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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: 35572

FusionGeneSummary for SPATA1_VPS26A

check button Fusion gene summary
Fusion gene informationFusion gene name: SPATA1_VPS26A
Fusion gene ID: 35572
HgeneTgene
Gene symbol

SPATA1

VPS26A

Gene ID

100505741

9559

Gene namespermatogenesis associated 1VPS26, retromer complex component A
SynonymsSP-2|SPAP1HB58|Hbeta58|PEP8A|VPS26
Cytomap

1p22.3

10q22.1

Type of geneprotein-codingprotein-coding
Descriptionspermatogenesis-associated protein 1sperm-specific protein SP-2vacuolar protein sorting-associated protein 26AVPS26 retromer complex comonent Avacuolar protein sorting 26 homolog Avesicle protein sorting 26A
Modification date2018051920180523
UniProtAcc

O75436

Ensembl transtripts involved in fusion geneENST00000370638, ENST00000373382, 
ENST00000263559, ENST00000395098, 
ENST00000546041, ENST00000490696, 
ENST00000541711, ENST00000489794, 
Fusion gene scores* DoF score1 X 1 X 1=16 X 4 X 4=96
# samples 16
** MAII scorelog2(1/1*10)=3.32192809488736log2(6/96*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SPATA1 [Title/Abstract] AND VPS26A [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

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
ChiTaRS3.1AI378347SPATA1chr1

84977412

+VPS26Achr10

70920847

-
* 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
intron-intronENST00000370638ENST00000373382SPATA1chr1

84977412

+VPS26Achr10

70920847

-
intron-intronENST00000370638ENST00000263559SPATA1chr1

84977412

+VPS26Achr10

70920847

-
intron-intronENST00000370638ENST00000395098SPATA1chr1

84977412

+VPS26Achr10

70920847

-
intron-intronENST00000370638ENST00000546041SPATA1chr1

84977412

+VPS26Achr10

70920847

-
intron-intronENST00000370638ENST00000490696SPATA1chr1

84977412

+VPS26Achr10

70920847

-
intron-intronENST00000370638ENST00000541711SPATA1chr1

84977412

+VPS26Achr10

70920847

-
intron-intronENST00000370638ENST00000489794SPATA1chr1

84977412

+VPS26Achr10

70920847

-

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FusionProtFeatures for SPATA1_VPS26A


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SPATA1

VPS26A

O75436

Lectin that binds to various sugars: galactose > mannose= fucose > N-acetylglucosamine > N-acetylgalactosamine(PubMed:10224141). Acts as a chemoattractant, probably involved inthe regulation of cell migration (PubMed:28301481).{ECO:0000269|PubMed:10224141, ECO:0000269|PubMed:28301481}. Acts as component of the retromer cargo-selectivecomplex (CSC). The CSC is believed to be the core functionalcomponent of retromer or respective retromer complex variantsacting to prevent missorting of selected transmembrane cargoproteins into the lysosomal degradation pathway. The recruitmentof the CSC to the endosomal membrane involves RAB7A and SNX3. TheSNX-BAR retromer mediates retrograde transport of cargo proteinsfrom endosomes to the trans-Golgi network (TGN) and is involved inendosome-to-plasma membrane transport for cargo protein recycling.The SNX3-retromer mediates the retrograde endosome-to-TGNtransport of WLS distinct from the SNX-BAR retromer pathway. TheSNX27-retromer is believed to be involved in endosome-to-plasmamembrane trafficking and recycling of a broad spectrum of cargoproteins (Probable). The CSC seems to act as recruitment hub forother proteins, such as the WASH complex and TBC1D5 (Probable).Required for retrograde transport of lysosomal enzyme receptorIGF2R (PubMed:15078902, PubMed:15078903). Required to regulatetranscytosis of the polymeric immunoglobulin receptor (pIgR-pIgA)(PubMed:15247922). Required for the endosomal localization ofWASHC2A (indicative for the WASH complex) (PubMed:22070227).Required for the endosomal localization of TBC1D5(PubMed:20923837). Mediates retromer cargo recognition of SORL1and is involved in trafficking of SORL1 implicated in sorting andprocessing of APP (PubMed:22279231). Involved in retromer-independent lysosomal sorting of F2R (PubMed:16407403). Involvedin recycling of ADRB2 (PubMed:21602791). Enhances the affinity ofSNX27 for PDZ-binding motifs in cargo proteins (By similarity).{ECO:0000250|UniProtKB:P40336, ECO:0000269|PubMed:15078902,ECO:0000269|PubMed:15078903, ECO:0000269|PubMed:15247922,ECO:0000269|PubMed:16407403, ECO:0000269|PubMed:22070227,ECO:0000269|PubMed:22279231, ECO:0000303|PubMed:20923837,ECO:0000303|PubMed:21602791, ECO:0000303|PubMed:21725319,ECO:0000303|PubMed:23563491, ECO:0000305}.

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 SPATA1_VPS26A


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 SPATA1_VPS26A


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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RelatedDrugs for SPATA1_VPS26A


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 SPATA1_VPS26A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneVPS26AC0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human