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MALAT1 Gene

RNA gene   GIFtS: 28
GCID: GC11P065266

Metastasis Associated Lung Adenocarcinoma Transcript 1 (Non-Protein...

  See MALAT1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 3

Aliases
Metastasis Associated Lung Adenocarcinoma Transcript 1 (Non-Protein
Coding)1 2
     LINC000472
hepcarcin1     MALAT-12
Long Intergenic Non-Protein Coding RNA 471     NCRNA000472
Metastasis Associated In Lung Adenocarcinoma Transcript 11     NEAT22
Non-Protein Coding RNA 471     PRO28532
Nuclear Enriched Abundant Transcript 21     mascRNA2
Nuclear Paraspeckle Assembly Transcript 2 (Non-Protein Coding)1     PRO10735
HCN2     

External Ids:    HGNC: 296651   Entrez Gene: 3789382   Ensembl: ENSG000002515627   OMIM: 6079245   UniProtKB: Q9UHZ23   

Export aliases for MALAT1 gene to outside databases

Previous GC identifers: GC11P065032 GC11U900628 GC11P061592


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for MALAT1 Gene:
MALAT1 (metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with MALAT1 include lung adenocarcinoma, and undifferentiated embryonal sarcoma of the liver.

Gene Wiki entry for MALAT1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000011.9  NC_018922.2  NT_167190.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the MALAT1 gene promoter:
         SREBP-1c   Nkx2-5   SREBP-1b   CREB   SREBP-1a   deltaCREB   FOXO1a   NF-Y   CBF(2)   FOXO1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat MALAT1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11q13.1   Ensembl cytogenetic band:  11q13.1   HGNC cytogenetic band: 11q13.1

MALAT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MALAT1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P065266:  view genomic region     (about GC identifiers)

Start:
65,265,233 bp from pter      End:
65,273,940 bp from pter
Size:
8,708 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for MALAT1

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
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UniProtKB/Swiss-Prot: MALAT_HUMAN, Q9UHZ2 (See protein sequence)
Recommended Name: Metastasis-associated lung adenocarcinoma transcript 1  
Size: 57 amino acids; 6289 Da

Explore the universe of human proteins at neXtProt for MALAT1: NX_Q9UHZ2


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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
LNCRNA: Long non-coding RNAs

ProtoNet protein and cluster: Q9UHZ2


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Phenotypes:
     2 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Malat1):
 no phenotypic analysis  normal 

Find genes that share phenotypes with MALAT1           About GenesLikeMe

Animal Models:
     MGI mouse knock-out Malat1tm1.2Dlsp for MALAT1

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for MALAT1
Interactions:

    Search GeneGlobe Interaction Network for MALAT1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for MALAT1 (MALAT)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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Unigene Clusters for MALAT1:

Metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)
Hs.621695  [show with all ESTs], Hs.642877  [show with all ESTs]
Unigene Representative Sequences: EF177381, BF675113
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000534336(lincRNA)(uc010roh.2) ENST00000508832(lincRNA)(uc001odz.3) ENST00000544868(lincRNA)

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Additional mRNA sequence: 

AJ535464.1 AJ535465.1 AJ535466.1 

Selected DOTS entries (see all 360):

DT.91900579  DT.95351792  DT.91927045  DT.95291680  DT.100735204  DT.100735190  DT.95377975  DT.91955986 
DT.100061127  DT.91925908  DT.100735117  DT.97869937  DT.100735119  DT.100735200  DT.95378317  DT.91905728 
DT.100735188  DT.99982642  DT.100735207  DT.98083654  DT.95378105  DT.92357998  DT.92407302  DT.100060487 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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Expression evidence for MALAT1:none

MALAT1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: ACGCAGGGAG
MALAT1 Expression
About this image


MALAT1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 8) fully expand
 
 Primitive Streak (Early Embryonic Tissues)    fully expand to see all 2 entries
         Notochord Cells Notochord
         Notochord
 
 Neural Tube (Nervous System)    fully expand to see all 2 entries
         Diencephalon
 
 Cartilage (Muscoskeletal System)
         Notochord Cells Notochord
 
 Adipose (Muscoskeletal System)
         White adipocyte-like cells
 
 Blood (Hematopoietic System)
         pre Conventional Dendritic Cells Peripheral Blood
MALAT1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene clusters: Hs.621695 Hs.642877
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MALAT1

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and mouse.

Orthologs for MALAT1 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Malat15 metastasis associated lung adenocarcinoma transcript more   --   19 (4.34 cM) 5795690 


ENSEMBL Gene Tree for MALAT1 (if available)
TreeFam Gene Tree for MALAT1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for MALAT1 (see all 275)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1383341561,2
C--65263234(+) AAAAA-/TTAT  
        
TTACG
1 -- us2k10--------
rs1136376201,2
C,F--65263287(+) GGATAC/TGGGAG 1 -- us2k11Minor allele frequency- T:0.50NA 2
rs1128296531,2
F--65263484(+) AGATCG/CAGACC 1 -- us2k11Minor allele frequency- C:0.50CSA 2
rs1408293781,2
--65263505(+) ACACGA/GTGAAA 1 -- us2k10--------
rs1921644871,2
--65263600(+) GTGAAC/TTGCTT 1 -- us2k10--------
rs789016881,2
C--65263640(+) CGAGAC/TCCCGC 1 -- us2k10--------
rs2003488031,2
C--65263702(-) TGTTTC/TTTTTT 1 -- us2k10--------
rs346340351,2
C--65263819(+) AGAGC-/AGAGAGT 1 -- us2k10--------
rs2009936391,2
--65263824(+) AGAGA-/GTACAGA 1 -- us2k10--------
rs41022171,2
C,F,A,H--65263895(+) TGCTGG/CAGAGG 1 -- us2k110Minor allele frequency- C:0.09NS EA NA WA 748

HapMap Linkage Disequilibrium report for MALAT1 (65265233 - 65273940 bp)

Structural Variations
     Database of Genomic Variants (DGV) 8 variations for MALAT1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv897717CNV Loss21882294
esv23728CNV Loss19812545
dgv1175n71CNV Loss21882294
nsv820139CNV Loss19587683
nsv897719CNV Loss21882294
nsv897718CNV Loss21882294
nsv897720CNV Loss21882294
nsv825951CNV Gain20364138

Site Specific Mutation Identification with PCR Assays
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DNA2.0 Custom Variant and Variant Library Synthesis for MALAT1

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 607924    OMIM disorders: --

4 diseases for MALAT1:    
About MalaCards
lung adenocarcinoma    undifferentiated embryonal sarcoma of the liver    adenocarcinoma    embryonal sarcoma


Find genes that share disorders with MALAT1           About GenesLikeMe


Export disorders for MALAT1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for MALAT1 gene, integrated from 10 sources (see all 33):
(articles sorted by number of sources associating them with MALAT1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. MALAT-1, a non protein-coding RNA is upregulated in the cerebellum, hippocampus and brain stem of human alcoholics. (PubMed id 22560368)1, 3 Kryger R....Jaquet V. (Alcohol 2012)
  2. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. (PubMed id 12970751)1, 3 Ji P....MA1ller-Tidow C. (Oncogene 2003)
  3. Construction of a 350-kb sequence-ready 11q13 cosmid contig encompassing the markers D11S4933 and D11S546: mapping of 11 genes and 3 tumor-associated translocation breakpoints. (PubMed id 10843802)1, 2 van Asseldonk M....Geurts van Kessel A. (Genomics 2000)
  4. Widespread purifying selection on RNA structure in mammals. (PubMed id 23847102)1 Smith M.A....Mattick J.S. (Nucleic Acids Res. 2013)
  5. Inducing cell proliferation inhibition, apoptosis, and motility reduction by silencing long noncoding ribonucleic acid metastasis-associated lung adenocarcinoma transcript 1 in urothelial carcinoma of the bladder. (PubMed id 23153939)1 Han Y....Cai Z. (Urology 2013)
  6. MALAT-1 interacts with hnRNP C in cell cycle regulation. (PubMed id 23973260)1 Yang F....Liang Z. (FEBS Lett. 2013)
  7. Circulating long non-coding RNAs in plasma of patients with gastric cancer. (PubMed id 23898077)1 Arita T....Otsuji E. (Anticancer Res. 2013)
  8. The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. (PubMed id 23243023)1 Gutschner T....Diederichs S. (Cancer Res. 2013)
  9. Long non-coding RNA metastasis associated in lung adenocarcinoma transcript 1 derived miniRNA as a novel plasma-based biomarker for diagnosing prostate cancer. (PubMed id 23726266)1 Ren S....Sun Y. (Eur. J. Cancer 2013)
  10. Characterization of translocations in mesenchymal hamartoma and undifferentiated embryonal sarcoma of the liver. (PubMed id 24120702)1 Mathews J....Pfeifer J.D. (Exp. Mol. Pathol. 2013)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 378938 HGNC: 29665 Ensembl:ENSG00000251562 euGenes: HUgn378938 ECgene: MALAT1
H-InvDB: MALAT1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for MALAT1 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for MALAT1 Genetics and Cytogenetics in Oncology and Haematology

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for MALAT1 gene:
Search GeneIP for patents involving MALAT1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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 Browse ESI BIO Cell Lines and PureStem Progenitors for MALAT1
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 inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for MALAT1
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Customized transgenic rodents for:
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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