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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:PTDSS2-IFITM1 (FusionGDB2 ID:69461)

Fusion Gene Summary for PTDSS2-IFITM1

check button Fusion gene summary
Fusion gene informationFusion gene name: PTDSS2-IFITM1
Fusion gene ID: 69461
HgeneTgene
Gene symbol

PTDSS2

IFITM1

Gene ID

81490

8519

Gene namephosphatidylserine synthase 2interferon induced transmembrane protein 1
SynonymsPSS29-27|CD225|DSPA2a|IFI17|LEU13
Cytomap

11p15.5

11p15.5

Type of geneprotein-codingprotein-coding
Descriptionphosphatidylserine synthase 2PSS-2ptdSer synthase 2serine-exchange enzyme IIinterferon-induced transmembrane protein 1dispanin subfamily A member 2ainterferon-induced protein 17interferon-inducible protein 9-27leu-13 antigen
Modification date2020031320200313
UniProtAcc.

A6NMD0

Ensembl transtripts involved in fusion geneENST00000308020, ENST00000530087, 
ENST00000528780, ENST00000328221, 
ENST00000408968, ENST00000525554, 
Fusion gene scores* DoF score9 X 3 X 6=1627 X 8 X 5=280
# samples 98
** MAII scorelog2(9/162*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/280*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PTDSS2 [Title/Abstract] AND IFITM1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPTDSS2(460288)-IFITM1(314922), # samples:2
Anticipated loss of major functional domain due to fusion event.PTDSS2-IFITM1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism 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
TgeneIFITM1

GO:0009615

response to virus

21253575|22479637

TgeneIFITM1

GO:0034341

response to interferon-gamma

21253575

TgeneIFITM1

GO:0035455

response to interferon-alpha

22479637

TgeneIFITM1

GO:0035456

response to interferon-beta

21253575

TgeneIFITM1

GO:0045071

negative regulation of viral genome replication

21253575

TgeneIFITM1

GO:0046597

negative regulation of viral entry into host cell

21253575|23358889


check buttonFusion gene breakpoints across PTDSS2 (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 IFITM1 (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
ChimerDB4LIHCTCGA-DD-AAD5-01APTDSS2chr11

460288

+IFITM1chr11

314922

+
ChimerDB4LIHCTCGA-DD-AAD5PTDSS2chr11

460288

+IFITM1chr11

314922

+
ChimerDB4LIHCTCGA-DD-AAD5PTDSS2chr11

460288

+IFITM1chr11

309013

+


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Fusion Gene ORF analysis for PTDSS2-IFITM1

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
Frame-shiftENST00000308020ENST00000528780PTDSS2chr11

460288

+IFITM1chr11

314922

+
In-frameENST00000308020ENST00000328221PTDSS2chr11

460288

+IFITM1chr11

314922

+
Frame-shiftENST00000308020ENST00000408968PTDSS2chr11

460288

+IFITM1chr11

314922

+
5CDS-3UTRENST00000308020ENST00000525554PTDSS2chr11

460288

+IFITM1chr11

314922

+
intron-3CDSENST00000530087ENST00000528780PTDSS2chr11

460288

+IFITM1chr11

314922

+
intron-3CDSENST00000530087ENST00000328221PTDSS2chr11

460288

+IFITM1chr11

314922

+
intron-3CDSENST00000530087ENST00000408968PTDSS2chr11

460288

+IFITM1chr11

314922

+
intron-3UTRENST00000530087ENST00000525554PTDSS2chr11

460288

+IFITM1chr11

314922

+
5CDS-intronENST00000308020ENST00000528780PTDSS2chr11

460288

+IFITM1chr11

309013

+
5CDS-intronENST00000308020ENST00000328221PTDSS2chr11

460288

+IFITM1chr11

309013

+
5CDS-intronENST00000308020ENST00000408968PTDSS2chr11

460288

+IFITM1chr11

309013

+
5CDS-intronENST00000308020ENST00000525554PTDSS2chr11

460288

+IFITM1chr11

309013

+
intron-intronENST00000530087ENST00000528780PTDSS2chr11

460288

+IFITM1chr11

309013

+
intron-intronENST00000530087ENST00000328221PTDSS2chr11

460288

+IFITM1chr11

309013

+
intron-intronENST00000530087ENST00000408968PTDSS2chr11

460288

+IFITM1chr11

309013

+
intron-intronENST00000530087ENST00000525554PTDSS2chr11

460288

+IFITM1chr11

309013

+

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)
ENST00000308020PTDSS2chr11460288+ENST00000328221IFITM1chr11314922+779460176490104

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
ENST00000308020ENST00000328221PTDSS2chr11460288+IFITM1chr11314922+0.474154530.52584547

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Fusion Genomic Features for PTDSS2-IFITM1


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)
PTDSS2chr11460288+IFITM1chr11314921+1.22E-050.99998784
PTDSS2chr11460288+IFITM1chr11314921+1.22E-050.99998784
PTDSS2chr11460288+IFITM1chr11314921+1.22E-050.99998784
PTDSS2chr11460288+IFITM1chr11314921+1.22E-050.99998784

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 PTDSS2-IFITM1


check button Go to

FGviewer for the breakpoints of chr11:460288-chr11:314922

.
- 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
.IFITM1

A6NMD0

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.

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
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+2121_6294.66666666666667488.0Topological domainCytoplasmic
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+21284_9694.66666666666667488.0Topological domainLumenal
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+21263_8394.66666666666667488.0TransmembraneHelical
TgeneIFITM1chr11:460288chr11:314922ENST0000032822113108_12562.0126.0Topological domainExtracellular
TgeneIFITM1chr11:460288chr11:314922ENST0000040896802108_12562.0126.0Topological domainExtracellular
TgeneIFITM1chr11:460288chr11:314922ENST0000052878013108_12562.0126.0Topological domainExtracellular
TgeneIFITM1chr11:460288chr11:314922ENST000003282211387_10762.0126.0TransmembraneHelical
TgeneIFITM1chr11:460288chr11:314922ENST000004089680287_10762.0126.0TransmembraneHelical
TgeneIFITM1chr11:460288chr11:314922ENST000005287801387_10762.0126.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+212118_12694.66666666666667488.0Topological domainCytoplasmic
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+212148_31394.66666666666667488.0Topological domainLumenal
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+212335_33594.66666666666667488.0Topological domainCytoplasmic
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+212357_37694.66666666666667488.0Topological domainLumenal
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+212398_40394.66666666666667488.0Topological domainCytoplasmic
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+212425_48794.66666666666667488.0Topological domainLumenal
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+212127_14794.66666666666667488.0TransmembraneHelical
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+212314_33494.66666666666667488.0TransmembraneHelical
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+212336_35694.66666666666667488.0TransmembraneHelical
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+212377_39794.66666666666667488.0TransmembraneHelical
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+212404_42494.66666666666667488.0TransmembraneHelical
HgenePTDSS2chr11:460288chr11:314922ENST00000308020+21297_11794.66666666666667488.0TransmembraneHelical
TgeneIFITM1chr11:460288chr11:314922ENST000003282211337_5762.0126.0IntramembraneHelical
TgeneIFITM1chr11:460288chr11:314922ENST000004089680237_5762.0126.0IntramembraneHelical
TgeneIFITM1chr11:460288chr11:314922ENST000005287801337_5762.0126.0IntramembraneHelical
TgeneIFITM1chr11:460288chr11:314922ENST00000328221131_3662.0126.0Topological domainCytoplasmic
TgeneIFITM1chr11:460288chr11:314922ENST000003282211358_8662.0126.0Topological domainCytoplasmic
TgeneIFITM1chr11:460288chr11:314922ENST00000408968021_3662.0126.0Topological domainCytoplasmic
TgeneIFITM1chr11:460288chr11:314922ENST000004089680258_8662.0126.0Topological domainCytoplasmic
TgeneIFITM1chr11:460288chr11:314922ENST00000528780131_3662.0126.0Topological domainCytoplasmic
TgeneIFITM1chr11:460288chr11:314922ENST000005287801358_8662.0126.0Topological domainCytoplasmic


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Fusion Gene Sequence for PTDSS2-IFITM1


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.
>In-frame_ENST00000308020_ENST00000328221_TCGA-DD-AAD5-01A_PTDSS2_chr11_460288_+_IFITM1_chr11_314922_length(transcript)=779nt_BP=460nt
CAATGCACCGCACACCCTTTACTGGCCGGCCCCGCGCTGCTCTCCTAAGACCCCGCGGGCCAGCGCCGCGACCCCTTCCCAGCGCTCCTC
GCGCTGTGTGCGGCGCGTCCTCTCGCCGGTGACCCGGTGTGCGTGGGGTCGAGGCGCCGGGCGGAGTGGCTCCGGGCCGAAACGCCATGC
GGAGGGGCGAGCGCAGGGACGCCGGAGGTCCGCGGCCCGAGTCCCCGGTGCCCGCGGGCAGGGCCTCGCTGGAGGAGCCGCCTGACGGGC
CGTCTGCCGGCCAAGCCACCGGGCCGGGCGAGGGCCGCCGCAGCACCGAGTCCGAGGTCTACGACGACGGCACCAACACCTTCTTCTGGC
GAGCCCACACCTTAACCGTGCTCTTCATCCTCACCTGTACGCTTGGCTATGTGACGCTGCTGGAGGAAACACCTCAGGACACGGCCTACA
ACACCAAGAGTCTAGGGACAGGAAGATGGTTGGCGACGTGACCGGGGCCCAGGCCTATGCCTCCACCGCCAAGTGCCTGAACATCTGGGC
CCTGATTCTGGGCATCCTCATGACCATTGGATTCATCCTGTTACTGGTATTCGGCTCTGTGACAGTCTACCATATTATGTTACAGATAAT
ACAGGAAAAACGGGGTTACTAGTAGCCGCCCATAGCCTGCAACCTTTGCACTCCACTGTGCAATGCTGGCCCTGCACGCTGGGGCTGTTG

>In-frame_ENST00000308020_ENST00000328221_TCGA-DD-AAD5-01A_PTDSS2_chr11_460288_+_IFITM1_chr11_314922_length(amino acids)=104AA_start in transcript=176_stop in transcript=490
MRRGERRDAGGPRPESPVPAGRASLEEPPDGPSAGQATGPGEGRRSTESEVYDDGTNTFFWRAHTLTVLFILTCTLGYVTLLEETPQDTA

--------------------------------------------------------------

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Fusion Gene PPI Analysis for PTDSS2-IFITM1


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
TgeneIFITM1chr11:460288chr11:314922ENST000003282211384_12562.0126.0CAV1
TgeneIFITM1chr11:460288chr11:314922ENST000004089680284_12562.0126.0CAV1
TgeneIFITM1chr11:460288chr11:314922ENST000005287801384_12562.0126.0CAV1


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 PTDSS2-IFITM1


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 PTDSS2-IFITM1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneIFITM1C0023893Liver Cirrhosis, Experimental1CTD_human