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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: 20633

FusionGeneSummary for MALAT1_MALAT1

check button Fusion gene summary
Fusion gene informationFusion gene name: MALAT1_MALAT1
Fusion gene ID: 20633
HgeneTgene
Gene symbol

MALAT1

MALAT1

Gene ID

378938

378938

Gene namemetastasis associated lung adenocarcinoma transcript 1metastasis associated lung adenocarcinoma transcript 1
SynonymsHCN|LINC00047|NCRNA00047|NEAT2|PRO2853HCN|LINC00047|NCRNA00047|NEAT2|PRO2853
Cytomap

11q13.1

11q13.1

Type of genencRNAncRNA
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)hepcarcinlong 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)
Modification date2018052720180527
UniProtAcc

Ensembl transtripts involved in fusion geneENST00000534336, ENST00000534336, 
Fusion gene scores* DoF score83 X 128 X 5=5312071 X 110 X 1=7810
# samples 141126
** MAII scorelog2(141/53120*10)=-5.23548807894813
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(126/7810*10)=-2.63189881464206
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MALAT1 [Title/Abstract] AND MALAT1 [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
ChiTaRS3.1AW891969MALAT1chr11

65266665

-MALAT1chr11

65266675

+
ChiTaRS3.1BG771150MALAT1chr11

65267577

+MALAT1chr11

65266791

+
ChiTaRS3.1CB265780MALAT1chr11

65267648

+MALAT1chr11

65266832

+
ChiTaRS3.1AW977290MALAT1chr11

65267278

-MALAT1chr11

65267672

-
ChiTaRS3.1AW858530MALAT1chr11

65266792

+MALAT1chr11

65266798

-
ChiTaRS3.1AW580841MALAT1chr11

65267741

-MALAT1chr11

65267766

+
ChiTaRS3.1EY123349MALAT1chr11

65267190

-MALAT1chr11

65267701

-
ChiTaRS3.1CB266111MALAT1chr11

65267648

+MALAT1chr11

65266832

+
ChiTaRS3.1DW410271MALAT1chr11

65267651

+MALAT1chr11

65266960

+
ChiTaRS3.1CB852741MALAT1chr11

65268121

+MALAT1chr11

65266782

+
ChiTaRS3.1BG011651MALAT1chr11

65266799

-MALAT1chr11

65266587

+
ChiTaRS3.1AA577941MALAT1chr11

65270528

+MALAT1chr11

65270428

-
ChiTaRS3.1AW996942MALAT1chr11

65268122

+MALAT1chr11

65267747

+
ChiTaRS3.1BG564122MALAT1chr11

65267539

+MALAT1chr11

65267186

+
ChiTaRS3.1BF577322MALAT1chr11

65271159

+MALAT1chr11

65266535

+
ChiTaRS3.1AA569443MALAT1chr11

65267608

-MALAT1chr11

65267785

+
ChiTaRS3.1DW433727MALAT1chr11

65268300

+MALAT1chr11

65266762

+
ChiTaRS3.1DW421327MALAT1chr11

65268470

+MALAT1chr11

65266695

+
ChiTaRS3.1BQ329707MALAT1chr11

65267369

-MALAT1chr11

65267892

-
ChiTaRS3.1DW407607MALAT1chr11

65266597

-MALAT1chr11

65269502

-
ChiTaRS3.1BQ632547MALAT1chr11

65266722

-MALAT1chr11

65268022

-
ChiTaRS3.1DW464867MALAT1chr11

65267625

+MALAT1chr11

65266715

+
ChiTaRS3.1BG427318MALAT1chr11

65272000

+MALAT1chr11

65266558

+
ChiTaRS3.1BU680148MALAT1chr11

65266756

-MALAT1chr11

65266572

+
ChiTaRS3.1CA424749MALAT1chr11

65272520

-MALAT1chr11

65272500

+
ChiTaRS3.1AW976079MALAT1chr11

65267411

-MALAT1chr11

65267994

-
ChiTaRS3.1AA578709MALAT1chr11

65267608

-MALAT1chr11

65267785

+
ChiTaRS3.1CB069039MALAT1chr11

65268086

+MALAT1chr11

65266832

+
ChiTaRS3.1AA777969MALAT1chr11

65266812

-MALAT1chr11

65269794

-
ChiTaRS3.1DW451889MALAT1chr11

65267830

+MALAT1chr11

65266597

+
ChiTaRS3.1BE766616MALAT1chr11

65272138

-MALAT1chr11

65272222

+
ChiTaRS3.1BU674886MALAT1chr11

65267054

-MALAT1chr11

65266874

+
ChiTaRS3.1BQ632546MALAT1chr11

65267132

-MALAT1chr11

65267661

-
ChiTaRS3.1BE767916MALAT1chr11

65271221

-MALAT1chr11

65271056

+
ChiTaRS3.1BU784876MALAT1chr11

65267066

-MALAT1chr11

65269637

-
ChiTaRS3.1DW419196MALAT1chr11

65267333

+MALAT1chr11

65266763

+
ChiTaRS3.1DW436856MALAT1chr11

65267649

+MALAT1chr11

65266635

+
ChiTaRS3.1AI824606MALAT1chr11

65268678

-MALAT1chr11

65269320

-
ChiTaRS3.1AW381344MALAT1chr11

65272267

+MALAT1chr11

65272296

-
ChiTaRS3.1BU678504MALAT1chr11

65266767

-MALAT1chr11

65266565

+
ChiTaRS3.1BF084924MALAT1chr11

65272267

+MALAT1chr11

65272105

-
ChiTaRS3.1BG961413MALAT1chr11

65266969

-MALAT1chr11

65267547

-
ChiTaRS3.1DW408943MALAT1chr11

65267546

+MALAT1chr11

65266564

+
ChiTaRS3.1DW467313MALAT1chr11

65271190

+MALAT1chr11

65270280

+
ChiTaRS3.1BE840873MALAT1chr11

65272619

-MALAT1chr11

65272767

+
ChiTaRS3.1BQ632833MALAT1chr11

65267661

+MALAT1chr11

65267132

+
* 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-3UTRENST00000534336ENST00000534336MALAT1chr11

65266665

-MALAT1chr11

65266675

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267577

+MALAT1chr11

65266791

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267648

+MALAT1chr11

65266832

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267278

-MALAT1chr11

65267672

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65266792

+MALAT1chr11

65266798

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267741

-MALAT1chr11

65267766

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267190

-MALAT1chr11

65267701

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267651

+MALAT1chr11

65266960

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65268121

+MALAT1chr11

65266782

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65266799

-MALAT1chr11

65266587

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65270528

+MALAT1chr11

65270428

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65268122

+MALAT1chr11

65267747

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267539

+MALAT1chr11

65267186

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65271159

+MALAT1chr11

65266535

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267608

-MALAT1chr11

65267785

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65268300

+MALAT1chr11

65266762

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65268470

+MALAT1chr11

65266695

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267369

-MALAT1chr11

65267892

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65266597

-MALAT1chr11

65269502

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65266722

-MALAT1chr11

65268022

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267625

+MALAT1chr11

65266715

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65272000

+MALAT1chr11

65266558

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65266756

-MALAT1chr11

65266572

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65272520

-MALAT1chr11

65272500

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267411

-MALAT1chr11

65267994

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65268086

+MALAT1chr11

65266832

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65266812

-MALAT1chr11

65269794

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267830

+MALAT1chr11

65266597

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65272138

-MALAT1chr11

65272222

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267054

-MALAT1chr11

65266874

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267132

-MALAT1chr11

65267661

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65271221

-MALAT1chr11

65271056

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267066

-MALAT1chr11

65269637

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267333

+MALAT1chr11

65266763

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267649

+MALAT1chr11

65266635

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65268678

-MALAT1chr11

65269320

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65272267

+MALAT1chr11

65272296

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65266767

-MALAT1chr11

65266565

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65272267

+MALAT1chr11

65272105

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65266969

-MALAT1chr11

65267547

-
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267546

+MALAT1chr11

65266564

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65271190

+MALAT1chr11

65270280

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65272619

-MALAT1chr11

65272767

+
3UTR-3UTRENST00000534336ENST00000534336MALAT1chr11

65267661

+MALAT1chr11

65267132

+

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FusionProtFeatures for MALAT1_MALAT1


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

MALAT1

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}. 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}.

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_MALAT1


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_MALAT1


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_MALAT1


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_MALAT1


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
TgeneMALAT1C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneMALAT1C0023903Liver neoplasms1CTD_human
TgeneMALAT1C0027626Neoplasm Invasiveness1CTD_human
TgeneMALAT1C0027627Neoplasm Metastasis1CTD_human
TgeneMALAT1C0032460Polycystic Ovary Syndrome1CTD_human
TgeneMALAT1C0236663Alcohol withdrawal syndrome1PSYGENET
TgeneMALAT1C0279626Squamous cell carcinoma of esophagus1CTD_human