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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: 20640

FusionGeneSummary for MALAT1_MLH1

check button Fusion gene summary
Fusion gene informationFusion gene name: MALAT1_MLH1
Fusion gene ID: 20640
HgeneTgene
Gene symbol

MALAT1

MLH1

Gene ID

378938

4292

Gene namemetastasis associated lung adenocarcinoma transcript 1mutL homolog 1
SynonymsHCN|LINC00047|NCRNA00047|NEAT2|PRO2853COCA2|FCC2|HNPCC|HNPCC2|hMLH1
Cytomap

11q13.1

3p22.2

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)DNA mismatch repair protein Mlh1mutL homolog 1, colon cancer, nonpolyposis type 2
Modification date2018052720180523
UniProtAcc

P40692

Ensembl transtripts involved in fusion geneENST00000534336, ENST00000536378, 
ENST00000231790, ENST00000458205, 
ENST00000539477, ENST00000455445, 
ENST00000435176, ENST00000492474, 
Fusion gene scores* DoF score83 X 128 X 5=531206 X 7 X 3=126
# samples 1418
** MAII scorelog2(141/53120*10)=-5.23548807894813
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/126*10)=-0.655351828612554
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MALAT1 [Title/Abstract] AND MLH1 [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
ChiTaRS3.1BG945974MALAT1chr11

65272105

-MLH1chr3

37055982

+
* 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-3CDSENST00000534336ENST00000536378MALAT1chr11

65272105

-MLH1chr3

37055982

+
3UTR-3CDSENST00000534336ENST00000231790MALAT1chr11

65272105

-MLH1chr3

37055982

+
3UTR-3CDSENST00000534336ENST00000458205MALAT1chr11

65272105

-MLH1chr3

37055982

+
3UTR-3CDSENST00000534336ENST00000539477MALAT1chr11

65272105

-MLH1chr3

37055982

+
3UTR-3CDSENST00000534336ENST00000455445MALAT1chr11

65272105

-MLH1chr3

37055982

+
3UTR-3CDSENST00000534336ENST00000435176MALAT1chr11

65272105

-MLH1chr3

37055982

+
3UTR-intronENST00000534336ENST00000492474MALAT1chr11

65272105

-MLH1chr3

37055982

+

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FusionProtFeatures for MALAT1_MLH1


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

MLH1

P40692

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}. Heterodimerizes with PMS2 to form MutL alpha, acomponent of the post-replicative DNA mismatch repair system(MMR). DNA repair is initiated by MutS alpha (MSH2-MSH6) or MutSbeta (MSH2-MSH3) binding to a dsDNA mismatch, then MutL alpha isrecruited to the heteroduplex. Assembly of the MutL-MutS-heteroduplex ternary complex in presence of RFC and PCNA issufficient to activate endonuclease activity of PMS2. Itintroduces single-strand breaks near the mismatch and thusgenerates new entry points for the exonuclease EXO1 to degrade thestrand containing the mismatch. DNA methylation would preventcleavage and therefore assure that only the newly mutated DNAstrand is going to be corrected. MutL alpha (MLH1-PMS2) interactsphysically with the clamp loader subunits of DNA polymerase III,suggesting that it may play a role to recruit the DNA polymeraseIII to the site of the MMR. Also implicated in DNA damagesignaling, a process which induces cell cycle arrest and can leadto apoptosis in case of major DNA damages. Heterodimerizes withMLH3 to form MutL gamma which plays a role in meiosis.{ECO:0000269|PubMed:16873062, ECO:0000269|PubMed:18206974,ECO:0000269|PubMed:20020535, ECO:0000269|PubMed:21120944,ECO:0000269|PubMed:9311737}.

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_MLH1


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_MLH1


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_MLH1


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_MLH1


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
TgeneMLH1C1333991Hereditary Non-Polyposis Colon Cancer Type 252CTD_human;UNIPROT
TgeneMLH1C1527249Colorectal Cancer6UNIPROT
TgeneMLH1C0009405Hereditary Nonpolyposis Colorectal Neoplasms5CTD_human
TgeneMLH1C0009404Colorectal Neoplasms3CTD_human
TgeneMLH1C0265325Turcot syndrome (disorder)2CTD_human;ORPHANET;UNIPROT
TgeneMLH1C0009375Colonic Neoplasms1CTD_human
TgeneMLH1C0024299Lymphoma1CTD_human;HPO
TgeneMLH1C0027627Neoplasm Metastasis1CTD_human
TgeneMLH1C0033578Prostatic Neoplasms1CTD_human
TgeneMLH1C0919267ovarian neoplasm1CTD_human