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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: 3228

FusionGeneSummary for ATL3_RTN3

check button Fusion gene summary
Fusion gene informationFusion gene name: ATL3_RTN3
Fusion gene ID: 3228
HgeneTgene
Gene symbol

ATL3

RTN3

Gene ID

25923

10313

Gene nameatlastin GTPase 3reticulon 3
SynonymsHSN1FASYIP|HAP|NSPL2|NSPLII|RTN3-A1
Cytomap

11q13.1

11q13.1

Type of geneprotein-codingprotein-coding
Descriptionatlastin-3reticulon-3ASY interacting proteinNSP-like protein 2NSP-like protein IIhomolog of ASY proteinneuroendocrine-specific protein-like 2neuroendocrine-specific protein-like II
Modification date2018051920180522
UniProtAcc

Q6DD88

O95197

Ensembl transtripts involved in fusion geneENST00000398868, ENST00000332645, 
ENST00000538786, ENST00000535789, 
ENST00000341307, ENST00000356000, 
ENST00000538995, ENST00000377819, 
ENST00000339997, ENST00000540798, 
ENST00000537981, ENST00000354497, 
Fusion gene scores* DoF score4 X 4 X 3=489 X 5 X 7=315
# samples 411
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(11/315*10)=-1.51784830486262
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ATL3 [Title/Abstract] AND RTN3 [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
HgeneATL3

GO:0051260

protein homooligomerization

18270207

TgeneRTN3

GO:0071787

endoplasmic reticulum tubular network formation

25612671


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
TCGARVLIHCTCGA-BC-A8YO-01AATL3chr11

63426233

-RTN3chr11

63517463

+
* 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-shiftENST00000398868ENST00000341307ATL3chr11

63426233

-RTN3chr11

63517463

+
Frame-shiftENST00000398868ENST00000356000ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000398868ENST00000538995ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000398868ENST00000377819ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000398868ENST00000339997ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000398868ENST00000540798ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000398868ENST00000537981ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000398868ENST00000354497ATL3chr11

63426233

-RTN3chr11

63517463

+
Frame-shiftENST00000332645ENST00000341307ATL3chr11

63426233

-RTN3chr11

63517463

+
Frame-shiftENST00000332645ENST00000356000ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000332645ENST00000538995ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000332645ENST00000377819ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000332645ENST00000339997ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000332645ENST00000540798ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000332645ENST00000537981ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000332645ENST00000354497ATL3chr11

63426233

-RTN3chr11

63517463

+
In-frameENST00000538786ENST00000341307ATL3chr11

63426233

-RTN3chr11

63517463

+
In-frameENST00000538786ENST00000356000ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000538786ENST00000538995ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000538786ENST00000377819ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000538786ENST00000339997ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000538786ENST00000540798ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000538786ENST00000537981ATL3chr11

63426233

-RTN3chr11

63517463

+
5CDS-intronENST00000538786ENST00000354497ATL3chr11

63426233

-RTN3chr11

63517463

+
intron-3CDSENST00000535789ENST00000341307ATL3chr11

63426233

-RTN3chr11

63517463

+
intron-3CDSENST00000535789ENST00000356000ATL3chr11

63426233

-RTN3chr11

63517463

+
intron-intronENST00000535789ENST00000538995ATL3chr11

63426233

-RTN3chr11

63517463

+
intron-intronENST00000535789ENST00000377819ATL3chr11

63426233

-RTN3chr11

63517463

+
intron-intronENST00000535789ENST00000339997ATL3chr11

63426233

-RTN3chr11

63517463

+
intron-intronENST00000535789ENST00000540798ATL3chr11

63426233

-RTN3chr11

63517463

+
intron-intronENST00000535789ENST00000537981ATL3chr11

63426233

-RTN3chr11

63517463

+
intron-intronENST00000535789ENST00000354497ATL3chr11

63426233

-RTN3chr11

63517463

+

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FusionProtFeatures for ATL3_RTN3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
ATL3

Q6DD88

RTN3

O95197

GTPase tethering membranes through formation of trans-homooligomers and mediating homotypic fusion of endoplasmicreticulum membranes. Functions in endoplasmic reticulum tubularnetwork biogenesis (PubMed:18270207, PubMed:19665976,PubMed:27619977). {ECO:0000269|PubMed:18270207,ECO:0000269|PubMed:19665976, ECO:0000269|PubMed:27619977}.

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 ATL3_RTN3


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 ATL3_RTN3


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
ATL3APP, RNF2, GDE1, LPAR6, RTN4, ASPH, ATP6V1C1, EEF1B2, EIF3B, HADHA, MRPL40, PGRMC1, PHB, POR, SRSF6, TPR, TROVE2, CANX, EEF1G, PHB2, NTRK1, ALDH1B1, ALDH3A2, ARCN1, ATP2B1, ATP5A1, ATP5E, BLMH, DVL3, ETFB, GART, ITGB1, RAB1A, RAB5C, RNF5, SLC4A2, SPAG1, SUPT6H, TAP1, TAP2, VAPB, LONP1, SEC22B, LPGAT1, USP15, TSSC4, RTN3, ZNF609, ESYT1, ATP13A2, ATL2, RAB14, TMEM161A, DALRD3, SNX14, SRPRB, FASTKD5, RBKS, TMEM109, ZCCHC6, ZNF768, L2HGDH, RABL3, PRSS56, LPAR4, CD70, GPR114, HS3ST2, APLNR, GRPR, MAS1, C5AR2, SLC2A12, SLC22A16, SLC17A2, CNGA3, LAMP3, SLC5A5, TRIM25RTN3FXR2, PTPN9, FAM160A2, RTN4, COL4A3BP, PLEKHF2, RAB33A, SPOP, RTN3, UGCG, TERF1, PRTFDC1, SNX1, CDIPT, PPP2R3C, ZNF391, ATP1B3, VAPA, TCTN2, TCTN3, XPO1, ATL3, FGFR1, GLP1R, BCL2, TRIM25, LMNA


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 ATL3_RTN3


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 ATL3_RTN3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATL3C3810194NEUROPATHY, HEREDITARY SENSORY, TYPE IF1UNIPROT