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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: 18022

FusionGeneSummary for JAM3_SEC13

check button Fusion gene summary
Fusion gene informationFusion gene name: JAM3_SEC13
Fusion gene ID: 18022
HgeneTgene
Gene symbol

JAM3

SEC13

Gene ID

83700

6396

Gene namejunctional adhesion molecule 3SEC13 homolog, nuclear pore and COPII coat complex component
SynonymsJAM-2|JAM-3|JAM-C|JAMCD3S1231E|SEC13L1|SEC13R|npp-20
Cytomap

11q25

3p25.3

Type of geneprotein-codingprotein-coding
Descriptionjunctional adhesion molecule Cprotein SEC13 homologGATOR complex protein SEC13SEC13 homolog, nuclear pore and COPII coating complex componentSEC13-like 1 isoformSEC13-like protein 1SEC13-related protein
Modification date2018051920180523
UniProtAcc

Q9BX67

P55735

Ensembl transtripts involved in fusion geneENST00000529443, ENST00000299106, 
ENST00000441717, ENST00000524969, 
ENST00000397109, ENST00000337354, 
ENST00000350697, ENST00000397117, 
ENST00000383801, ENST00000492602, 
Fusion gene scores* DoF score4 X 4 X 3=488 X 5 X 4=160
# samples 46
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/160*10)=-1.41503749927884
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: JAM3 [Title/Abstract] AND SEC13 [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
HgeneJAM3

GO:0001525

angiogenesis

20592283

HgeneJAM3

GO:0090022

regulation of neutrophil chemotaxis

15194813

TgeneSEC13

GO:0090110

cargo loading into COPII-coated vesicle

17499046|18843296


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
TCGALDLGGTCGA-DU-7015-01AJAM3chr11

134010665

+SEC13chr3

10347376

-
* 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-shiftENST00000529443ENST00000397109JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000529443ENST00000337354JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000529443ENST00000350697JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000529443ENST00000397117JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000529443ENST00000383801JAM3chr11

134010665

+SEC13chr3

10347376

-
5CDS-intronENST00000529443ENST00000492602JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000299106ENST00000397109JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000299106ENST00000337354JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000299106ENST00000350697JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000299106ENST00000397117JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000299106ENST00000383801JAM3chr11

134010665

+SEC13chr3

10347376

-
5CDS-intronENST00000299106ENST00000492602JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000441717ENST00000397109JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000441717ENST00000337354JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000441717ENST00000350697JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000441717ENST00000397117JAM3chr11

134010665

+SEC13chr3

10347376

-
Frame-shiftENST00000441717ENST00000383801JAM3chr11

134010665

+SEC13chr3

10347376

-
5CDS-intronENST00000441717ENST00000492602JAM3chr11

134010665

+SEC13chr3

10347376

-
3UTR-3CDSENST00000524969ENST00000397109JAM3chr11

134010665

+SEC13chr3

10347376

-
3UTR-3CDSENST00000524969ENST00000337354JAM3chr11

134010665

+SEC13chr3

10347376

-
3UTR-3CDSENST00000524969ENST00000350697JAM3chr11

134010665

+SEC13chr3

10347376

-
3UTR-3CDSENST00000524969ENST00000397117JAM3chr11

134010665

+SEC13chr3

10347376

-
3UTR-3CDSENST00000524969ENST00000383801JAM3chr11

134010665

+SEC13chr3

10347376

-
3UTR-intronENST00000524969ENST00000492602JAM3chr11

134010665

+SEC13chr3

10347376

-

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FusionProtFeatures for JAM3_SEC13


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
JAM3

Q9BX67

SEC13

P55735

Participates in cell-cell adhesion. It is a counter-receptor for ITGAM, mediating leukocyte-platelet interactions andis involved in the regulation of transepithelial migration ofpolymorphonuclear neutrophils (PMN). The soluble form is amediator of angiogenesis. {ECO:0000269|PubMed:12208882,ECO:0000269|PubMed:15194813, ECO:0000269|PubMed:20592283}. Functions as a component of the nuclear pore complex(NPC) and the COPII coat. At the endoplasmic reticulum, SEC13 isinvolved in the biogenesis of COPII-coated vesicles.{ECO:0000269|PubMed:8972206}. As a component of the GATOR subcomplex GATOR2, functionswithin the amino acid-sensing branch of the TORC1 signalingpathway. Indirectly activates mTORC1 and the TORC1 signalingpathway through the inhibition of the GATOR1 subcomplex(PubMed:23723238). It is negatively regulated by the upstreamamino acid sensors SESN2 and CASTOR1 (PubMed:25457612,PubMed:27487210). {ECO:0000269|PubMed:23723238,ECO:0000269|PubMed:25457612, ECO:0000269|PubMed:27487210}.

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 JAM3_SEC13


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 JAM3_SEC13


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
JAM3PARD3, TJP1, ITGAM, JAM2, JAM3, RHOUSEC13SEC16B, NUP37, NUP160, NUP133, NUP107, NUP85, SEC31A, RAB11A, SEC13, SIRT7, STAM2, CUL3, SEC23A, SLC12A2, RAD52, BAG3, CLDN12, MAPK9, EGFR, POLR2E, PRPF19, PSMB1, CSNK1A1, CSNK1E, FUS, TRAF5, RNF2, BCR, SPDL1, NUP98, SEH1L, MIOS, PRPF38A, WDR59, WDR24, STX7, ACY1, NUP43, MED4, TFG, QRICH1, SESN2, HSPB1, AHSA1, FLNB, NAPRT, SARS, SEC23B, SEPHS1, SEC24B, IFI16, EWSR1, B9D2, XPO1, CLTB, CLTC, FLNA, GAK, PICALM, AP1S2, SEC16A, GTSE1, MCM2, PPWD1, ZBTB5, CCDC94, FLYWCH2, WDR92, EDEM3, BRCA1


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 JAM3_SEC13


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 JAM3_SEC13


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneJAM3C3151000HEMORRHAGIC DESTRUCTION OF THE BRAIN, SUBEPENDYMAL CALCIFICATION, AND CATARACTS1CTD_human;ORPHANET;UNIPROT