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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

MALAT1 Gene

RNA gene   GIFtS: 30
GCID: GC11P065266

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

  See 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)
About This Section

Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 6.4

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

External Ids:    HGNC: 296651   Entrez Gene: 3789382   Ensembl: ENSG000002515627   OMIM: 6079245   UniProtKB: Q9UHZ23   
ORGUL members:    fRNAdb10:FR273624 FR077061 FR207589 FR264225      
NCBI13:BK001411 BK001418    
NONCODE14:n380683 n379853 n381725 n343070      
Rfam:RF01871    
RNAdb15:LIT2013 LIT2012 RNZ7067 EVF32835    

Export aliases for MALAT1 gene to outside databases

Previous GC identifers: GC11P065032 GC11U900628 GC11P061592


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 adenocarcinoma.

Gene Wiki entry for MALAT1 Gene

fRNAdb sequence ontologies for MALAT1 - the ORGUL cluster for this gene includes several descriptions:
Metastasis associated lung adenocarcinoma transcript 1 - MALAT 1 (metastasis associated lung adenocarcinoma transcript 1) is also known as NEAT2 (noncoding nuclear-enriched abundant transcript 2). It is a large, infrequently spliced RNA, which is highly conserved amongst mammals. It is highly expressed in the nucleus [1]. It is associated with metastasis, and positively regulates cell motility via the transcriptional and/or post-transcriptional regulation of motility-related genes [2].
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.

View fRNAdb secondary structures for MALAT1

(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000011.9  NT_167190.1  NC_018922.2  
Regulatory elements:
   SABiosciences 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

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

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

MALAT1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Phenotypes:
     2 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Malat1):
 no phenotypic analysis  normal 

MALAT1 for phenotypes           About GeneDecksing

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

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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for MALAT1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for MALAT1 (MALAT)

Search CenterWatch for drugs/clinical trials and news about MALAT1

(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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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About This Section
2 fRNAdb Secondary structures:


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)

miRNA
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Additional mRNA sequence: 

AJ535464.1 AJ535465.1 AJ535466.1 

24/360 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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

Expression evidence for MALAT1:RNAdb

MALAT1 expression in normal human tissues (normalized intensities)      MALAT1 embryonic expression: see
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 
 5/7 selected tissues (see all 7) fully expand
 
 Brain (Nervous System)    fully expand to see all 3 entries
         Hypothalamus
         brain/midbrain   
 
 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
 
 Blood (Hematopoietic System)
         pre Conventional Dendritic Cells Peripheral Blood
 
 Cartilage (Muscoskeletal System)
         Notochord Cells Notochord

Genevestigator expression for MALAT1

SOURCE GeneReport for Unigene clusters: Hs.621695 Hs.642877
    SABiosciences Custom PCR Arrays for MALAT1
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In Situ
Assay Products:
 

 
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(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)
About This Section

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)
About This Section
  --

(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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/275 SNPs in MALAT1 are shown (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

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
OMIM gene information: 607924OMIM information:   
12 diseases for MALAT1:    About MalaCards
lung adenocarcinoma    adenocarcinoma    endometrial stromal sarcoma    multiple endocrine neoplasia
cervical cancer    sarcoma    renal cell carcinoma    cervicitis
alcoholism    neuroblastoma    colorectal cancer    lung cancer


MALAT1 for disorders           About GeneDecksing


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)
About This Section

PubMed articles for MALAT1 gene, integrated from 9 sources (see all 32):
(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 th e cerebellum, hippocampus and brain stem of human alcoholics. (PubMed id 22560368)1, 3 Kryger R....Jaquet V. (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....Muller-Tidow C. (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. (2000)
  4. Widespread purifying selection on RNA structure in mam mals. (PubMed id 23847102)1 Smith M.A....Mattick J.S. (2013)
  5. The noncoding RNA MALAT1 is a critical regulator of th e metastasis phenotype of lung cancer cells. (PubMed id 23243023)1 Gutschner T....Diederichs S. (2013)
  6. Inducing cell proliferation inhibition, apoptosis, and motility reduction by silencing long noncoding ribonucleic acid metastasis-asso ciated lung adenocarcinoma transcript 1 in urothelial carcinoma of the bladder. (PubMed id 23153939)1 Han Y....Cai Z. (2013)
  7. Long noncoding RNA MALAT1 controls cell cycle progress ion by regulating the expression of oncogenic transcription factor B-MYB. (PubMed id 23555285)1 Tripathi V....Prasanth K.V. (2013)
  8. Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. (PubMed id 22858678)1 Eismann M....Diederichs S. (2012)
  9. Long non-coding RNA MALAT-1 overexpression predicts tu mor recurrence of hepatocellular carcinoma after liver transplantation. (PubMed id 21678027)1 Lai M.C....Zheng S.S. (2012)
  10. Formation of triple-helical structures by the 3'-end s equences of MALAT1 and MENb noncoding RNAs. (PubMed id 23129630)1 Brown J.A....Steitz J.A. (2012)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 378938 HGNC: 29665 Ensembl:ENSG00000251562 euGenes: HUgn378938 ECgene: MALAT1
H-InvDB: MALAT1

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
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.)
About This Section
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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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transforming growth factor, beta 1
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The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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