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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 20664

FusionGeneSummary for MALAT1_SETDB1

check button Fusion gene summary
Fusion gene informationFusion gene name: MALAT1_SETDB1
Fusion gene ID: 20664
HgeneTgene
Gene symbol

MALAT1

SETDB1

Gene ID

378938

9869

Gene namemetastasis associated lung adenocarcinoma transcript 1SET domain bifurcated 1
SynonymsHCN|LINC00047|NCRNA00047|NEAT2|PRO2853ESET|H3-K9-HMTase4|KG1T|KMT1E|TDRD21
Cytomap

11q13.1

1q21.3

Type of genencRNAprotein-coding
Descriptionhepcarcinlong intergenic non-protein coding RNA 47metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)nuclear enriched abundant transcript 2nuclear paraspeckle assembly transcript 2 (non-protein coding)histone-lysine N-methyltransferase SETDB1ERG-associated protein with SET domainERG-associated protein with a SET domain, ESETH3-K9-HMTase 4histone H3-K9 methyltransferase 4histone-lysine N-methyltransferase, H3lysine-9 specific 4lysine N-methyltrans
Modification date2018052720180519
UniProtAcc

Q15047

Ensembl transtripts involved in fusion geneENST00000534336, ENST00000271640, 
ENST00000368962, ENST00000368969, 
ENST00000368963, ENST00000459773, 
Fusion gene scores* DoF score83 X 128 X 5=531202 X 2 X 1=4
# samples 1412
** MAII scorelog2(141/53120*10)=-5.23548807894813
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/4*10)=2.32192809488736
Context

PubMed: MALAT1 [Title/Abstract] AND SETDB1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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

check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1BF992583MALAT1chr11

65267932

-SETDB1chr1

150900286

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
3UTR-3CDSENST00000534336ENST00000271640MALAT1chr11

65267932

-SETDB1chr1

150900286

-
3UTR-3CDSENST00000534336ENST00000368962MALAT1chr11

65267932

-SETDB1chr1

150900286

-
3UTR-3CDSENST00000534336ENST00000368969MALAT1chr11

65267932

-SETDB1chr1

150900286

-
3UTR-3CDSENST00000534336ENST00000368963MALAT1chr11

65267932

-SETDB1chr1

150900286

-
3UTR-3UTRENST00000534336ENST00000459773MALAT1chr11

65267932

-SETDB1chr1

150900286

-

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FusionProtFeatures for MALAT1_SETDB1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
MALAT1

SETDB1

Q15047

Lectin that binds to various sugars: galactose > mannose= fucose > N-acetylglucosamine > N-acetylgalactosamine(PubMed:10224141). Acts as a chemoattractant, probably involved inthe regulation of cell migration (PubMed:28301481).{ECO:0000269|PubMed:10224141, ECO:0000269|PubMed:28301481}. Histone methyltransferase that specificallytrimethylates 'Lys-9' of histone H3. H3 'Lys-9' trimethylationrepresents a specific tag for epigenetic transcriptionalrepression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins tomethylated histones. Mainly functions in euchromatin regions,thereby playing a central role in the silencing of euchromaticgenes. H3 'Lys-9' trimethylation is coordinated with DNAmethylation. Probably forms a complex with MBD1 and ATF7IP thatrepresses transcription and couples DNA methylation and histone'Lys-9' trimethylation. Its activity is dependent on MBD1 and isheritably maintained through DNA replication by being recruited byCAF-1. SETDB1 is targeted to histone H3 by TRIM28/TIF1B, a factorrecruited by KRAB zinc-finger proteins. Probably forms acorepressor complex required for activated KRAS-mediated promoterhypermethylation and transcriptional silencing of tumor suppressorgenes (TSGs) or other tumor-related genes in colorectal cancer(CRC) cells (PubMed:24623306). Also required to maintain atranscriptionally repressive state of genes in undifferentiatedembryonic stem cells (ESCs) (PubMed:24623306). Associates atpromoter regions of tumor suppressor genes (TSGs) leading to theirgene silencing (PubMed:24623306). The SETDB1-TRIM28-ZNF274 complexmay play a role in recruiting ATRX to the 3'-exons of zinc-fingercoding genes with atypical chromatin signatures to establish ormaintain/protect H3K9me3 at these transcriptionally active regions(PubMed:27029610). {ECO:0000269|PubMed:12869583,ECO:0000269|PubMed:14536086, ECO:0000269|PubMed:15327775,ECO:0000269|PubMed:17952062, ECO:0000269|PubMed:24623306,ECO:0000269|PubMed:27029610}.

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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FusionGeneSequence for MALAT1_SETDB1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for MALAT1_SETDB1


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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RelatedDrugs for MALAT1_SETDB1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for MALAT1_SETDB1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMALAT1C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneMALAT1C0023903Liver neoplasms1CTD_human
HgeneMALAT1C0027626Neoplasm Invasiveness1CTD_human
HgeneMALAT1C0027627Neoplasm Metastasis1CTD_human
HgeneMALAT1C0032460Polycystic Ovary Syndrome1CTD_human
HgeneMALAT1C0236663Alcohol withdrawal syndrome1PSYGENET
HgeneMALAT1C0279626Squamous cell carcinoma of esophagus1CTD_human
TgeneSETDB1C0025202melanoma1CTD_human
TgeneSETDB1C0036341Schizophrenia1PSYGENET
TgeneSETDB1C0178417Anhedonia1PSYGENET
TgeneSETDB1C0345967Malignant mesothelioma1CTD_human