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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: 35509

FusionGeneSummary for SPAG17_LRSAM1

check button Fusion gene summary
Fusion gene informationFusion gene name: SPAG17_LRSAM1
Fusion gene ID: 35509
HgeneTgene
Gene symbol

SPAG17

LRSAM1

Gene ID

200162

90678

Gene namesperm associated antigen 17leucine rich repeat and sterile alpha motif containing 1
SynonymsCT143|PF6CMT2P|RIFLE|TAL
Cytomap

1p12

9q33.3-q34.11

Type of geneprotein-codingprotein-coding
Descriptionsperm-associated antigen 17projection protein PF6 homologE3 ubiquitin-protein ligase LRSAM1RING-type E3 ubiquitin transferase LRSAM1Tsg101-associated ligase
Modification date2018052320180523
UniProtAcc

Q6Q759

Q6UWE0

Ensembl transtripts involved in fusion geneENST00000336338, ENST00000492438, 
ENST00000300417, ENST00000373324, 
ENST00000323301, ENST00000373322, 
ENST00000483302, 
Fusion gene scores* DoF score4 X 4 X 3=485 X 6 X 5=150
# samples 45
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/150*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SPAG17 [Title/Abstract] AND LRSAM1 [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
TgeneLRSAM1

GO:0000209

protein polyubiquitination

18077552

TgeneLRSAM1

GO:0051865

protein autoubiquitination

15256501|23245322

TgeneLRSAM1

GO:0070086

ubiquitin-dependent endocytosis

15256501


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
TCGARVMESOTCGA-3H-AB3S-01ASPAG17chr1

118550667

-LRSAM1chr9

130221282

+
* 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-shiftENST00000336338ENST00000300417SPAG17chr1

118550667

-LRSAM1chr9

130221282

+
Frame-shiftENST00000336338ENST00000373324SPAG17chr1

118550667

-LRSAM1chr9

130221282

+
Frame-shiftENST00000336338ENST00000323301SPAG17chr1

118550667

-LRSAM1chr9

130221282

+
Frame-shiftENST00000336338ENST00000373322SPAG17chr1

118550667

-LRSAM1chr9

130221282

+
5CDS-intronENST00000336338ENST00000483302SPAG17chr1

118550667

-LRSAM1chr9

130221282

+
intron-3CDSENST00000492438ENST00000300417SPAG17chr1

118550667

-LRSAM1chr9

130221282

+
intron-3CDSENST00000492438ENST00000373324SPAG17chr1

118550667

-LRSAM1chr9

130221282

+
intron-3CDSENST00000492438ENST00000323301SPAG17chr1

118550667

-LRSAM1chr9

130221282

+
intron-3CDSENST00000492438ENST00000373322SPAG17chr1

118550667

-LRSAM1chr9

130221282

+
intron-intronENST00000492438ENST00000483302SPAG17chr1

118550667

-LRSAM1chr9

130221282

+

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FusionProtFeatures for SPAG17_LRSAM1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SPAG17

Q6Q759

LRSAM1

Q6UWE0

Component of the central pair apparatus of ciliaryaxonemes. Plays a critical role in the function and structure ofmotile cilia. May play a role in endochondral bone formation, mostlikely because of a function in primary cilia of chondrocytes andosteoblasts. {ECO:0000250|UniProtKB:Q5S003}. E3 ubiquitin-protein ligase that mediatesmonoubiquitination of TSG101 at multiple sites, leading toinactivate the ability of TSG101 to sort endocytic (EGF receptors)and exocytic (HIV-1 viral proteins) cargos (PubMed:15256501).Bacterial recognition protein that defends the cytoplasm frominvasive pathogens (PubMed:23245322). Localizes to severalintracellular bacterial pathogens and generates the bacteria-associated ubiquitin signal leading to autophagy-mediatedintracellular bacteria degradation (xenophagy) (PubMed:23245322,PubMed:25484098). {ECO:0000269|PubMed:15256501,ECO:0000269|PubMed:23245322, ECO:0000269|PubMed:25484098}.

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 SPAG17_LRSAM1


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 SPAG17_LRSAM1


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
SPAG17TRIM25LRSAM1TSG101, GPR108, NINL, KLC1, FAM178B, UBE2J1, UBE2N, UBE2D1, UBE2D2, UBE2D3, UBE2D4, UBE2E1, UBE2H, UBE2K, UBE2W, UEVLD, ATXN7, TERF1, ATXN1, YTHDF1, USP2, USP21, HSP90AA1, MKRN3, MDM4, RNF111, VPS11, TRIM74, TRIM17, ANKMY2, DR1, HSF1, HSPBP1, CBS, CTPS2, DBNL, DDX5, EHD4, ERO1L, GOPC, P3H1, PLIN3, MTMR2, PPME1, UBE3A, LRSAM1, EGFR, AP3B1, LRRC46, LIPF, PHF23, MAGEA1, UTP6


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 SPAG17_LRSAM1


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 SPAG17_LRSAM1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneLRSAM1C0007959Charcot-Marie-Tooth Disease1CTD_human
TgeneLRSAM1C3280797CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2P1ORPHANET;UNIPROT