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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: 33140

FusionGeneSummary for SEMA3D_RBM28

check button Fusion gene summary
Fusion gene informationFusion gene name: SEMA3D_RBM28
Fusion gene ID: 33140
HgeneTgene
Gene symbol

SEMA3D

RBM28

Gene ID

223117

55131

Gene namesemaphorin 3DRNA binding motif protein 28
SynonymsSema-Z2|coll-2ANES
Cytomap

7q21.11

7q32.1

Type of geneprotein-codingprotein-coding
Descriptionsemaphorin-3Dcollapsin 2sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3DRNA-binding protein 282810480G15Rik
Modification date2018052320180523
UniProtAcc

O95025

Q9NW13

Ensembl transtripts involved in fusion geneENST00000284136, ENST00000444867, 
ENST00000484038, 
ENST00000223073, 
ENST00000481788, ENST00000415472, 
Fusion gene scores* DoF score2 X 3 X 2=123 X 3 X 3=27
# samples 23
** MAII scorelog2(2/12*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SEMA3D [Title/Abstract] AND RBM28 [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
TCGARVPRADTCGA-CH-5788-01ASEMA3Dchr7

84782924

-RBM28chr7

127979845

-
* 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-3CDSENST00000284136ENST00000223073SEMA3Dchr7

84782924

-RBM28chr7

127979845

-
intron-intronENST00000284136ENST00000481788SEMA3Dchr7

84782924

-RBM28chr7

127979845

-
intron-intronENST00000284136ENST00000415472SEMA3Dchr7

84782924

-RBM28chr7

127979845

-
5UTR-3CDSENST00000444867ENST00000223073SEMA3Dchr7

84782924

-RBM28chr7

127979845

-
5UTR-intronENST00000444867ENST00000481788SEMA3Dchr7

84782924

-RBM28chr7

127979845

-
5UTR-intronENST00000444867ENST00000415472SEMA3Dchr7

84782924

-RBM28chr7

127979845

-
intron-3CDSENST00000484038ENST00000223073SEMA3Dchr7

84782924

-RBM28chr7

127979845

-
intron-intronENST00000484038ENST00000481788SEMA3Dchr7

84782924

-RBM28chr7

127979845

-
intron-intronENST00000484038ENST00000415472SEMA3Dchr7

84782924

-RBM28chr7

127979845

-

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FusionProtFeatures for SEMA3D_RBM28


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SEMA3D

O95025

RBM28

Q9NW13

Induces the collapse and paralysis of neuronal growthcones. Could potentially act as repulsive cues toward specificneuronal populations. Binds to neuropilin (By similarity).{ECO:0000250}. Nucleolar component of the spliceosomalribonucleoprotein complexes. {ECO:0000269|PubMed:17081119}.

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 SEMA3D_RBM28


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 SEMA3D_RBM28


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
SEMA3DRBM28NOP56, SIRT7, CUL3, CUL1, CAND1, RPL5, RPS17, RRP12, DKC1, CTPS1, POLR3F, POLR3G, ZNF622, ESR1, HDAC11, HECW2, LIN28A, TARBP2, BRCA1, OBSL1, EED, RNF2, NOL12, RPL14, RPL8, DHX8, NIFK, NPM1, ZC3H3, PRR11, ILF2, NTRK1, NOP2, PES1, DDX18, NIP7, RRP15, SDAD1, TOP1, IFI16, HNRNPU, KIF11, RPL10, SORT1, FBXW7, ZNF746, RPL30, ZC3HAV1, ZNF2, RPL18, H2AFY2, KIAA0020, KNOP1, GPATCH4, RPL18A, RRP8, WDR46, RPS14, RPL37A, RBM4, PRDM5, MAK16, STAU1, DGCR8, GLTSCR2, ZBTB48, SART3, PDGFB, MECP2, HIST1H1E, SRP68, RBM34, RPL28, CNBP, MTF1


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 SEMA3D_RBM28


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 SEMA3D_RBM28


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSEMA3DC0036341Schizophrenia1PSYGENET
TgeneRBM28C2677535Alopecia, Neurologic Defects, and Endocrinopathy Syndrome1CTD_human;ORPHANET;UNIPROT