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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:CTDSPL2-B2M (FusionGDB2 ID:20198)

Fusion Gene Summary for CTDSPL2-B2M

check button Fusion gene summary
Fusion gene informationFusion gene name: CTDSPL2-B2M
Fusion gene ID: 20198
HgeneTgene
Gene symbol

CTDSPL2

B2M

Gene ID

51496

567

Gene nameCTD small phosphatase like 2beta-2-microglobulin
SynonymsHSPC058|HSPC129|SCP4IMD43
Cytomap

15q15.3-q21.1

15q21.1

Type of geneprotein-codingprotein-coding
DescriptionCTD small phosphatase-like protein 2CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2CTDSP-like 2beta-2-microglobulinbeta chain of MHC class I moleculesbeta-2-microglobin
Modification date2020031320200329
UniProtAcc

Q05D32

P61769

Ensembl transtripts involved in fusion geneENST00000260327, ENST00000396780, 
ENST00000558373, ENST00000558966, 
ENST00000561189, 		ENST00000559220, 
ENST00000558401, ENST00000544417, 
ENST00000559916, 
Fusion gene scores* DoF score8 X 6 X 7=33664 X 31 X 17=33728
# samples 1471
** MAII scorelog2(14/336*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(71/33728*10)=-5.56998393724517
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CTDSPL2 [Title/Abstract] AND B2M [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCTDSPL2(44751398)-B2M(45007621), # samples:1
CTDSPL2(44719970)-B2M(45009805), # samples:1
Anticipated loss of major functional domain due to fusion event.CTDSPL2-B2M seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CTDSPL2-B2M seems lost the major protein functional domain in Tgene partner, which is a CGC 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
TgeneB2M

GO:0002726

positive regulation of T cell cytokine production

24643698

TgeneB2M

GO:0007611

learning or memory

26147761

TgeneB2M

GO:0050680

negative regulation of epithelial cell proliferation

28213472

TgeneB2M

GO:0050768

negative regulation of neurogenesis

26147761

TgeneB2M

GO:0090647

modulation of age-related behavioral decline

26147761

TgeneB2M

GO:1900121

negative regulation of receptor binding

9465039

TgeneB2M

GO:1990000

amyloid fibril formation

28468825

TgeneB2M

GO:2000774

positive regulation of cellular senescence

28213472

TgeneB2M

GO:2000978

negative regulation of forebrain neuron differentiation

26147761


check buttonFusion gene breakpoints across CTDSPL2 (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 B2M (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
ChimerDB4OVTCGA-04-1530-01ACTDSPL2chr15

44751398

+B2Mchr15

45007621

+
ChimerDB4SKCMTCGA-W3-AA1V-06BCTDSPL2chr15

44719970

+B2Mchr15

45009805

+


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Fusion Gene ORF analysis for CTDSPL2-B2M

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-intronENST00000260327ENST00000559220CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
5CDS-intronENST00000396780ENST00000559220CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
5CDS-intronENST00000558373ENST00000559220CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
5CDS-intronENST00000558966ENST00000559220CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
5UTR-3UTRENST00000260327ENST00000558401CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
5UTR-3UTRENST00000260327ENST00000559220CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
5UTR-3UTRENST00000396780ENST00000558401CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
5UTR-3UTRENST00000396780ENST00000559220CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
5UTR-intronENST00000260327ENST00000544417CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
5UTR-intronENST00000260327ENST00000559916CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
5UTR-intronENST00000396780ENST00000544417CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
5UTR-intronENST00000396780ENST00000559916CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
Frame-shiftENST00000260327ENST00000544417CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
Frame-shiftENST00000260327ENST00000558401CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
Frame-shiftENST00000260327ENST00000559916CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
Frame-shiftENST00000396780ENST00000544417CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
Frame-shiftENST00000396780ENST00000558401CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
Frame-shiftENST00000396780ENST00000559916CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
Frame-shiftENST00000558373ENST00000544417CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
Frame-shiftENST00000558373ENST00000558401CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
Frame-shiftENST00000558373ENST00000559916CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
Frame-shiftENST00000558966ENST00000544417CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
Frame-shiftENST00000558966ENST00000558401CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
Frame-shiftENST00000558966ENST00000559916CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
intron-3CDSENST00000561189ENST00000544417CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
intron-3CDSENST00000561189ENST00000558401CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
intron-3CDSENST00000561189ENST00000559916CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
intron-3UTRENST00000558373ENST00000558401CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
intron-3UTRENST00000558373ENST00000559220CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
intron-3UTRENST00000558966ENST00000558401CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
intron-3UTRENST00000558966ENST00000559220CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
intron-3UTRENST00000561189ENST00000558401CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
intron-3UTRENST00000561189ENST00000559220CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
intron-intronENST00000558373ENST00000544417CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
intron-intronENST00000558373ENST00000559916CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
intron-intronENST00000558966ENST00000544417CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
intron-intronENST00000558966ENST00000559916CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
intron-intronENST00000561189ENST00000544417CTDSPL2chr15

44719970

+B2Mchr15

45009805

+
intron-intronENST00000561189ENST00000559220CTDSPL2chr15

44751398

+B2Mchr15

45007621

+
intron-intronENST00000561189ENST00000559916CTDSPL2chr15

44719970

+B2Mchr15

45009805

+

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 CTDSPL2-B2M


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)
CTDSPL2chr1544719970+B2Mchr1545009804+5.87E-050.99994135
CTDSPL2chr1544751398+B2Mchr1545007620+2.40E-050.9999759
CTDSPL2chr1544719970+B2Mchr1545009804+5.87E-050.99994135
CTDSPL2chr1544751398+B2Mchr1545007620+2.40E-050.9999759

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 CTDSPL2-B2M


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/:44751398/:45007621)
- 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
CTDSPL2

Q05D32

B2M

P61769

FUNCTION: Probable phosphatase. {ECO:0000250}.FUNCTION: Component of the class I major histocompatibility complex (MHC). Involved in the presentation of peptide antigens to the immune system. Exogenously applied M.tuberculosis EsxA or EsxA-EsxB (or EsxA expressed in host) binds B2M and decreases its export to the cell surface (total protein levels do not change), probably leading to defects in class I antigen presentation (PubMed:25356553). {ECO:0000269|PubMed:25356553}.

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 CTDSPL2-B2M


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 CTDSPL2-B2M


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 CTDSPL2-B2M


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 CTDSPL2-B2M


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