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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: 20623

FusionGeneSummary for MALAT1_HDAC3

check button Fusion gene summary
Fusion gene informationFusion gene name: MALAT1_HDAC3
Fusion gene ID: 20623
HgeneTgene
Gene symbol

MALAT1

HDAC3

Gene ID

378938

8841

Gene namemetastasis associated lung adenocarcinoma transcript 1histone deacetylase 3
SynonymsHCN|LINC00047|NCRNA00047|NEAT2|PRO2853HD3|RPD3|RPD3-2
Cytomap

11q13.1

5q31.3

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 deacetylase 3SMAP45
Modification date2018052720180520
UniProtAcc

O15379

Ensembl transtripts involved in fusion geneENST00000534336, ENST00000305264, 
ENST00000469207, 
Fusion gene scores* DoF score83 X 128 X 5=531201 X 1 X 1=1
# samples 1412
** MAII scorelog2(141/53120*10)=-5.23548807894813
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/1*10)=4.32192809488736
Context

PubMed: MALAT1 [Title/Abstract] AND HDAC3 [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
TgeneHDAC3

GO:0000122

negative regulation of transcription by RNA polymerase II

16569215|18417529|18854353

TgeneHDAC3

GO:0001934

positive regulation of protein phosphorylation

25190803

TgeneHDAC3

GO:0006476

protein deacetylation

17172643|21030595

TgeneHDAC3

GO:0031647

regulation of protein stability

25190803

TgeneHDAC3

GO:0042307

positive regulation of protein import into nucleus

25190803

TgeneHDAC3

GO:0045944

positive regulation of transcription by RNA polymerase II

25190803

TgeneHDAC3

GO:0071498

cellular response to fluid shear stress

25190803


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
ChiTaRS3.1AI133081MALAT1chr11

65268585

-HDAC3chr5

141008217

-
ChiTaRS3.1AF130111MALAT1chr11

65268585

-HDAC3chr5

141008217

-
* 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-intronENST00000534336ENST00000305264MALAT1chr11

65268585

-HDAC3chr5

141008217

-
3UTR-intronENST00000534336ENST00000469207MALAT1chr11

65268585

-HDAC3chr5

141008217

-

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FusionProtFeatures for MALAT1_HDAC3


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

HDAC3

O15379

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}. Responsible for the deacetylation of lysine residues onthe N-terminal part of the core histones (H2A, H2B, H3 and H4),and some other non-histone substrates. Histone deacetylation givesa tag for epigenetic repression and plays an important role intranscriptional regulation, cell cycle progression anddevelopmental events. Histone deacetylases act via the formationof large multiprotein complexes. Participates in the BCL6transcriptional repressor activity by deacetylating the H3 'Lys-27' (H3K27) on enhancer elements, antagonizing EP300acetyltransferase activity and repressing proximal geneexpression. Probably participates in the regulation oftranscription through its binding to the zinc-finger transcriptionfactor YY1; increases YY1 repression activity. Required to represstranscription of the POU1F1 transcription factor. Acts as amolecular chaperone for shuttling phosphorylated NR2C1 to PMLbodies for sumoylation (PubMed:21444723, PubMed:23911289).Contributes, together with XBP1 isoform 1, to the activation ofNFE2L2-mediated HMOX1 transcription factor gene expression in aPI(3)K/mTORC2/Akt-dependent signaling pathway leading toendothelial cell (EC) survival under disturbed flow/oxidativestress (PubMed:25190803). {ECO:0000269|PubMed:21444723,ECO:0000269|PubMed:23911289, ECO:0000269|PubMed:25190803}.

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_HDAC3


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_HDAC3


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_HDAC3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneHDAC3O15379DB02546VorinostatHistone deacetylase 3small moleculeapproved|investigational

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RelatedDiseases for MALAT1_HDAC3


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
TgeneHDAC3C0036341Schizophrenia4PSYGENET
TgeneHDAC3C0018799Heart Diseases1CTD_human