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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:TMEM97-SKAP1 (FusionGDB2 ID:91653)

Fusion Gene Summary for TMEM97-SKAP1

check button Fusion gene summary
Fusion gene informationFusion gene name: TMEM97-SKAP1
Fusion gene ID: 91653
HgeneTgene
Gene symbol

TMEM97

SKAP1

Gene ID

27346

8631

Gene nametransmembrane protein 97src kinase associated phosphoprotein 1
SynonymsMAC30HEL-S-81p|SCAP1|SKAP55
Cytomap

17q11.2

17q21.32

Type of geneprotein-codingprotein-coding
Descriptionsigma intracellular receptor 2meningioma-associated protein 30sigma-2 receptorsigma2 receptorsrc kinase-associated phosphoprotein 1SKAP-55epididymis secretory sperm binding protein Li 81ppp55src family-associated phosphoprotein 1src kinase-associated phosphoprotein of 55 kDa
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000226230, ENST00000583381, 
ENST00000582113, ENST00000336687, 
ENST00000336915, ENST00000584924, 
Fusion gene scores* DoF score4 X 3 X 3=3624 X 12 X 10=2880
# samples 529
** MAII scorelog2(5/36*10)=0.473931188332412
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(29/2880*10)=-3.31194400631474
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TMEM97 [Title/Abstract] AND SKAP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTMEM97(26646391)-SKAP1(46474147), # samples:1
Anticipated loss of major functional domain due to fusion event.TMEM97-SKAP1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
TMEM97-SKAP1 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
HgeneTMEM97

GO:0042632

cholesterol homeostasis

19583955

TgeneSKAP1

GO:0002821

positive regulation of adaptive immune response

12652296

TgeneSKAP1

GO:0033625

positive regulation of integrin activation

12652296

TgeneSKAP1

GO:0034116

positive regulation of heterotypic cell-cell adhesion

12652296

TgeneSKAP1

GO:0045944

positive regulation of transcription by RNA polymerase II

11909961

TgeneSKAP1

GO:1903039

positive regulation of leukocyte cell-cell adhesion

12652296


check buttonFusion gene breakpoints across TMEM97 (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 SKAP1 (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-C8-A275-01ATMEM97chr17

26646391

+SKAP1chr17

46474147

-


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Fusion Gene ORF analysis for TMEM97-SKAP1

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
In-frameENST00000226230ENST00000336915TMEM97chr17

26646391

+SKAP1chr17

46474147

-
Frame-shiftENST00000226230ENST00000584924TMEM97chr17

26646391

+SKAP1chr17

46474147

-
5UTR-3CDSENST00000583381ENST00000336915TMEM97chr17

26646391

+SKAP1chr17

46474147

-
5UTR-3CDSENST00000583381ENST00000584924TMEM97chr17

26646391

+SKAP1chr17

46474147

-
In-frameENST00000582113ENST00000336915TMEM97chr17

26646391

+SKAP1chr17

46474147

-
Frame-shiftENST00000582113ENST00000584924TMEM97chr17

26646391

+SKAP1chr17

46474147

-
intron-3CDSENST00000336687ENST00000336915TMEM97chr17

26646391

+SKAP1chr17

46474147

-
intron-3CDSENST00000336687ENST00000584924TMEM97chr17

26646391

+SKAP1chr17

46474147

-

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)
ENST00000226230TMEM97chr1726646391+ENST00000336915SKAP1chr1746474147-16892711681304378
ENST00000582113TMEM97chr1726646391+ENST00000336915SKAP1chr1746474147-1578160571193378

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
ENST00000226230ENST00000336915TMEM97chr1726646391+SKAP1chr1746474147-0.0023045240.9976955
ENST00000582113ENST00000336915TMEM97chr1726646391+SKAP1chr1746474147-0.0025863580.9974137

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Fusion Genomic Features for TMEM97-SKAP1


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.

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 TMEM97-SKAP1


check button Go to

FGviewer for the breakpoints of chr17:26646391-chr17:46474147

.
- 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
..
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: 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
HgeneTMEM97chr17:26646391chr17:46474147ENST00000226230+131_942.0177.0Topological domainCytoplasmic
HgeneTMEM97chr17:26646391chr17:46474147ENST00000226230+1310_3042.0177.0TransmembraneHelical%3B Name%3D1
TgeneSKAP1chr17:26646391chr17:46474147ENST00000336915013220_23015.333333333333334448.0Compositional biasNote=Poly-Glu
TgeneSKAP1chr17:26646391chr17:46474147ENST00000584924012220_23015.333333333333334360.0Compositional biasNote=Poly-Glu
TgeneSKAP1chr17:26646391chr17:46474147ENST00000336915013107_21015.333333333333334448.0DomainPH
TgeneSKAP1chr17:26646391chr17:46474147ENST00000336915013294_35515.333333333333334448.0DomainSH3
TgeneSKAP1chr17:26646391chr17:46474147ENST00000584924012107_21015.333333333333334360.0DomainPH
TgeneSKAP1chr17:26646391chr17:46474147ENST00000584924012294_35515.333333333333334360.0DomainSH3

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTMEM97chr17:26646391chr17:46474147ENST00000226230+1310_15842.0177.0DomainEXPERA
HgeneTMEM97chr17:26646391chr17:46474147ENST00000226230+13121_14042.0177.0Topological domainExtracellular
HgeneTMEM97chr17:26646391chr17:46474147ENST00000226230+13162_17642.0177.0Topological domainCytoplasmic
HgeneTMEM97chr17:26646391chr17:46474147ENST00000226230+1331_6842.0177.0Topological domainExtracellular
HgeneTMEM97chr17:26646391chr17:46474147ENST00000226230+1390_9942.0177.0Topological domainCytoplasmic
HgeneTMEM97chr17:26646391chr17:46474147ENST00000226230+13100_12042.0177.0TransmembraneHelical%3B Name%3D3
HgeneTMEM97chr17:26646391chr17:46474147ENST00000226230+13141_16142.0177.0TransmembraneHelical%3B Name%3D4
HgeneTMEM97chr17:26646391chr17:46474147ENST00000226230+1369_8942.0177.0TransmembraneHelical%3B Name%3D2


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Fusion Gene Sequence for TMEM97-SKAP1


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_ENST00000226230_ENST00000336915_TCGA-C8-A275-01A_TMEM97_chr17_26646391_+_SKAP1_chr17_46474147_length(transcript)=1689nt_BP=271nt
GAGCCTCCTCTTCTCGCCAGCCAATGGAAGCGGTCTGCCTAGCCCTCGCGGGGGCAAGGCGGCGACCGAGGCGCGTGGGTCTGGGAAGGC
GCGCGGATTTGGCCCCTCTTCTCACATCAGCGGGTCCAGGCCCAACCGACAGACTATGGGGGCTCCGGCAACCAGGCGCTGCGTGGAGTG
GCTGCTGGGCCTCTACTTCCTCAGCCACATCCCCATCACCCTGTTCATGGACCTGCAGGCGGTGCTGCCGCGCGAGCTCTACCCAGTCGA
GATGCTGAAGAGTTTCTGGCAGAAGGTTTGCGGAATGAGAACCTCAGCGCTGTTGCAAGGGATCACAGAGACCATATTCTACGGGGCTTT
CAGCAAATCAAAGCCAGGTACTATTGGGATTTTCAGCCCCAAGGGGGAGACATTGGACAGGACAGCTCTGATGATAATCACAGCGGGACT
CTTGGCCTGTCCCTCACATCCGATGCACCCTTTTTGTCAGATTATCAGGATGAGGGAATGGAAGACATCGTAAAAGGAGCTCAAGAACTT
GATAACGTAATCAAGCAAGGATACTTGGAGAAGAAAAGCAAAGATCATAGTTTCTTTGGATCGGAGTGGCAGAAGCGATGGTGTGTTGTC
AGCAGAGGTCTCTTCTACTACTATGCTAATGAGAAGAGCAAGCAGCCCAAAGGGACCTTCCTCATTAAGGGCTACGGTGTACGGATGGCC
CCCCACCTGCGAAGAGATTCCAAGAAAGAATCCTGCTTTGAACTGACCTCCCAGGATAGGCGCAGCTATGAGTTTACAGCTACTAGTCCA
GCAGAAGCCAGAGACTGGGTGGATCAAATAAGTTTCTTGTTAAAGGATCTGAGCTCCTTAACCATTCCATATGAAGAGGATGAGGAGGAA
GAAGAAAAAGAAGAGACATATGATGATATTGATGGTTTTGACTCCCCAAGTTGTGGTTCCCAGTGCAGACCCACTATCTTGCCTGGGAGT
GTGGGGATAAAAGAGCCTACAGAGGAGAAAGAAGAAGAAGATATTTATGAAGTCTTGCCAGATGAAGAGCATGATCTAGAAGAGGATGAG
AGTGGCACTCGACGAAAAGGAGTAGACTATGCCAGTTACTACCAGGGCCTATGGGATTGCCATGGTGACCAGCCAGATGAACTGTCCTTC
CAACGGGGTGACCTCATCCGTATTCTGAGCAAGGAGTATAACATGTATGGCTGGTGGGTGGGAGAACTGAACAGCCTCGTTGGGATTGTT
CCAAAGGAGTATCTCACCACTGCCTTTGAAGTGGAAGAAAGATGAAACCCAGGAAATATATTCTTCCCTCTCTCCTGCCTTTATGAGGAA
ACTGATCATCAAAAGTTCCCACTCCCTACTTCTGCCACCCCACCAACGCCTTGGACTCCTCTCTTTGCTGAAGAGACCCAAGTCTCTTGA
CACCTCAGAGTGACTGTAAGCTACCAGTAAGACAAGTGGGAAGAGGCACGTTCATCAAACCTGTTACTAAACCAGCCTAGTCATAGCTCA
TCCCCATCTCTAAATGTGTCCACACAACCACATCTGCCTTTTCCACAAGCTTTTCACAAAGAAGGTGAGAGAGAAGGAAACCTTGGGAGG

>In-frame_ENST00000226230_ENST00000336915_TCGA-C8-A275-01A_TMEM97_chr17_26646391_+_SKAP1_chr17_46474147_length(amino acids)=378AA_start in transcript=168_stop in transcript=1304
MRGVAAGPLLPQPHPHHPVHGPAGGAAARALPSRDAEEFLAEGLRNENLSAVARDHRDHILRGFQQIKARYYWDFQPQGGDIGQDSSDDN
HSGTLGLSLTSDAPFLSDYQDEGMEDIVKGAQELDNVIKQGYLEKKSKDHSFFGSEWQKRWCVVSRGLFYYYANEKSKQPKGTFLIKGYG
VRMAPHLRRDSKKESCFELTSQDRRSYEFTATSPAEARDWVDQISFLLKDLSSLTIPYEEDEEEEEKEETYDDIDGFDSPSCGSQCRPTI
LPGSVGIKEPTEEKEEEDIYEVLPDEEHDLEEDESGTRRKGVDYASYYQGLWDCHGDQPDELSFQRGDLIRILSKEYNMYGWWVGELNSL

--------------------------------------------------------------
>In-frame_ENST00000582113_ENST00000336915_TCGA-C8-A275-01A_TMEM97_chr17_26646391_+_SKAP1_chr17_46474147_length(transcript)=1578nt_BP=160nt
TCACATCAGCGGGTCCAGGCCCAACCGACAGACTATGGGGGCTCCGGCAACCAGGCGCTGCGTGGAGTGGCTGCTGGGCCTCTACTTCCT
CAGCCACATCCCCATCACCCTGTTCATGGACCTGCAGGCGGTGCTGCCGCGCGAGCTCTACCCAGTCGAGATGCTGAAGAGTTTCTGGCA
GAAGGTTTGCGGAATGAGAACCTCAGCGCTGTTGCAAGGGATCACAGAGACCATATTCTACGGGGCTTTCAGCAAATCAAAGCCAGGTAC
TATTGGGATTTTCAGCCCCAAGGGGGAGACATTGGACAGGACAGCTCTGATGATAATCACAGCGGGACTCTTGGCCTGTCCCTCACATCC
GATGCACCCTTTTTGTCAGATTATCAGGATGAGGGAATGGAAGACATCGTAAAAGGAGCTCAAGAACTTGATAACGTAATCAAGCAAGGA
TACTTGGAGAAGAAAAGCAAAGATCATAGTTTCTTTGGATCGGAGTGGCAGAAGCGATGGTGTGTTGTCAGCAGAGGTCTCTTCTACTAC
TATGCTAATGAGAAGAGCAAGCAGCCCAAAGGGACCTTCCTCATTAAGGGCTACGGTGTACGGATGGCCCCCCACCTGCGAAGAGATTCC
AAGAAAGAATCCTGCTTTGAACTGACCTCCCAGGATAGGCGCAGCTATGAGTTTACAGCTACTAGTCCAGCAGAAGCCAGAGACTGGGTG
GATCAAATAAGTTTCTTGTTAAAGGATCTGAGCTCCTTAACCATTCCATATGAAGAGGATGAGGAGGAAGAAGAAAAAGAAGAGACATAT
GATGATATTGATGGTTTTGACTCCCCAAGTTGTGGTTCCCAGTGCAGACCCACTATCTTGCCTGGGAGTGTGGGGATAAAAGAGCCTACA
GAGGAGAAAGAAGAAGAAGATATTTATGAAGTCTTGCCAGATGAAGAGCATGATCTAGAAGAGGATGAGAGTGGCACTCGACGAAAAGGA
GTAGACTATGCCAGTTACTACCAGGGCCTATGGGATTGCCATGGTGACCAGCCAGATGAACTGTCCTTCCAACGGGGTGACCTCATCCGT
ATTCTGAGCAAGGAGTATAACATGTATGGCTGGTGGGTGGGAGAACTGAACAGCCTCGTTGGGATTGTTCCAAAGGAGTATCTCACCACT
GCCTTTGAAGTGGAAGAAAGATGAAACCCAGGAAATATATTCTTCCCTCTCTCCTGCCTTTATGAGGAAACTGATCATCAAAAGTTCCCA
CTCCCTACTTCTGCCACCCCACCAACGCCTTGGACTCCTCTCTTTGCTGAAGAGACCCAAGTCTCTTGACACCTCAGAGTGACTGTAAGC
TACCAGTAAGACAAGTGGGAAGAGGCACGTTCATCAAACCTGTTACTAAACCAGCCTAGTCATAGCTCATCCCCATCTCTAAATGTGTCC
ACACAACCACATCTGCCTTTTCCACAAGCTTTTCACAAAGAAGGTGAGAGAGAAGGAAACCTTGGGAGGAGGACATTACTGGTTGTTCTG

>In-frame_ENST00000582113_ENST00000336915_TCGA-C8-A275-01A_TMEM97_chr17_26646391_+_SKAP1_chr17_46474147_length(amino acids)=378AA_start in transcript=57_stop in transcript=1193
MRGVAAGPLLPQPHPHHPVHGPAGGAAARALPSRDAEEFLAEGLRNENLSAVARDHRDHILRGFQQIKARYYWDFQPQGGDIGQDSSDDN
HSGTLGLSLTSDAPFLSDYQDEGMEDIVKGAQELDNVIKQGYLEKKSKDHSFFGSEWQKRWCVVSRGLFYYYANEKSKQPKGTFLIKGYG
VRMAPHLRRDSKKESCFELTSQDRRSYEFTATSPAEARDWVDQISFLLKDLSSLTIPYEEDEEEEEKEETYDDIDGFDSPSCGSQCRPTI
LPGSVGIKEPTEEKEEEDIYEVLPDEEHDLEEDESGTRRKGVDYASYYQGLWDCHGDQPDELSFQRGDLIRILSKEYNMYGWWVGELNSL

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Fusion Gene PPI Analysis for TMEM97-SKAP1


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
TgeneSKAP1chr17:26646391chr17:46474147ENST00000336915013290_29515.333333333333334448.0FYB1
TgeneSKAP1chr17:26646391chr17:46474147ENST00000584924012290_29515.333333333333334360.0FYB1


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 TMEM97-SKAP1


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 TMEM97-SKAP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneSKAP1C0919267ovarian neoplasm1CTD_human
TgeneSKAP1C1140680Malignant neoplasm of ovary1CTD_human