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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:SDC1-PUM2 (FusionGDB2 ID:79802)

Fusion Gene Summary for SDC1-PUM2

check button Fusion gene summary
Fusion gene informationFusion gene name: SDC1-PUM2
Fusion gene ID: 79802
HgeneTgene
Gene symbol

SDC1

PUM2

Gene ID

6382

23369

Gene namesyndecan 1pumilio RNA binding family member 2
SynonymsCD138|SDC|SYND1|syndecanPUMH2|PUML2
Cytomap

2p24.1

2p24.1

Type of geneprotein-codingprotein-coding
Descriptionsyndecan-1CD138 antigenheparan sulfate proteoglycan fibroblast growth factor receptorsyndecan proteoglycan 1pumilio homolog 2pumilio-2
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000254351, ENST00000381150, 
ENST00000403076, ENST00000482879, 
ENST00000420234, ENST00000319801, 
ENST00000338086, ENST00000361078, 
ENST00000403432, ENST00000536417, 
Fusion gene scores* DoF score4 X 4 X 3=4811 X 9 X 5=495
# samples 413
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/495*10)=-1.92891690193852
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SDC1 [Title/Abstract] AND PUM2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPUM2(20550358)-SDC1(20405185), # samples:1
PUM2(20550571)-SDC1(20405185), # samples:1
SDC1(20402848)-PUM2(20463221), # samples:3
Anticipated loss of major functional domain due to fusion event.SDC1-PUM2 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
SDC1-PUM2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* 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
TgenePUM2

GO:0010608

posttranscriptional regulation of gene expression

25100735

TgenePUM2

GO:0043488

regulation of mRNA stability

26724866

TgenePUM2

GO:0051983

regulation of chromosome segregation

26724866

TgenePUM2

GO:1900246

positive regulation of RIG-I signaling pathway

25340845


check buttonFusion gene breakpoints across SDC1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across PUM2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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-HF-A5NB-01ASDC1chr2

20402848

-PUM2chr2

20463221

-


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Fusion Gene ORF analysis for SDC1-PUM2

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-intronENST00000254351ENST00000420234SDC1chr2

20402848

-PUM2chr2

20463221

-
5CDS-intronENST00000381150ENST00000420234SDC1chr2

20402848

-PUM2chr2

20463221

-
Frame-shiftENST00000381150ENST00000319801SDC1chr2

20402848

-PUM2chr2

20463221

-
Frame-shiftENST00000381150ENST00000338086SDC1chr2

20402848

-PUM2chr2

20463221

-
Frame-shiftENST00000381150ENST00000361078SDC1chr2

20402848

-PUM2chr2

20463221

-
Frame-shiftENST00000381150ENST00000403432SDC1chr2

20402848

-PUM2chr2

20463221

-
Frame-shiftENST00000381150ENST00000536417SDC1chr2

20402848

-PUM2chr2

20463221

-
In-frameENST00000254351ENST00000319801SDC1chr2

20402848

-PUM2chr2

20463221

-
In-frameENST00000254351ENST00000338086SDC1chr2

20402848

-PUM2chr2

20463221

-
In-frameENST00000254351ENST00000361078SDC1chr2

20402848

-PUM2chr2

20463221

-
In-frameENST00000254351ENST00000403432SDC1chr2

20402848

-PUM2chr2

20463221

-
In-frameENST00000254351ENST00000536417SDC1chr2

20402848

-PUM2chr2

20463221

-
intron-3CDSENST00000403076ENST00000319801SDC1chr2

20402848

-PUM2chr2

20463221

-
intron-3CDSENST00000403076ENST00000338086SDC1chr2

20402848

-PUM2chr2

20463221

-
intron-3CDSENST00000403076ENST00000361078SDC1chr2

20402848

-PUM2chr2

20463221

-
intron-3CDSENST00000403076ENST00000403432SDC1chr2

20402848

-PUM2chr2

20463221

-
intron-3CDSENST00000403076ENST00000536417SDC1chr2

20402848

-PUM2chr2

20463221

-
intron-3CDSENST00000482879ENST00000319801SDC1chr2

20402848

-PUM2chr2

20463221

-
intron-3CDSENST00000482879ENST00000338086SDC1chr2

20402848

-PUM2chr2

20463221

-
intron-3CDSENST00000482879ENST00000361078SDC1chr2

20402848

-PUM2chr2

20463221

-
intron-3CDSENST00000482879ENST00000403432SDC1chr2

20402848

-PUM2chr2

20463221

-
intron-3CDSENST00000482879ENST00000536417SDC1chr2

20402848

-PUM2chr2

20463221

-
intron-intronENST00000403076ENST00000420234SDC1chr2

20402848

-PUM2chr2

20463221

-
intron-intronENST00000482879ENST00000420234SDC1chr2

20402848

-PUM2chr2

20463221

-

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 SDC1-PUM2


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)

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.
genomic feature

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 SDC1-PUM2


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/chr2:20550358/chr2:20405185)
- 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
..
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: 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
HgeneSDC1chr2:20402848chr2:20463221ENST00000254351-4523_254254311.0Topological domainExtracellular
HgeneSDC1chr2:20402848chr2:20463221ENST00000381150-5623_254254311.0Topological domainExtracellular
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019706_1048573988.0DomainPUM-HD
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120706_10486521065.0DomainPUM-HD
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120706_10486521067.0DomainPUM-HD
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221706_10486521065.0DomainPUM-HD
TgenePUM2chr2:20402848chr2:20463221ENST0000031980110191002_1006573988.0RegionUracil-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019741_745573988.0RegionAdenine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019777_781573988.0RegionUracil-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019813_817573988.0RegionAdenine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019851_855573988.0RegionNon-specific-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019887_891573988.0RegionAdenine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019923_927573988.0RegionUracil-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019959_963573988.0RegionGuanine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST0000033808611201002_10066521065.0RegionUracil-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120741_7456521065.0RegionAdenine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120777_7816521065.0RegionUracil-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120813_8176521065.0RegionAdenine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120851_8556521065.0RegionNon-specific-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120887_8916521065.0RegionAdenine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120923_9276521065.0RegionUracil-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120959_9636521065.0RegionGuanine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST0000036107811201002_10066521067.0RegionUracil-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120741_7456521067.0RegionAdenine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120777_7816521067.0RegionUracil-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120813_8176521067.0RegionAdenine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120851_8556521067.0RegionNon-specific-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120887_8916521067.0RegionAdenine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120923_9276521067.0RegionUracil-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120959_9636521067.0RegionGuanine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST0000040343212211002_10066521065.0RegionUracil-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221741_7456521065.0RegionAdenine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221777_7816521065.0RegionUracil-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221813_8176521065.0RegionAdenine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221851_8556521065.0RegionNon-specific-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221887_8916521065.0RegionAdenine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221923_9276521065.0RegionUracil-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221959_9636521065.0RegionGuanine-nucleotide binding in RNA target
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019726_761573988.0RepeatPumilio 1
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019762_797573988.0RepeatPumilio 2
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019798_835573988.0RepeatPumilio 3
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019836_871573988.0RepeatPumilio 4
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019872_907573988.0RepeatPumilio 5
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019908_943573988.0RepeatPumilio 6
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019944_979573988.0RepeatPumilio 7
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019983_1022573988.0RepeatPumilio 8
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120726_7616521065.0RepeatPumilio 1
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120762_7976521065.0RepeatPumilio 2
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120798_8356521065.0RepeatPumilio 3
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120836_8716521065.0RepeatPumilio 4
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120872_9076521065.0RepeatPumilio 5
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120908_9436521065.0RepeatPumilio 6
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120944_9796521065.0RepeatPumilio 7
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120983_10226521065.0RepeatPumilio 8
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120726_7616521067.0RepeatPumilio 1
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120762_7976521067.0RepeatPumilio 2
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120798_8356521067.0RepeatPumilio 3
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120836_8716521067.0RepeatPumilio 4
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120872_9076521067.0RepeatPumilio 5
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120908_9436521067.0RepeatPumilio 6
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120944_9796521067.0RepeatPumilio 7
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120983_10226521067.0RepeatPumilio 8
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221726_7616521065.0RepeatPumilio 1
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221762_7976521065.0RepeatPumilio 2
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221798_8356521065.0RepeatPumilio 3
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221836_8716521065.0RepeatPumilio 4
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221872_9076521065.0RepeatPumilio 5
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221908_9436521065.0RepeatPumilio 6
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221944_9796521065.0RepeatPumilio 7
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221983_10226521065.0RepeatPumilio 8

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneSDC1chr2:20402848chr2:20463221ENST00000254351-45276_310254311.0Topological domainCytoplasmic
HgeneSDC1chr2:20402848chr2:20463221ENST00000381150-56276_310254311.0Topological domainCytoplasmic
HgeneSDC1chr2:20402848chr2:20463221ENST00000254351-45255_275254311.0TransmembraneHelical
HgeneSDC1chr2:20402848chr2:20463221ENST00000381150-56255_275254311.0TransmembraneHelical
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019278_488573988.0Compositional biasNote=Ala-rich
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019359_405573988.0Compositional biasNote=Gln-rich
TgenePUM2chr2:20402848chr2:20463221ENST000003198011019520_687573988.0Compositional biasNote=Ser-rich
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120278_4886521065.0Compositional biasNote=Ala-rich
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120359_4056521065.0Compositional biasNote=Gln-rich
TgenePUM2chr2:20402848chr2:20463221ENST000003380861120520_6876521065.0Compositional biasNote=Ser-rich
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120278_4886521067.0Compositional biasNote=Ala-rich
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120359_4056521067.0Compositional biasNote=Gln-rich
TgenePUM2chr2:20402848chr2:20463221ENST000003610781120520_6876521067.0Compositional biasNote=Ser-rich
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221278_4886521065.0Compositional biasNote=Ala-rich
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221359_4056521065.0Compositional biasNote=Gln-rich
TgenePUM2chr2:20402848chr2:20463221ENST000004034321221520_6876521065.0Compositional biasNote=Ser-rich


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Fusion Gene Sequence for SDC1-PUM2


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 SDC1-PUM2


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
TgenePUM2chr2:20402848chr2:20463221ENST0000031980110191_260573.3333333333334988.0SNAPIN
TgenePUM2chr2:20402848chr2:20463221ENST0000033808611201_260652.33333333333341065.0SNAPIN
TgenePUM2chr2:20402848chr2:20463221ENST0000036107811201_260652.33333333333341067.0SNAPIN
TgenePUM2chr2:20402848chr2:20463221ENST0000040343212211_260652.33333333333341065.0SNAPIN


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 SDC1-PUM2


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 SDC1-PUM2


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