Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:LINC00469-DNMT1 (FusionGDB2 ID:HG283982TG1786)

Fusion Gene Summary for LINC00469-DNMT1

check button Fusion gene summary
Fusion gene informationFusion gene name: LINC00469-DNMT1
Fusion gene ID: hg283982tg1786
HgeneTgene
Gene symbol

LINC00469

DNMT1

Gene ID

283982

1786

Gene namelong intergenic non-protein coding RNA 469DNA methyltransferase 1
SynonymsC17orf54ADCADN|AIM|CXXC9|DNMT|HSN1E|MCMT|m.HsaI
Cytomap('LINC00469')('DNMT1')

17q25.1

19p13.2

Type of genencRNAprotein-coding
Description-DNA (cytosine-5)-methyltransferase 1CXXC-type zinc finger protein 9DNA (cytosine-5-)-methyltransferase 1DNA MTase HsaIDNA methyltransferase HsaI
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000321800, 
Fusion gene scores* DoF score1 X 1 X 1=15 X 4 X 5=100
# samples 15
** MAII scorelog2(1/1*10)=3.32192809488736log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LINC00469 [Title/Abstract] AND DNMT1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLINC00469(71819827)-DNMT1(10292753), # 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
TgeneDNMT1

GO:0010216

maintenance of DNA methylation

18754681|21745816



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
ChimerDB4LUADTCGA-50-5946-02ALINC00469chr17

71819827

-DNMT1chr19

10292753

-


Top

Fusion Gene ORF analysis for LINC00469-DNMT1

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
5UTR-3CDSENST00000321800ENST00000340748LINC00469chr17

71819827

-DNMT1chr19

10292753

-
5UTR-3CDSENST00000321800ENST00000359526LINC00469chr17

71819827

-DNMT1chr19

10292753

-
5UTR-3CDSENST00000321800ENST00000540357LINC00469chr17

71819827

-DNMT1chr19

10292753

-
5UTR-intronENST00000321800ENST00000589538LINC00469chr17

71819827

-DNMT1chr19

10292753

-

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

Top

Fusion Genomic Features for LINC00469-DNMT1


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)


Top

Fusion Protein Features for LINC00469-DNMT1


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/:71819827/:10292753)
- 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


Top

Fusion Gene Sequence for LINC00469-DNMT1


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.

Top

Fusion Gene PPI Analysis for LINC00469-DNMT1


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


Top

Related Drugs for LINC00469-DNMT1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for LINC00469-DNMT1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC3807295CEREBELLAR ATAXIA, DEAFNESS, AND NARCOLEPSY, AUTOSOMAL DOMINANT11CLINGEN;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC3279885Hereditary Sensory and Autonomic Neuropathy Type Ie5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0036341Schizophrenia4PSYGENET
TgeneC0005586Bipolar Disorder2PSYGENET
TgeneC0006142Malignant neoplasm of breast2CTD_human
TgeneC0024623Malignant neoplasm of stomach2CTD_human
TgeneC0038356Stomach Neoplasms2CTD_human
TgeneC0678222Breast Carcinoma2CTD_human
TgeneC1257931Mammary Neoplasms, Human2CTD_human
TgeneC1384666hearing impairment2CTD_human;GENOMICS_ENGLAND
TgeneC1458155Mammary Neoplasms2CTD_human
TgeneC1708349Hereditary Diffuse Gastric Cancer2CTD_human
TgeneC4704874Mammary Carcinoma, Human2CTD_human
TgeneC0001418Adenocarcinoma1CTD_human
TgeneC0003469Anxiety Disorders1CTD_human
TgeneC0003865Arthritis, Adjuvant-Induced1CTD_human
TgeneC0004096Asthma1CTD_human
TgeneC0007097Carcinoma1CTD_human
TgeneC0007102Malignant tumor of colon1CTD_human
TgeneC0009375Colonic Neoplasms1CTD_human
TgeneC0020071Hereditary Sensory Autonomic Neuropathy, Type 11CTD_human
TgeneC0020072Hereditary Sensory Autonomic Neuropathy, Type 21CTD_human
TgeneC0020074HSAN Type IV1CTD_human
TgeneC0020075Hereditary Sensory Autonomic Neuropathy, Type 51CTD_human
TgeneC0025149Medulloblastoma1CTD_human
TgeneC0027626Neoplasm Invasiveness1CTD_human
TgeneC0027889Hereditary Sensory and Autonomic Neuropathies1CTD_human
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0086405Hereditary Sensory Radicular Neuropathy1CTD_human
TgeneC0205641Adenocarcinoma, Basal Cell1CTD_human
TgeneC0205642Adenocarcinoma, Oxyphilic1CTD_human
TgeneC0205643Carcinoma, Cribriform1CTD_human
TgeneC0205644Carcinoma, Granular Cell1CTD_human
TgeneC0205645Adenocarcinoma, Tubular1CTD_human
TgeneC0205696Anaplastic carcinoma1CTD_human
TgeneC0205697Carcinoma, Spindle-Cell1CTD_human
TgeneC0205698Undifferentiated carcinoma1CTD_human
TgeneC0205699Carcinomatosis1CTD_human
TgeneC0205833Medullomyoblastoma1CTD_human
TgeneC0278510Childhood Medulloblastoma1CTD_human
TgeneC0278876Adult Medulloblastoma1CTD_human
TgeneC0282612Prostatic Intraepithelial Neoplasias1CTD_human
TgeneC0338630Senile Paranoid Dementia1CTD_human
TgeneC0376280Anxiety States, Neurotic1CTD_human
TgeneC0376358Malignant neoplasm of prostate1CTD_human
TgeneC0497327Dementia1CTD_human
TgeneC0525045Mood Disorders1PSYGENET
TgeneC0699739Sensory Neuropathy, Hereditary1CTD_human
TgeneC0751071Familial Dementia1CTD_human
TgeneC0751291Desmoplastic Medulloblastoma1CTD_human
TgeneC0887833Carcinoma, Pancreatic Ductal1CTD_human
TgeneC0971858Arthritis, Collagen-Induced1CTD_human
TgeneC0993582Arthritis, Experimental1CTD_human
TgeneC1275668Melanotic medulloblastoma1CTD_human
TgeneC1279420Anxiety neurosis (finding)1CTD_human
TgeneC2931852Clear-cell metastatic renal cell carcinoma1CTD_human