binding site (site 1) in integrins. In theabsence of CX3CR1, binds to a second site (site 2) in integrinswhich is distinct from site 1 and enhances the binding of otherintegrin ligands to site 1 (PubMed:23125415, PubMed:24789099). Thesoluble form is chemotactic for T-cells and monocytes and not forneutrophils. The membrane-bound form promotes adhesion of thoseleukocytes to endothelial cells. May play a role in regulatingleukocyte adhesion and migration processes at the endothelium(PubMed:9024663, PubMed:9177350). {ECO:0000269|PubMed:21829356,ECO:0000269|PubMed:23125415, ECO:0000269|PubMed:24789099,ECO:0000269|PubMed:9024663, ECO:0000269|PubMed:9177350,ECO:0000269|PubMed:9931005}.

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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FusionGeneSequence for USB1_CX3CL1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for USB1_CX3CL1


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
USB1ELAVL1, RNU6-1, PRPF19, CDC5L, PLRG1, SMAD4, RNU5A-1, PPIE, XAB2, GPATCH1, DHX35, CRNKL1, BUD31, AQR, RBM22, WDR83, SNW1, CWF19L2, ISY1, CDC40, BCAS2, CCDC12, DGCR14, SYF2, EAPP, KNSTRN, CSNK2A1, SNX27, SMIM12, TOMM5, SNRNP200CX3CL1CX3CR1, CX3CL1


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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RelatedDrugs for USB1_CX3CL1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for USB1_CX3CL1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCX3CL1C0011853Diabetes Mellitus, Experimental1CTD_human
TgeneCX3CL1C0020517Hypersensitivity1CTD_human
TgeneCX3CL1C0032285Pneumonia1CTD_human
TgeneCX3CL1C0033578Prostatic Neoplasms1CTD_human
TgeneCX3CL1C0151744Myocardial Ischemia1CTD_human