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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:TYMS-PABPC1L (FusionGDB2 ID:HG7298TG80336)

Fusion Gene Summary for TYMS-PABPC1L

check button Fusion gene summary
Fusion gene informationFusion gene name: TYMS-PABPC1L
Fusion gene ID: hg7298tg80336
HgeneTgene
Gene symbol

TYMS

PABPC1L

Gene ID

7298

80336

Gene namethymidylate synthetasepoly(A) binding protein cytoplasmic 1 like
SynonymsHST422|TMS|TSC20orf119|EPAB|PABPC1L1|dJ1069P2.3
Cytomap('TYMS')('PABPC1L')

18p11.32

20q13.12

Type of geneprotein-codingprotein-coding
Descriptionthymidylate synthaseTSasepolyadenylate-binding protein 1-likeembryonic poly(A) binding protein
Modification date2020032220200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000323224, ENST00000323274, 
ENST00000323250, ENST00000581920, 
Fusion gene scores* DoF score13 X 7 X 9=8196 X 5 X 5=150
# samples 136
** MAII scorelog2(13/819*10)=-2.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/150*10)=-1.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TYMS [Title/Abstract] AND PABPC1L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTYMS(662320)-PABPC1L(43561698), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneTYMS

GO:0006231

dTMP biosynthetic process

8845352|11278511|15093541

HgeneTYMS

GO:0017148

negative regulation of translation

1924359

HgeneTYMS

GO:0035999

tetrahydrofolate interconversion

15093541



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-BR-8080-01ATYMSchr18

662320

+PABPC1Lchr20

43561698

+


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Fusion Gene ORF analysis for TYMS-PABPC1L

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-5UTRENST00000323224ENST00000372819TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-5UTRENST00000323224ENST00000372824TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-5UTRENST00000323274ENST00000372819TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-5UTRENST00000323274ENST00000372824TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-intronENST00000323224ENST00000217073TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-intronENST00000323224ENST00000217074TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-intronENST00000323224ENST00000217075TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-intronENST00000323224ENST00000255136TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-intronENST00000323224ENST00000490798TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-intronENST00000323224ENST00000537323TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-intronENST00000323274ENST00000217073TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-intronENST00000323274ENST00000217074TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-intronENST00000323274ENST00000217075TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-intronENST00000323274ENST00000255136TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-intronENST00000323274ENST00000490798TYMSchr18

662320

+PABPC1Lchr20

43561698

+
5CDS-intronENST00000323274ENST00000537323TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-5UTRENST00000323250ENST00000372819TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-5UTRENST00000323250ENST00000372824TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-5UTRENST00000581920ENST00000372819TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-5UTRENST00000581920ENST00000372824TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-intronENST00000323250ENST00000217073TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-intronENST00000323250ENST00000217074TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-intronENST00000323250ENST00000217075TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-intronENST00000323250ENST00000255136TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-intronENST00000323250ENST00000490798TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-intronENST00000323250ENST00000537323TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-intronENST00000581920ENST00000217073TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-intronENST00000581920ENST00000217074TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-intronENST00000581920ENST00000217075TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-intronENST00000581920ENST00000255136TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-intronENST00000581920ENST00000490798TYMSchr18

662320

+PABPC1Lchr20

43561698

+
intron-intronENST00000581920ENST00000537323TYMSchr18

662320

+PABPC1Lchr20

43561698

+

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 TYMS-PABPC1L


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)


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Fusion Protein Features for TYMS-PABPC1L


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/:662320/:43561698)
- 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

- 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 TYMS-PABPC1L


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 TYMS-PABPC1L


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 TYMS-PABPC1L


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 TYMS-PABPC1L


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTYMSC0009402Colorectal Carcinoma11CTD_human
HgeneTYMSC0009404Colorectal Neoplasms11CTD_human
HgeneTYMSC0007102Malignant tumor of colon6CTD_human
HgeneTYMSC0009375Colonic Neoplasms6CTD_human
HgeneTYMSC0013221Drug toxicity4CTD_human
HgeneTYMSC0024623Malignant neoplasm of stomach4CTD_human
HgeneTYMSC0038356Stomach Neoplasms4CTD_human
HgeneTYMSC0041755Adverse reaction to drug4CTD_human
HgeneTYMSC1708349Hereditary Diffuse Gastric Cancer4CTD_human
HgeneTYMSC0006142Malignant neoplasm of breast3CTD_human
HgeneTYMSC0678222Breast Carcinoma3CTD_human
HgeneTYMSC1257931Mammary Neoplasms, Human3CTD_human
HgeneTYMSC1458155Mammary Neoplasms3CTD_human
HgeneTYMSC4704874Mammary Carcinoma, Human3CTD_human
HgeneTYMSC0024121Lung Neoplasms2CTD_human
HgeneTYMSC0242379Malignant neoplasm of lung2CTD_human
HgeneTYMSC2239176Liver carcinoma2CTD_human
HgeneTYMSC0002871Anemia1CTD_human
HgeneTYMSC0006111Brain Diseases1CTD_human
HgeneTYMSC0007113Rectal Carcinoma1CTD_human
HgeneTYMSC0007137Squamous cell carcinoma1CTD_human
HgeneTYMSC0008924Cleft upper lip1CTD_human
HgeneTYMSC0008925Cleft Palate1CTD_human
HgeneTYMSC0012243Digestive System Neoplasms1CTD_human
HgeneTYMSC0018671Head and Neck Neoplasms1CTD_human
HgeneTYMSC0018675Head Neoplasms1CTD_human
HgeneTYMSC0024301Lymphoma, Follicular1CTD_human
HgeneTYMSC0024302Reticulosarcoma1CTD_human
HgeneTYMSC0024304Lymphoma, Mixed-Cell1CTD_human
HgeneTYMSC0024305Lymphoma, Non-Hodgkin1CTD_human
HgeneTYMSC0024306Lymphoma, Undifferentiated1CTD_human
HgeneTYMSC0027533Neck Neoplasms1CTD_human
HgeneTYMSC0027643Neoplasm Recurrence, Local1CTD_human
HgeneTYMSC0027765nervous system disorder1CTD_human
HgeneTYMSC0030297Pancreatic Neoplasm1CTD_human
HgeneTYMSC0033578Prostatic Neoplasms1CTD_human
HgeneTYMSC0034885Rectal Neoplasms1CTD_human
HgeneTYMSC0040411Tongue Neoplasms1CTD_human
HgeneTYMSC0079740High Grade Lymphoma (neoplasm)1CTD_human
HgeneTYMSC0079741Lymphoma, Intermediate-Grade1CTD_human
HgeneTYMSC0079745Lymphoma, Large-Cell, Follicular1CTD_human
HgeneTYMSC0079747Low Grade Lymphoma (neoplasm)1CTD_human
HgeneTYMSC0079757Diffuse Mixed-Cell Lymphoma1CTD_human
HgeneTYMSC0079758Lymphoma, Mixed-Cell, Follicular1CTD_human
HgeneTYMSC0079765Lymphoma, Small Cleaved-Cell, Follicular1CTD_human
HgeneTYMSC0079770Lymphoma, Small Noncleaved-Cell1CTD_human
HgeneTYMSC0085584Encephalopathies1CTD_human
HgeneTYMSC0152013Adenocarcinoma of lung (disorder)1CTD_human
HgeneTYMSC0153349Malignant neoplasm of tongue1CTD_human
HgeneTYMSC0206754Neuroendocrine Tumors1CTD_human
HgeneTYMSC0220994Hyperammonemia1CTD_human
HgeneTYMSC0278996Malignant Head and Neck Neoplasm1CTD_human
HgeneTYMSC0346647Malignant neoplasm of pancreas1CTD_human
HgeneTYMSC0376358Malignant neoplasm of prostate1CTD_human
HgeneTYMSC0746787Cancer of Neck1CTD_human
HgeneTYMSC0751075Cancer of Digestive System1CTD_human
HgeneTYMSC0751177Cancer of Head1CTD_human
HgeneTYMSC0887900Upper Aerodigestive Tract Neoplasms1CTD_human
HgeneTYMSC0919267ovarian neoplasm1CTD_human
HgeneTYMSC1140680Malignant neoplasm of ovary1CTD_human
HgeneTYMSC1837218Cleft palate, isolated1CTD_human
HgeneTYMSC1956130Lymphoma, Follicular, Grade 11CTD_human
HgeneTYMSC1956131Lymphoma, Follicular, Grade 31CTD_human
HgeneTYMSC1956132Lymphoma, Follicular, Grade 21CTD_human
HgeneTYMSC3714542Lymphoma, Diffuse1CTD_human
HgeneTYMSC4721532Lymphoma, Non-Hodgkin, Familial1CTD_human