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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: 19792

FusionGeneSummary for LINC00886_SEMA4D

check button Fusion gene summary
Fusion gene informationFusion gene name: LINC00886_SEMA4D
Fusion gene ID: 19792
HgeneTgene
Gene symbol

LINC00886

SEMA4D

Gene ID

730091

10507

Gene namelong intergenic non-protein coding RNA 886semaphorin 4D
Synonyms-C9orf164|CD100|COLL4|M-sema-G|SEMAJ|coll-4
Cytomap

3q25.31

9q22.2

Type of genencRNAprotein-coding
Description-semaphorin-4DA8BB18GR3sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Dsema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, 4D
Modification date2018032920180527
UniProtAcc

Q92854

Ensembl transtripts involved in fusion geneENST00000472943, ENST00000339861, 
ENST00000420987, ENST00000455551, 
ENST00000343780, ENST00000450295, 
ENST00000438547, ENST00000356444, 
ENST00000422704, ENST00000420101, 
ENST00000469653, 
Fusion gene scores* DoF score1 X 1 X 1=13 X 4 X 2=24
# samples 14
** MAII scorelog2(1/1*10)=3.32192809488736log2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: LINC00886 [Title/Abstract] AND SEMA4D [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
TgeneSEMA4D

GO:0001934

positive regulation of protein phosphorylation

16055703

TgeneSEMA4D

GO:0007162

negative regulation of cell adhesion

15218527

TgeneSEMA4D

GO:0030335

positive regulation of cell migration

16055703

TgeneSEMA4D

GO:0071526

semaphorin-plexin signaling pathway

15218527


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
ChiTaRS3.1AA442974LINC00886chr3

156527598

-SEMA4Dchr9

92065405

-
* 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-intronENST00000472943ENST00000339861LINC00886chr3

156527598

-SEMA4Dchr9

92065405

-
intron-intronENST00000472943ENST00000420987LINC00886chr3

156527598

-SEMA4Dchr9

92065405

-
intron-intronENST00000472943ENST00000455551LINC00886chr3

156527598

-SEMA4Dchr9

92065405

-
intron-intronENST00000472943ENST00000343780LINC00886chr3

156527598

-SEMA4Dchr9

92065405

-
intron-intronENST00000472943ENST00000450295LINC00886chr3

156527598

-SEMA4Dchr9

92065405

-
intron-intronENST00000472943ENST00000438547LINC00886chr3

156527598

-SEMA4Dchr9

92065405

-
intron-intronENST00000472943ENST00000356444LINC00886chr3

156527598

-SEMA4Dchr9

92065405

-
intron-intronENST00000472943ENST00000422704LINC00886chr3

156527598

-SEMA4Dchr9

92065405

-
intron-intronENST00000472943ENST00000420101LINC00886chr3

156527598

-SEMA4Dchr9

92065405

-
intron-intronENST00000472943ENST00000469653LINC00886chr3

156527598

-SEMA4Dchr9

92065405

-

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FusionProtFeatures for LINC00886_SEMA4D


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LINC00886

SEMA4D

Q92854

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}. Cell surface receptor for PLXN1B and PLXNB2 that playsan important role in cell-cell signaling. Promotes reorganizationof the actin cytoskeleton and plays a role in axonal growth coneguidance in the developing central nervous system. Regulatesdendrite and axon branching and morphogenesis. Promotes themigration of cerebellar granule cells and of endothelial cells.Plays a role in the immune system; induces B-cells to aggregateand improves their viability (in vitro). Promotes signaling viaSRC and PTK2B/PYK2, which then mediates activation ofphosphatidylinositol 3-kinase and of the AKT1 signaling cascade.Interaction with PLXNB1 mediates activation of RHOA.{ECO:0000269|PubMed:16055703, ECO:0000269|PubMed:19788569,ECO:0000269|PubMed:20877282, ECO:0000269|PubMed:8876214}.

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 LINC00886_SEMA4D


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 LINC00886_SEMA4D


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 LINC00886_SEMA4D


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 LINC00886_SEMA4D


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