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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:PTPN12-UBR1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PTPN12-UBR1
FusionPDB ID: 70205
FusionGDB2.0 ID: 70205
HgeneTgene
Gene symbol

PTPN12

UBR1

Gene ID

5782

197131

Gene nameprotein tyrosine phosphatase non-receptor type 12ubiquitin protein ligase E3 component n-recognin 1
SynonymsPTP-PEST|PTPG1JBS
Cytomap

7q11.23

15q15.2

Type of geneprotein-codingprotein-coding
Descriptiontyrosine-protein phosphatase non-receptor type 12protein-tyrosine phosphatase G1E3 ubiquitin-protein ligase UBR1E3a ligaseN-recognin-1RING-type E3 ubiquitin transferase UBR1ubiquitin ligase E3 alpha-Iubiquitin-protein ligase E3-alphaubiquitin-protein ligase E3-alpha-1ubiquitin-protein ligase E3-alpha-I
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000248594, ENST00000415482, 
ENST00000435495, 		ENST00000382177, 
ENST00000568782, ENST00000290650, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score22 X 21 X 16=73926 X 6 X 3=108
# samples 446
** MAII scorelog2(44/7392*10)=-4.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/108*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: PTPN12 [Title/Abstract] AND UBR1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PTPN12(77230123)-UBR1(43294902), # samples:1
Anticipated loss of major functional domain due to fusion event.PTPN12-UBR1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
PTPN12-UBR1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
PTPN12-UBR1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
PTPN12-UBR1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
HgenePTPN12

GO:0006470

protein dephosphorylation

27134172

HgenePTPN12

GO:0035335

peptidyl-tyrosine dephosphorylation

27134172

TgeneUBR1

GO:0071233

cellular response to leucine

20298436


check buttonFusion gene breakpoints across PTPN12 (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 UBR1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4Non-CancerTCGA-BG-A2AD-11APTPN12chr7

77230123

+UBR1chr15

43294902

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000248594PTPN12chr777230123+ENST00000290650UBR1chr1543294902-514096722707901
ENST00000415482PTPN12chr777230123+ENST00000290650UBR1chr1543294902-4841668842408774
ENST00000435495PTPN12chr777230123+ENST00000290650UBR1chr1543294902-4711538502278742

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
ENST00000248594ENST00000290650PTPN12chr777230123+UBR1chr1543294902-0.0003079240.9996921
ENST00000415482ENST00000290650PTPN12chr777230123+UBR1chr1543294902-0.0002628280.9997372
ENST00000435495ENST00000290650PTPN12chr777230123+UBR1chr1543294902-0.0010922470.9989078

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>70205_70205_1_PTPN12-UBR1_PTPN12_chr7_77230123_ENST00000248594_UBR1_chr15_43294902_ENST00000290650_length(amino acids)=901AA_BP=320
LGVGVGASAAARLVLWESGGCSWKLWCREPSRCRRSRRLGRWGGGGSRGAWRGREGGTCWGNELGKTERALCRAGGRRGGQRPQPGGRGR
MEQVEILRKFIQRVQAMKSPDHNGEDNFARDFMRLRRLSTKYRTEKIYPTATGEKEENVKKNRYKDILPFDHSRVKLTLKTPSQDSDYIN
ANFIKGVYGPKAYVATQGPLANTVIDFWRMIWEYNVVIIVMACREFEMGRKKCERYWPLYGEDPITFAPFKISCEDEQARTDYFIRTLLL
EFQNESRRLYQFHYVNWPDHDVPSSFDSILDMISLMRKYQEHEDVPICIHCRYFEAVQLSSQQRIHVDLFDLESGEYLCPLCKSLCNTVI
PIIPLQPQKINSENADALAQLLTLARWIQTVLARISGYNIRHAKGENPIPIFFNQGMGDSTLEFHSILSFGVESSIKYSNSIKEMVILFA
TTIYRIGLKVPPDERDPRVPMLTWSTCAFTIQAIENLLGDEGKPLFGALQNRQHNGLKALMQFAVAQRITCPQVLIQKHLVRLLSVVLPN
IKSEDTPCLLSIDLFHVLVGAVLAFPSLYWDDPVDLQPSSVSSSYNHLYLFHLITMAHMLQILLTVDTGLPLAQVQEDSEEAHSASSFFA
EISQYTSGSIGCDIPGWYLWVSLKNGITPYLRCAALFFHYLLGVTPPEELHTNSAEGEYSALCSYLSLPTNLFLLFQEYWDTVRPLLQRW
CADPALLNCLKQKNTVVRYPRKRNSLIELPDDYSCLLNQASHFRCPRSADDERKHPVLCLFCGAILCSQNICCQEIVNGEEVGACIFHAL
HCGAGVCIFLKIRECRVVLVEGKARGCAYPAPYLDEYGETDPGLKRGNPLHLSRERYRKLHLVWQQHCIIEEIARSQETNQMLFGFNWQL

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

>70205_70205_2_PTPN12-UBR1_PTPN12_chr7_77230123_ENST00000415482_UBR1_chr15_43294902_ENST00000290650_length(amino acids)=774AA_BP=193
MSTKYRTEKIYPTATGEKEENVKKNRYKDILPFDHSRVKLTLKTPSQDSDYINANFIKGVYGPKAYVATQGPLANTVIDFWRMIWEYNVV
IIVMACREFEMGRKKCERYWPLYGEDPITFAPFKISCEDEQARTDYFIRTLLLEFQNESRRLYQFHYVNWPDHDVPSSFDSILDMISLMR
KYQEHEDVPICIHCRYFEAVQLSSQQRIHVDLFDLESGEYLCPLCKSLCNTVIPIIPLQPQKINSENADALAQLLTLARWIQTVLARISG
YNIRHAKGENPIPIFFNQGMGDSTLEFHSILSFGVESSIKYSNSIKEMVILFATTIYRIGLKVPPDERDPRVPMLTWSTCAFTIQAIENL
LGDEGKPLFGALQNRQHNGLKALMQFAVAQRITCPQVLIQKHLVRLLSVVLPNIKSEDTPCLLSIDLFHVLVGAVLAFPSLYWDDPVDLQ
PSSVSSSYNHLYLFHLITMAHMLQILLTVDTGLPLAQVQEDSEEAHSASSFFAEISQYTSGSIGCDIPGWYLWVSLKNGITPYLRCAALF
FHYLLGVTPPEELHTNSAEGEYSALCSYLSLPTNLFLLFQEYWDTVRPLLQRWCADPALLNCLKQKNTVVRYPRKRNSLIELPDDYSCLL
NQASHFRCPRSADDERKHPVLCLFCGAILCSQNICCQEIVNGEEVGACIFHALHCGAGVCIFLKIRECRVVLVEGKARGCAYPAPYLDEY

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

>70205_70205_3_PTPN12-UBR1_PTPN12_chr7_77230123_ENST00000435495_UBR1_chr15_43294902_ENST00000290650_length(amino acids)=742AA_BP=161
MSTKYRTEKIYPTATGEKEENVKKNRYKDILPFDHSRVKLTLKTPSQDSDYINANFIKIIVMACREFEMGRKKCERYWPLYGEDPITFAP
FKISCEDEQARTDYFIRTLLLEFQNESRRLYQFHYVNWPDHDVPSSFDSILDMISLMRKYQEHEDVPICIHCRYFEAVQLSSQQRIHVDL
FDLESGEYLCPLCKSLCNTVIPIIPLQPQKINSENADALAQLLTLARWIQTVLARISGYNIRHAKGENPIPIFFNQGMGDSTLEFHSILS
FGVESSIKYSNSIKEMVILFATTIYRIGLKVPPDERDPRVPMLTWSTCAFTIQAIENLLGDEGKPLFGALQNRQHNGLKALMQFAVAQRI
TCPQVLIQKHLVRLLSVVLPNIKSEDTPCLLSIDLFHVLVGAVLAFPSLYWDDPVDLQPSSVSSSYNHLYLFHLITMAHMLQILLTVDTG
LPLAQVQEDSEEAHSASSFFAEISQYTSGSIGCDIPGWYLWVSLKNGITPYLRCAALFFHYLLGVTPPEELHTNSAEGEYSALCSYLSLP
TNLFLLFQEYWDTVRPLLQRWCADPALLNCLKQKNTVVRYPRKRNSLIELPDDYSCLLNQASHFRCPRSADDERKHPVLCLFCGAILCSQ
NICCQEIVNGEEVGACIFHALHCGAGVCIFLKIRECRVVLVEGKARGCAYPAPYLDEYGETDPGLKRGNPLHLSRERYRKLHLVWQQHCI

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

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Fusion Protein Functional Features


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/chr7:77230123/chr15:43294902)
- 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: 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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePTPN12chr7:77230123chr15:43294902ENST00000248594+81863_67231.66666666666666781.0RegionSubstrate binding
HgenePTPN12chr7:77230123chr15:43294902ENST00000435495+71763_67101.66666666666667651.0RegionSubstrate binding

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePTPN12chr7:77230123chr15:43294902ENST00000248594+81828_293231.66666666666666781.0DomainTyrosine-protein phosphatase
HgenePTPN12chr7:77230123chr15:43294902ENST00000435495+71728_293101.66666666666667651.0DomainTyrosine-protein phosphatase
HgenePTPN12chr7:77230123chr15:43294902ENST00000248594+818231_237231.66666666666666781.0RegionSubstrate binding
HgenePTPN12chr7:77230123chr15:43294902ENST00000435495+717231_237101.66666666666667651.0RegionSubstrate binding
TgeneUBR1chr7:77230123chr15:43294902ENST000002906503047864_8691169.66666666666671750.0Compositional biasNote=Poly-Pro
TgeneUBR1chr7:77230123chr15:43294902ENST000003821772946864_8691152.01599.6666666666667Compositional biasNote=Poly-Pro
TgeneUBR1chr7:77230123chr15:43294902ENST0000029065030471098_12011169.66666666666671750.0Zinc fingerNote=RING-type%3B atypical
TgeneUBR1chr7:77230123chr15:43294902ENST00000290650304797_1681169.66666666666671750.0Zinc fingerUBR-type
TgeneUBR1chr7:77230123chr15:43294902ENST0000038217729461098_12011152.01599.6666666666667Zinc fingerNote=RING-type%3B atypical
TgeneUBR1chr7:77230123chr15:43294902ENST00000382177294697_1681152.01599.6666666666667Zinc fingerUBR-type


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
PTPN12
UBR1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgenePTPN12chr7:77230123chr15:43294902ENST00000248594+818345_438231.66666666666666781.0TGFB1I1
HgenePTPN12chr7:77230123chr15:43294902ENST00000435495+717345_438101.66666666666667651.0TGFB1I1


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Related Drugs to PTPN12-UBR1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to PTPN12-UBR1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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