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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: 35607

FusionGeneSummary for SPCS3_SKAP2

check button Fusion gene summary
Fusion gene informationFusion gene name: SPCS3_SKAP2
Fusion gene ID: 35607
HgeneTgene
Gene symbol

SPCS3

SKAP2

Gene ID

60559

8935

Gene namesignal peptidase complex subunit 3src kinase associated phosphoprotein 2
SynonymsPRO3567|SPC22/23|SPC3|YLR066WPRAP|RA70|SAPS|SCAP2|SKAP-HOM|SKAP55R
Cytomap

4q34.2

7p15.2

Type of geneprotein-codingprotein-coding
Descriptionsignal peptidase complex subunit 3SPase 22 kDa subunitSPase 22/23 kDa subunitmicrosomal signal peptidase 22/23 kDa subunitmicrosomal signal peptidase 23 kDa subunitsignal peptidase complex subunit 3 homologsrc kinase-associated phosphoprotein 2Fyn-associated phosphoprotein SKAP55 homologuePyk2/RAFTK-associated proteinSKAP-55HOMSKAP55 homologretinoic acid-induced protein 70src family-associated phosphoprotein 2src kinase-associated phosphoprotein of 5
Modification date2018052320180523
UniProtAcc

P61009

O75563

Ensembl transtripts involved in fusion geneENST00000503362, ENST00000507001, 
ENST00000345317, ENST00000539623, 
ENST00000489977, 
Fusion gene scores* DoF score3 X 3 X 3=276 X 6 X 5=180
# samples 38
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(8/180*10)=-1.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SPCS3 [Title/Abstract] AND SKAP2 [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
HgeneSPCS3

GO:0006508

proteolysis

27499293


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
TCGALDSARCTCGA-DX-A8BR-01ASPCS3chr4

177245408

+SKAP2chr7

26729981

-
* 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-shiftENST00000503362ENST00000345317SPCS3chr4

177245408

+SKAP2chr7

26729981

-
Frame-shiftENST00000503362ENST00000539623SPCS3chr4

177245408

+SKAP2chr7

26729981

-
5CDS-5UTRENST00000503362ENST00000489977SPCS3chr4

177245408

+SKAP2chr7

26729981

-
intron-3CDSENST00000507001ENST00000345317SPCS3chr4

177245408

+SKAP2chr7

26729981

-
intron-3CDSENST00000507001ENST00000539623SPCS3chr4

177245408

+SKAP2chr7

26729981

-
intron-5UTRENST00000507001ENST00000489977SPCS3chr4

177245408

+SKAP2chr7

26729981

-

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FusionProtFeatures for SPCS3_SKAP2


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SPCS3

P61009

SKAP2

O75563

Component of the microsomal signal peptidase complexwhich removes signal peptides and other N-terminal peptides fromnascent proteins as they are translocated into the lumen of theendoplasmic reticulum. {ECO:0000269|PubMed:27499293}. May be involved in B-cell and macrophage adhesionprocesses. In B-cells, may act by coupling the B-cell receptor(BCR) to integrin activation. May play a role in src signalingpathway. {ECO:0000269|PubMed:12893833,ECO:0000269|PubMed:9837776}.

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 SPCS3_SKAP2


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 SPCS3_SKAP2


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
SPCS3FBXO6, TCTN2, TCTN3, EVC2, TCTN1, TMEM17, TMEM216, TMEM67, MCM2, SEC11C, PTPRO, TRIM25SKAP2PRAM1, FYN, LYN, HCK, KHDRBS1, FASLG, PTK2B, SRC, GRB2, APP, SKAP1, RGS3, ABHD5, FRMD1, SNRPN


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 SPCS3_SKAP2


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 SPCS3_SKAP2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneSKAP2C0023893Liver Cirrhosis, Experimental1CTD_human