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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: 19474

FusionGeneSummary for LARP4B_SMCO3

check button Fusion gene summary
Fusion gene informationFusion gene name: LARP4B_SMCO3
Fusion gene ID: 19474
HgeneTgene
Gene symbol

LARP4B

SMCO3

Gene ID

23185

440087

Gene nameLa ribonucleoprotein domain family member 4Bsingle-pass membrane protein with coiled-coil domains 3
SynonymsKIAA0217|LARP5C12orf69
Cytomap

10p15.3

12p12.3

Type of geneprotein-codingprotein-coding
Descriptionla-related protein 4BLa ribonucleoprotein domain family, member 5la-related protein 5single-pass membrane and coiled-coil domain-containing protein 3
Modification date2018051920180519
UniProtAcc

Q92615

A2RU48

Ensembl transtripts involved in fusion geneENST00000316157, ENST00000469487, 
ENST00000316048, 
Fusion gene scores* DoF score7 X 6 X 5=2101 X 1 X 1=1
# samples 71
** MAII scorelog2(7/210*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: LARP4B [Title/Abstract] AND SMCO3 [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
TCGALDLUSCTCGA-22-1012-01ALARP4Bchr10

882343

-SMCO3chr12

14959630

-
* 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
5CDS-5UTRENST00000316157ENST00000316048LARP4Bchr10

882343

-SMCO3chr12

14959630

-
intron-5UTRENST00000469487ENST00000316048LARP4Bchr10

882343

-SMCO3chr12

14959630

-

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FusionProtFeatures for LARP4B_SMCO3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LARP4B

Q92615

SMCO3

A2RU48

Stimulates mRNA translation.{ECO:0000269|PubMed:20573744}.

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 LARP4B_SMCO3


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 LARP4B_SMCO3


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
LARP4BGNB2L1, ELAVL1, SIRT7, CUL3, COPS5, CDV3, HSP90AA1, MMS19, CDK18, HECW2, LIN28A, FHL3, RBFOX2, NTRK1, IFI16, XPO1, NPM1, RPL10, STRAP, FAM136A, ASB3, IL13RA2, TRIM25SMCO3MAPK9, TRIM39, OBFC1, FUS


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 LARP4B_SMCO3


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 LARP4B_SMCO3


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