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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:SPTAN1-GLE1 (FusionGDB2 ID:85513)

Fusion Gene Summary for SPTAN1-GLE1

check button Fusion gene summary
Fusion gene informationFusion gene name: SPTAN1-GLE1
Fusion gene ID: 85513
HgeneTgene
Gene symbol

SPTAN1

GLE1

Gene ID

6709

2733

Gene namespectrin alpha, non-erythrocytic 1GLE1 RNA export mediator
SynonymsEIEE5|NEAS|SPTA2CAAHC|CAAHD|GLE1L|LCCS|LCCS1|hGLE1
Cytomap

9q34.11

9q34.11

Type of geneprotein-codingprotein-coding
Descriptionspectrin alpha chain, non-erythrocytic 1alpha-II spectrinalpha-fodrinepididymis secretory sperm binding proteinfodrin alpha chainspectrin, non-erythroid alpha chainspectrin, non-erythroid alpha subunitnucleoporin GLE1GLE1 RNA export mediator homologGLE1 RNA export mediator-likeGLE1-like proteinGLE1-like, RNA export mediator
Modification date2020031320200313
UniProtAcc.

Q53GS7

Ensembl transtripts involved in fusion geneENST00000358161, ENST00000372739, 
ENST00000372731, ENST00000475367, 
ENST00000309971, ENST00000372770, 
ENST00000539582, ENST00000494417, 
Fusion gene scores* DoF score20 X 20 X 10=40004 X 7 X 6=168
# samples 267
** MAII scorelog2(26/4000*10)=-3.94341647163363
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/168*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SPTAN1 [Title/Abstract] AND GLE1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSPTAN1(131314975)-GLE1(131277808), # samples:2
SPTAN1(131337624)-GLE1(131284947), # samples:2
GLE1(131277918)-SPTAN1(131386607), # 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

check buttonFusion gene breakpoints across SPTAN1 (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 GLE1 (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
ChimerDB4BRCATCGA-AO-A03O-01ASPTAN1chr9

131314975

+GLE1chr9

131277808

+
ChimerDB4UCECTCGA-D1-A3JP-01ASPTAN1chr9

131337624

+GLE1chr9

131284947

+
ChimerDB4BRCATCGA-AO-A03O-01ASPTAN1chr9

131314975

-GLE1chr9

131277808

+
ChimerDB4UCECTCGA-D1-A3JP-01ASPTAN1chr9

131337624

-GLE1chr9

131284947

+
ChimerDB4STADTCGA-HU-A4H2-01ASPTAN1chr9

131314975

-GLE1chr9

131295792

+


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Fusion Gene ORF analysis for SPTAN1-GLE1

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
5UTR-3CDSENST00000358161ENST00000309971SPTAN1chr9

131314975

+GLE1chr9

131277808

+
5UTR-3CDSENST00000358161ENST00000372770SPTAN1chr9

131314975

+GLE1chr9

131277808

+
5UTR-5UTRENST00000358161ENST00000539582SPTAN1chr9

131314975

+GLE1chr9

131277808

+
5UTR-intronENST00000358161ENST00000494417SPTAN1chr9

131314975

+GLE1chr9

131277808

+
5UTR-3CDSENST00000372739ENST00000309971SPTAN1chr9

131314975

+GLE1chr9

131277808

+
5UTR-3CDSENST00000372739ENST00000372770SPTAN1chr9

131314975

+GLE1chr9

131277808

+
5UTR-5UTRENST00000372739ENST00000539582SPTAN1chr9

131314975

+GLE1chr9

131277808

+
5UTR-intronENST00000372739ENST00000494417SPTAN1chr9

131314975

+GLE1chr9

131277808

+
5UTR-3CDSENST00000372731ENST00000309971SPTAN1chr9

131314975

+GLE1chr9

131277808

+
5UTR-3CDSENST00000372731ENST00000372770SPTAN1chr9

131314975

+GLE1chr9

131277808

+
5UTR-5UTRENST00000372731ENST00000539582SPTAN1chr9

131314975

+GLE1chr9

131277808

+
5UTR-intronENST00000372731ENST00000494417SPTAN1chr9

131314975

+GLE1chr9

131277808

+
intron-3CDSENST00000475367ENST00000309971SPTAN1chr9

131314975

+GLE1chr9

131277808

+
intron-3CDSENST00000475367ENST00000372770SPTAN1chr9

131314975

+GLE1chr9

131277808

+
intron-5UTRENST00000475367ENST00000539582SPTAN1chr9

131314975

+GLE1chr9

131277808

+
intron-intronENST00000475367ENST00000494417SPTAN1chr9

131314975

+GLE1chr9

131277808

+
In-frameENST00000358161ENST00000309971SPTAN1chr9

131337624

+GLE1chr9

131284947

+
In-frameENST00000358161ENST00000372770SPTAN1chr9

131337624

+GLE1chr9

131284947

+
5CDS-intronENST00000358161ENST00000539582SPTAN1chr9

131337624

+GLE1chr9

131284947

+
5CDS-intronENST00000358161ENST00000494417SPTAN1chr9

131337624

+GLE1chr9

131284947

+
In-frameENST00000372739ENST00000309971SPTAN1chr9

131337624

+GLE1chr9

131284947

+
In-frameENST00000372739ENST00000372770SPTAN1chr9

131337624

+GLE1chr9

131284947

+
5CDS-intronENST00000372739ENST00000539582SPTAN1chr9

131337624

+GLE1chr9

131284947

+
5CDS-intronENST00000372739ENST00000494417SPTAN1chr9

131337624

+GLE1chr9

131284947

+
In-frameENST00000372731ENST00000309971SPTAN1chr9

131337624

+GLE1chr9

131284947

+
In-frameENST00000372731ENST00000372770SPTAN1chr9

131337624

+GLE1chr9

131284947

+
5CDS-intronENST00000372731ENST00000539582SPTAN1chr9

131337624

+GLE1chr9

131284947

+
5CDS-intronENST00000372731ENST00000494417SPTAN1chr9

131337624

+GLE1chr9

131284947

+
intron-3CDSENST00000475367ENST00000309971SPTAN1chr9

131337624

+GLE1chr9

131284947

+
intron-3CDSENST00000475367ENST00000372770SPTAN1chr9

131337624

+GLE1chr9

131284947

+
intron-intronENST00000475367ENST00000539582SPTAN1chr9

131337624

+GLE1chr9

131284947

+
intron-intronENST00000475367ENST00000494417SPTAN1chr9

131337624

+GLE1chr9

131284947

+
5UTR-3CDSENST00000358161ENST00000309971SPTAN1chr9

131314975

-GLE1chr9

131295792

+
5UTR-3CDSENST00000358161ENST00000372770SPTAN1chr9

131314975

-GLE1chr9

131295792

+
5UTR-3CDSENST00000358161ENST00000539582SPTAN1chr9

131314975

-GLE1chr9

131295792

+
5UTR-3UTRENST00000358161ENST00000494417SPTAN1chr9

131314975

-GLE1chr9

131295792

+
5UTR-3CDSENST00000372739ENST00000309971SPTAN1chr9

131314975

-GLE1chr9

131295792

+
5UTR-3CDSENST00000372739ENST00000372770SPTAN1chr9

131314975

-GLE1chr9

131295792

+
5UTR-3CDSENST00000372739ENST00000539582SPTAN1chr9

131314975

-GLE1chr9

131295792

+
5UTR-3UTRENST00000372739ENST00000494417SPTAN1chr9

131314975

-GLE1chr9

131295792

+
5UTR-3CDSENST00000372731ENST00000309971SPTAN1chr9

131314975

-GLE1chr9

131295792

+
5UTR-3CDSENST00000372731ENST00000372770SPTAN1chr9

131314975

-GLE1chr9

131295792

+
5UTR-3CDSENST00000372731ENST00000539582SPTAN1chr9

131314975

-GLE1chr9

131295792

+
5UTR-3UTRENST00000372731ENST00000494417SPTAN1chr9

131314975

-GLE1chr9

131295792

+
intron-3CDSENST00000475367ENST00000309971SPTAN1chr9

131314975

-GLE1chr9

131295792

+
intron-3CDSENST00000475367ENST00000372770SPTAN1chr9

131314975

-GLE1chr9

131295792

+
intron-3CDSENST00000475367ENST00000539582SPTAN1chr9

131314975

-GLE1chr9

131295792

+
intron-3UTRENST00000475367ENST00000494417SPTAN1chr9

131314975

-GLE1chr9

131295792

+

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 SPTAN1-GLE1


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)
SPTAN1chr9131337624+GLE1chr9131284946+5.59E-060.9999944
SPTAN1chr9131314975+GLE1chr9131277807+2.97E-101
SPTAN1chr9131337624+GLE1chr9131284946+5.59E-060.9999944
SPTAN1chr9131314975+GLE1chr9131277807+2.97E-101

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.

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Fusion Protein Features for SPTAN1-GLE1


check button Go to

FGviewer for the breakpoints of chr9:131337624-chr9:131284947

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.GLE1

Q53GS7

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Required for the export of mRNAs containing poly(A) tails from the nucleus into the cytoplasm. May be involved in the terminal step of the mRNA transport through the nuclear pore complex (NPC). {ECO:0000269|PubMed:12668658, ECO:0000269|PubMed:16000379, ECO:0000269|PubMed:9618489}.

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
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+55645_146217.02473.0RepeatSpectrin 1
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+55745_146217.02478.0RepeatSpectrin 1
TgeneGLE1chr9:131337624chr9:131284947ENST00000309971216151_277144.0699.0Coiled coilOntology_term=ECO:0000255
TgeneGLE1chr9:131337624chr9:131284947ENST00000309971216305_356144.0699.0Coiled coilOntology_term=ECO:0000255
TgeneGLE1chr9:131337624chr9:131284947ENST00000372770214151_277144.0660.0Coiled coilOntology_term=ECO:0000255
TgeneGLE1chr9:131337624chr9:131284947ENST00000372770214305_356144.0660.0Coiled coilOntology_term=ECO:0000255
TgeneGLE1chr9:131337624chr9:131284947ENST00000309971216444_483144.0699.0RegionNote=Mediates the shuttling between the nucleus and the cytoplasm
TgeneGLE1chr9:131337624chr9:131284947ENST00000372770214444_483144.0660.0RegionNote=Mediates the shuttling between the nucleus and the cytoplasm

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5562336_2347217.02473.0Calcium binding1
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5562379_2390217.02473.0Calcium binding2
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5572336_2347217.02478.0Calcium binding1
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5572379_2390217.02478.0Calcium binding2
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5562323_2358217.02473.0DomainEF-hand 1
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5562366_2401217.02473.0DomainEF-hand 2
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5562404_2439217.02473.0DomainEF-hand 3
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+556967_1026217.02473.0DomainSH3
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5572323_2358217.02478.0DomainEF-hand 1
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5572366_2401217.02478.0DomainEF-hand 2
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5572404_2439217.02478.0DomainEF-hand 3
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+557967_1026217.02478.0DomainSH3
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5561096_1166217.02473.0RepeatSpectrin 10
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5561233_1336217.02473.0RepeatSpectrin 11
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5561339_1442217.02473.0RepeatSpectrin 12
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5561446_1549217.02473.0RepeatSpectrin 13
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+556150_251217.02473.0RepeatSpectrin 2
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5561552_1656217.02473.0RepeatSpectrin 14
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5561659_1762217.02473.0RepeatSpectrin 15
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5561764_1868217.02473.0RepeatSpectrin 16
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5561871_1974217.02473.0RepeatSpectrin 17
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5561978_2081217.02473.0RepeatSpectrin 18
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5562092_2194217.02473.0RepeatSpectrin 19
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+5562206_2310217.02473.0RepeatSpectrin 20
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+556256_358217.02473.0RepeatSpectrin 3
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+556361_465217.02473.0RepeatSpectrin 4
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+556468_570217.02473.0RepeatSpectrin 5
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+556574_676217.02473.0RepeatSpectrin 6
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+556679_781217.02473.0RepeatSpectrin 7
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+556785_888217.02473.0RepeatSpectrin 8
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372731+556891_969217.02473.0RepeatSpectrin 9
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5571096_1166217.02478.0RepeatSpectrin 10
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5571233_1336217.02478.0RepeatSpectrin 11
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5571339_1442217.02478.0RepeatSpectrin 12
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5571446_1549217.02478.0RepeatSpectrin 13
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+557150_251217.02478.0RepeatSpectrin 2
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5571552_1656217.02478.0RepeatSpectrin 14
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5571659_1762217.02478.0RepeatSpectrin 15
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5571764_1868217.02478.0RepeatSpectrin 16
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5571871_1974217.02478.0RepeatSpectrin 17
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5571978_2081217.02478.0RepeatSpectrin 18
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5572092_2194217.02478.0RepeatSpectrin 19
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+5572206_2310217.02478.0RepeatSpectrin 20
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+557256_358217.02478.0RepeatSpectrin 3
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+557361_465217.02478.0RepeatSpectrin 4
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+557468_570217.02478.0RepeatSpectrin 5
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+557574_676217.02478.0RepeatSpectrin 6
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+557679_781217.02478.0RepeatSpectrin 7
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+557785_888217.02478.0RepeatSpectrin 8
HgeneSPTAN1chr9:131337624chr9:131284947ENST00000372739+557891_969217.02478.0RepeatSpectrin 9


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Fusion Gene Sequence for SPTAN1-GLE1


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 SPTAN1-GLE1


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
TgeneGLE1chr9:131337624chr9:131284947ENST00000309971216656_698144.0699.0NUP42
TgeneGLE1chr9:131337624chr9:131284947ENST00000372770214656_698144.0660.0NUP42


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
TgeneGLE1chr9:131337624chr9:131284947ENST000003099712161_29144.0699.0NUP155
TgeneGLE1chr9:131337624chr9:131284947ENST000003727702141_29144.0660.0NUP155


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 SPTAN1-GLE1


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 SPTAN1-GLE1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSPTAN1C0037769West Syndrome2ORPHANET
HgeneSPTAN1C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneSPTAN1C0270715Degenerative Diseases, Central Nervous System1CTD_human
HgeneSPTAN1C0524851Neurodegenerative Disorders1CTD_human
HgeneSPTAN1C0751733Degenerative Diseases, Spinal Cord1CTD_human
HgeneSPTAN1C3150731EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 51CTD_human;GENOMICS_ENGLAND
TgeneGLE1C1854664LETHAL CONGENITAL CONTRACTURE SYNDROME 13CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneGLE1C2678471Lethal Arthrogryposis With Anterior Horn Cell Disease3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneGLE1C0002736Amyotrophic Lateral Sclerosis1ORPHANET