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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: 35136

FusionGeneSummary for SNHG3_LRBA

check button Fusion gene summary
Fusion gene informationFusion gene name: SNHG3_LRBA
Fusion gene ID: 35136
HgeneTgene
Gene symbol

SNHG3

LRBA

Gene ID

8420

987

Gene namesmall nucleolar RNA host gene 3LPS responsive beige-like anchor protein
SynonymsNCRNA00014|RNU17C|RNU17D|U17HG|U17HG-A|U17HG-ABBGL|CDC4L|CVID8|LAB300|LBA
Cytomap

1p35.3

4q31.3

Type of genencRNAprotein-coding
DescriptionU17 small nucleolar RNA hostsmall nucleolar RNA host gene (non-protein coding) 3small nucleolar RNA host gene 3 (non-protein coding)lipopolysaccharide-responsive and beige-like anchor proteinCDC4-like proteinLPS-responsive vesicle trafficking, beach and anchor containingvesicle trafficking, beach and anchor containing
Modification date2018051920180519
UniProtAcc

P50851

Ensembl transtripts involved in fusion geneENST00000364938, ENST00000535741, 
ENST00000510413, ENST00000503716, 
ENST00000357115, ENST00000507224, 
Fusion gene scores* DoF score15 X 7 X 4=42015 X 15 X 7=1575
# samples 1518
** MAII scorelog2(15/420*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(18/1575*10)=-3.12928301694497
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SNHG3 [Title/Abstract] AND LRBA [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
ChiTaRS3.1DA643621SNHG3chr1

28834673

+LRBAchr4

151336756

-
* 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-intronENST00000364938ENST00000535741SNHG3chr1

28834673

+LRBAchr4

151336756

-
intron-intronENST00000364938ENST00000510413SNHG3chr1

28834673

+LRBAchr4

151336756

-
intron-intronENST00000364938ENST00000503716SNHG3chr1

28834673

+LRBAchr4

151336756

-
intron-intronENST00000364938ENST00000357115SNHG3chr1

28834673

+LRBAchr4

151336756

-
intron-intronENST00000364938ENST00000507224SNHG3chr1

28834673

+LRBAchr4

151336756

-

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FusionProtFeatures for SNHG3_LRBA


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SNHG3

LRBA

P50851

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}. May be involved in coupling signal transduction andvesicle trafficking to enable polarized secretion and/or membranedeposition of immune effector molecules. {ECO:0000250}.

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 SNHG3_LRBA


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 SNHG3_LRBA


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 SNHG3_LRBA


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 SNHG3_LRBA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneLRBAC3553512IMMUNODEFICIENCY, COMMON VARIABLE, 8, WITH AUTOIMMUNITY1ORPHANET;UNIPROT