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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: 35135

FusionGeneSummary for SNHG3_IGHA1

check button Fusion gene summary
Fusion gene informationFusion gene name: SNHG3_IGHA1
Fusion gene ID: 35135
HgeneTgene
Gene symbol

SNHG3

IGHA1

Gene ID

8420

3493

Gene namesmall nucleolar RNA host gene 3immunoglobulin heavy constant alpha 1
SynonymsNCRNA00014|RNU17C|RNU17D|U17HG|U17HG-A|U17HG-ABIgA1
Cytomap

1p35.3

14q32.33

Type of genencRNAother
DescriptionU17 small nucleolar RNA hostsmall nucleolar RNA host gene (non-protein coding) 3small nucleolar RNA host gene 3 (non-protein coding)immunoglobulin alpha 1immunoglobulin heavy chain constant region alpha 1
Modification date2018051920180523
UniProtAcc

P01876

Ensembl transtripts involved in fusion geneENST00000364938, ENST00000390547, 
Fusion gene scores* DoF score15 X 7 X 4=4205 X 4 X 3=60
# samples 154
** MAII scorelog2(15/420*10)=-1.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/60*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SNHG3 [Title/Abstract] AND IGHA1 [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
TgeneIGHA1

GO:0019731

antibacterial humoral response

23250751

TgeneIGHA1

GO:0060267

positive regulation of respiratory burst

24145934


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
TCGALDSTADTCGA-CG-5716-01ASNHG3chr1

28832596

+IGHA1chr14

106173768

-
* 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-3CDSENST00000364938ENST00000390547SNHG3chr1

28832596

+IGHA1chr14

106173768

-

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FusionProtFeatures for SNHG3_IGHA1


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

IGHA1

P01876

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}. Constant region of immunoglobulin heavy chains.Immunoglobulins, also known as antibodies, are membrane-bound orsecreted glycoproteins produced by B lymphocytes. In therecognition phase of humoral immunity, the membrane-boundimmunoglobulins serve as receptors which, upon binding of aspecific antigen, trigger the clonal expansion and differentiationof B lymphocytes into immunoglobulins-secreting plasma cells.Secreted immunoglobulins mediate the effector phase of humoralimmunity, which results in the elimination of bound antigens(PubMed:22158414, PubMed:20176268). The antigen binding site isformed by the variable domain of one heavy chain, together withthat of its associated light chain. Thus, each immunoglobulin hastwo antigen binding sites with remarkable affinity for aparticular antigen. The variable domains are assembled by aprocess called V-(D)-J rearrangement and can then be subjected tosomatic hypermutations which, after exposure to antigen andselection, allow affinity maturation for a particular antigen(PubMed:17576170, PubMed:20176268). Ig alpha is the majorimmunoglobulin class in body secretions (PubMed:2241915).{ECO:0000303|PubMed:17576170, ECO:0000303|PubMed:20176268,ECO:0000303|PubMed:22158414, ECO:0000303|PubMed:2241915}.

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_IGHA1


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_IGHA1


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
SNHG3UTP23, TRIM25IGHA1CDK2AP1, SGK1, CDK5RAP3, POT1, RNF115, CDH1, PARK2, CCDC148, SSFA2, EAPP, GDPD1, POLL, ACOT8, PRAP1, GTF2B, KIR2DS2, TMEM237, DXO, FN3KRP, ICE2, INPP5A, CCRL2, MTMR14, DDX31, FRMD1, ZNF491, SNX27, PCK2, HBM, ARHGAP12, NPB, ZBBX, PLEKHG6, RCAN2, UQCRQ, DDX17, RCAN1, GKN1, TSFM, ALDH2, SNRPF, ZCCHC17, RNGTT


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_IGHA1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneIGHA1P01876DB01593ZincImmunoglobulin heavy constant alpha 1 {ECO:0000303|PubMed:11340299, ECO:0000303|Ref.11}small moleculeapproved|investigational

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RelatedDiseases for SNHG3_IGHA1


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