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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:GREM1-TP53RK (FusionGDB2 ID:HG26585TG112858)

Fusion Gene Summary for GREM1-TP53RK

check button Fusion gene summary
Fusion gene informationFusion gene name: GREM1-TP53RK
Fusion gene ID: hg26585tg112858
HgeneTgene
Gene symbol

GREM1

TP53RK

Gene ID

26585

112858

Gene namegremlin 1, DAN family BMP antagonistTP53 regulating kinase
SynonymsC15DUPq|CKTSF1B1|CRAC1|CRCS4|DAND2|DRM|DUP15q|GREMLIN|HMPS|HMPS1|IHG-2|MPSH|PIG2BUD32|C20orf64|GAMOS4|Nori-2|Nori-2p|PRPK|TPRKB|dJ101A2
Cytomap('GREM1')('TP53RK')

15q13.3

20q13.12

Type of geneprotein-codingprotein-coding
Descriptiongremlin-1DAN domain family member 2cell proliferation-inducing gene 2 proteincolorectal adenoma and carcinoma 1cysteine knot superfamily 1, BMP antagonist 1down-regulated in Mos-transformed cells proteingremlin 1, cysteine knot superfamily, homologEKC/KEOPS complex subunit TP53RKatypical serine/threonine protein kinase TP53RKp53-related protein kinase
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000300177, ENST00000322805, 
ENST00000560830, ENST00000560677, 
Fusion gene scores* DoF score1 X 1 X 1=11 X 1 X 1=1
# samples 11
** MAII scorelog2(1/1*10)=3.32192809488736log2(1/1*10)=3.32192809488736
Context

PubMed: GREM1 [Title/Abstract] AND TP53RK [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGREM1(33025331)-TP53RK(45315095), # 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
HgeneGREM1

GO:0000902

cell morphogenesis

16545136

HgeneGREM1

GO:0008284

positive regulation of cell proliferation

16545136

HgeneGREM1

GO:0030514

negative regulation of BMP signaling pathway

15539560

HgeneGREM1

GO:0051973

positive regulation of telomerase activity

16545136

HgeneGREM1

GO:0060394

negative regulation of pathway-restricted SMAD protein phosphorylation

15539560

HgeneGREM1

GO:0090090

negative regulation of canonical Wnt signaling pathway

15539560

TgeneTP53RK

GO:0006468

protein phosphorylation

11546806



check button Fusion gene information
* 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


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Fusion Gene ORF analysis for GREM1-TP53RK

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

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 GREM1-TP53RK


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 GREM1-TP53RK


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/:33025331/:45315095)
- 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 GREM1-TP53RK


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 GREM1-TP53RK


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 GREM1-TP53RK


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 GREM1-TP53RK


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGREM1C1832587POLYPOSIS SYNDROME, HEREDITARY MIXED, 18CLINGEN;GENOMICS_ENGLAND;ORPHANET
HgeneGREM1C0009402Colorectal Carcinoma2CTD_human
HgeneGREM1C0009404Colorectal Neoplasms2CTD_human
HgeneGREM1C0024623Malignant neoplasm of stomach1CTD_human
HgeneGREM1C0032580Adenomatous Polyposis Coli1CTD_human
HgeneGREM1C0034069Pulmonary Fibrosis1CTD_human
HgeneGREM1C0038356Stomach Neoplasms1CTD_human
HgeneGREM1C1708349Hereditary Diffuse Gastric Cancer1CTD_human
HgeneGREM1C2677290COLORECTAL CANCER, SUSCEPTIBILITY TO, 41ORPHANET
HgeneGREM1C2677291COLORECTAL CANCER, SUSCEPTIBILITY TO, ON CHROMOSOME 151ORPHANET
HgeneGREM1C2713442Polyposis, Adenomatous Intestinal1CTD_human
HgeneGREM1C2713443Familial Intestinal Polyposis1CTD_human
HgeneGREM1C4721507Alveolitis, Fibrosing1CTD_human
TgeneC0795949Galloway Mowat syndrome1CTD_human;ORPHANET
TgeneC4540270GALLOWAY-MOWAT SYNDROME 41GENOMICS_ENGLAND;UNIPROT