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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:SLC19A1-C9orf3 (FusionGDB2 ID:82365)

Fusion Gene Summary for SLC19A1-C9orf3

check button Fusion gene summary
Fusion gene informationFusion gene name: SLC19A1-C9orf3
Fusion gene ID: 82365
HgeneTgene
Gene symbol

SLC19A1

C9orf3

Gene ID

6573

84909

Gene namesolute carrier family 19 member 1aminopeptidase O (putative)
SynonymsCHMD|FOLT|IFC-1|IFC1|REFC|RFC|RFC1|RFT-1|hRFC|hSLC19A1AP-O|APO|C90RF3|C9orf3|ONPEP
Cytomap

21q22.3

9q22.32

Type of geneprotein-codingprotein-coding
Descriptionreduced folate transporterfolate transporter 1intestinal folate carrier 1placental folate transporterreduced folate carrier 1reduced folate carrier proteinreduced folate transporter 1solute carrier family 19 (folate transporter), member 1aminopeptidase O
Modification date2020031320200313
UniProtAcc

P41440

.
Ensembl transtripts involved in fusion geneENST00000311124, ENST00000380010, 
ENST00000485649, ENST00000567670, 
ENST00000468508, 		ENST00000297979, 
ENST00000375315, ENST00000277198, 
ENST00000395357, ENST00000425634, 
ENST00000433691, ENST00000473778, 
Fusion gene scores* DoF score8 X 7 X 5=28039 X 9 X 14=4914
# samples 843
** MAII scorelog2(8/280*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(43/4914*10)=-3.5144892927727
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SLC19A1 [Title/Abstract] AND C9orf3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSLC19A1(46945731)-C9orf3(97848964), # 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
HgeneSLC19A1

GO:0051958

methotrexate transport

22554803

HgeneSLC19A1

GO:0098838

folate transmembrane transport

22554803

HgeneSLC19A1

GO:1904447

folate import across plasma membrane

14609557|22554803


check buttonFusion gene breakpoints across SLC19A1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across C9orf3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChimerDB4STADTCGA-D7-6822-01ASLC19A1chr21

46945731

-C9orf3chr9

97848964

+


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Fusion Gene ORF analysis for SLC19A1-C9orf3

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-3UTRENST00000311124ENST00000297979SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-3UTRENST00000311124ENST00000375315SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-3UTRENST00000380010ENST00000297979SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-3UTRENST00000380010ENST00000375315SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-3UTRENST00000485649ENST00000297979SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-3UTRENST00000485649ENST00000375315SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-3UTRENST00000567670ENST00000297979SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-3UTRENST00000567670ENST00000375315SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000311124ENST00000277198SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000311124ENST00000395357SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000311124ENST00000425634SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000311124ENST00000433691SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000311124ENST00000473778SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000380010ENST00000277198SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000380010ENST00000395357SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000380010ENST00000425634SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000380010ENST00000433691SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000380010ENST00000473778SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000485649ENST00000277198SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000485649ENST00000395357SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000485649ENST00000425634SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000485649ENST00000433691SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000485649ENST00000473778SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000567670ENST00000277198SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000567670ENST00000395357SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000567670ENST00000425634SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000567670ENST00000433691SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
5CDS-intronENST00000567670ENST00000473778SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
intron-3UTRENST00000468508ENST00000297979SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
intron-3UTRENST00000468508ENST00000375315SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
intron-intronENST00000468508ENST00000277198SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
intron-intronENST00000468508ENST00000395357SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
intron-intronENST00000468508ENST00000425634SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
intron-intronENST00000468508ENST00000433691SLC19A1chr21

46945731

-C9orf3chr9

97848964

+
intron-intronENST00000468508ENST00000473778SLC19A1chr21

46945731

-C9orf3chr9

97848964

+

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 SLC19A1-C9orf3


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)
SLC19A1chr2146945730-C9orf3chr997848963+0.0002618680.99973816
SLC19A1chr2146945730-C9orf3chr997848963+0.0002618680.99973816

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for SLC19A1-C9orf3


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/:46945731/:97848964)
- 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
SLC19A1

P41440

.
FUNCTION: Transporter that mediates the import of reduced folates and a subset of cyclic dinucleotides (PubMed:7826387, PubMed:9041240, PubMed:10787414, PubMed:15337749, PubMed:16115875, PubMed:31126740, PubMed:31511694). Has high affinity for N5-methyltetrahydrofolate, the predominant circulating form of folate (PubMed:10787414, PubMed:14609557, PubMed:22554803). Also able to mediate the import of antifolate drug methotrexate (PubMed:7615551, PubMed:7641195, PubMed:9767079, PubMed:22554803). Acts as an importer of immunoreactive cyclic dinucleotides, such as cyclic GMP-AMP (2'-3'-cGAMP), an immune messenger produced in response to DNA virus in the cytosol, and its linkage isomer 3'-3'-cGAMP (PubMed:31126740, PubMed:31511694). Mechanistically, acts as an antiporter, which export of intracellular organic anions to facilitate uptake of its substrates (PubMed:22554803, PubMed:31126740, PubMed:31511694). 5-amino-4-imidazolecarboxamide riboside (AICAR), when phosphorylated to AICAR monophosphate, can serve as an organic anion for antiporter activity (PubMed:22554803). {ECO:0000269|PubMed:10787414, ECO:0000269|PubMed:14609557, ECO:0000269|PubMed:15337749, ECO:0000269|PubMed:16115875, ECO:0000269|PubMed:22554803, ECO:0000269|PubMed:31126740, ECO:0000269|PubMed:31511694, ECO:0000269|PubMed:7615551, ECO:0000269|PubMed:7641195, ECO:0000269|PubMed:7826387, ECO:0000269|PubMed:9041240, ECO:0000269|PubMed:9767079}.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}.

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 SLC19A1-C9orf3


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 SLC19A1-C9orf3


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 SLC19A1-C9orf3


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 SLC19A1-C9orf3


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