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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:SPTLC2-ACTB (FusionGDB2 ID:HG9517TG60)

Fusion Gene Summary for SPTLC2-ACTB

check button Fusion gene summary
Fusion gene informationFusion gene name: SPTLC2-ACTB
Fusion gene ID: hg9517tg60
HgeneTgene
Gene symbol

SPTLC2

ACTB

Gene ID

9517

60

Gene nameserine palmitoyltransferase long chain base subunit 2actin beta
SynonymsHSN1C|LCB2|LCB2A|NSAN1C|SPT2|hLCB2aBRWS1|PS1TP5BP1
Cytomap('SPTLC2')('ACTB')

14q24.3

7p22.1

Type of geneprotein-codingprotein-coding
Descriptionserine palmitoyltransferase 2LCB 2SPT 2long chain base biosynthesis protein 2aserine palmitoyltransferase, subunit IIserine-palmitoyl-CoA transferase 2actin, cytoplasmic 1I(2)-actinPS1TP5-binding protein 1beta cytoskeletal actin
Modification date2020031320200327
UniProtAcc.

P60709

Ensembl transtripts involved in fusion geneENST00000216484, ENST00000556264, 
Fusion gene scores* DoF score9 X 10 X 5=45052 X 37 X 11=21164
# samples 1158
** MAII scorelog2(11/450*10)=-2.03242147769238
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(58/21164*10)=-5.1894156123924
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SPTLC2 [Title/Abstract] AND ACTB [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSPTLC2(77972521)-ACTB(5567258), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneSPTLC2

GO:0030148

sphingolipid biosynthetic process

25332431|26573920

HgeneSPTLC2

GO:0046513

ceramide biosynthetic process

25691431

HgeneSPTLC2

GO:1904504

positive regulation of lipophagy

25332431

TgeneACTB

GO:0098974

postsynaptic actin cytoskeleton organization

18341992



check button Fusion gene information
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand


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Fusion Gene ORF analysis for SPTLC2-ACTB

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

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for SPTLC2-ACTB


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for SPTLC2-ACTB


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:77972521/:5567258)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

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

P60709

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Actin is a highly conserved protein that polymerizes to produce filaments that form cross-linked networks in the cytoplasm of cells (PubMed:29581253). Actin exists in both monomeric (G-actin) and polymeric (F-actin) forms, both forms playing key functions, such as cell motility and contraction (PubMed:29581253). In addition to their role in the cytoplasmic cytoskeleton, G- and F-actin also localize in the nucleus, and regulate gene transcription and motility and repair of damaged DNA (PubMed:29925947). {ECO:0000269|PubMed:29581253, ECO:0000269|PubMed:29925947}.

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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Fusion Gene Sequence for SPTLC2-ACTB


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for SPTLC2-ACTB


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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Related Drugs for SPTLC2-ACTB


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for SPTLC2-ACTB


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSPTLC2C3150896NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE IC5CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneSPTLC2C0020071Hereditary Sensory Autonomic Neuropathy, Type 13GENOMICS_ENGLAND;ORPHANET
HgeneSPTLC2C0007959Charcot-Marie-Tooth Disease1GENOMICS_ENGLAND
HgeneSPTLC2C0013364Dysautonomia, Familial1GENOMICS_ENGLAND
TgeneC1855722Iris Coloboma with Ptosis, Hypertelorism, and Mental Retardation6CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC1846331Juvenile-onset dystonia2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC1853623Fryns-Aftimos Syndrome2GENOMICS_ENGLAND
TgeneC2239176Liver carcinoma2CTD_human
TgeneC0003129Anoxemia1CTD_human
TgeneC0003130Anoxia1CTD_human
TgeneC0005586Bipolar Disorder1PSYGENET
TgeneC0005818Blood Platelet Disorders1GENOMICS_ENGLAND
TgeneC0007097Carcinoma1CTD_human
TgeneC0009363Congenital ocular coloboma (disorder)1CTD_human
TgeneC0013393Dysostoses1CTD_human
TgeneC0013421Dystonia1CTD_human
TgeneC0014859Esophageal Neoplasms1CTD_human
TgeneC0018784Sensorineural Hearing Loss (disorder)1CTD_human
TgeneC0019193Hepatitis, Toxic1CTD_human
TgeneC0024121Lung Neoplasms1CTD_human
TgeneC0024667Animal Mammary Neoplasms1CTD_human
TgeneC0024668Mammary Neoplasms, Experimental1CTD_human
TgeneC0027626Neoplasm Invasiveness1CTD_human
TgeneC0029408Degenerative polyarthritis1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0086743Osteoarthrosis Deformans1CTD_human
TgeneC0151744Myocardial Ischemia1CTD_human
TgeneC0205696Anaplastic carcinoma1CTD_human
TgeneC0205697Carcinoma, Spindle-Cell1CTD_human
TgeneC0205698Undifferentiated carcinoma1CTD_human
TgeneC0205699Carcinomatosis1CTD_human
TgeneC0242184Hypoxia1CTD_human
TgeneC0242379Malignant neoplasm of lung1CTD_human
TgeneC0263579Pigmented hairy epidermal nevus1ORPHANET
TgeneC0265541Cranioschisis1CTD_human
TgeneC0272183Qualitative abnormality of granulocyte1GENOMICS_ENGLAND
TgeneC0376634Craniofacial Abnormalities1CTD_human
TgeneC0393588Dystonia, Paroxysmal1CTD_human
TgeneC0393610Dystonia, Diurnal1CTD_human
TgeneC0497552Congenital neurologic anomalies1CTD_human
TgeneC0546837Malignant neoplasm of esophagus1CTD_human
TgeneC0700292Hypoxemia1CTD_human
TgeneC0751093Dystonia, Limb1CTD_human
TgeneC0860207Drug-Induced Liver Disease1CTD_human
TgeneC1257925Mammary Carcinoma, Animal1CTD_human
TgeneC1262760Hepatitis, Drug-Induced1CTD_human
TgeneC1691779Sensory hearing loss1CTD_human
TgeneC1858042Becker Nevus Syndrome1ORPHANET
TgeneC3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneC4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneC4279912Chemically-Induced Liver Toxicity1CTD_human
TgeneC4554007Uveoretinal Coloboma1CTD_human