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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

MALAT1 Gene

RNA gene GIFtS: 31
GCID: GC11P065266

metastasis associated lung adenocarcinoma transcript 1 (non-protein...

Explore 12 diseases affiliated with
MALAT1 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 6

Aliases
Metastasis Associated Lung Adenocarcinoma Transcript 1 (Non-Protein Coding)¹ ²		NCRNA00047¹ ²
HCN¹ ²		NEAT2¹ ²
LINC00047¹ ²		PRO1073¹ ⁵
MALAT-1¹ ²		PRO2853²

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

ORGUL members:	fRNAdb¹⁰:FR273624 FR077061
	NCBI:BK001411 BK001418
	NONCODE:n379853 n381725 n343070 n380683
	Rfam:RF01871
	RNAdb:LIT2013 LIT2012

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

Gene Wiki entry for MALAT1

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.

(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000011.9 NC_018922.1 NT_167190.1

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

Browse SwitchGear Promoter luciferase reporter plasmids

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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)

n343070
FR0273624
FR0077061
n380683
n381725
n379853
RF01871

lncRNA
undefined
Full Legend

65265232 65269828 65274423 chr11

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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 MOPED and PaxDb: --

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

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,
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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for MALAT1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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
Search CenterWatch for drugs/clinical trials and news about MALAT1

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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About This Section

Unigene Cluster for MALAT1:

Metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)

Hs.621695 [show with all ESTs]

Unigene Representative Sequence: EF177381

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 cDNA sequence:

AF001541.1 AF001542.1 AF113016.1 AJ535464.1 AJ535465.1 AJ535466.1 AK130345.1 AL050210.1

BC018448.1 BC025986.1 BC063689.1 BC104662.1 BX538238.1 BX640764.1 EF177381.1 FJ209305.1

NR_002819.2 X17272.1

24/360 DOTS entries (see all 360):

DT.91900579 DT.95351792 DT.91927045 DT.95291680 DT.100735204 DT.100735190 DT.95377975 DT.100061127

DT.91955986 DT.91925908 DT.100735117 DT.100735119 DT.97869937 DT.100735200 DT.95378317 DT.91905728

DT.99982642 DT.100735188 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)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: ACGCAGGGAG

About this image

MALAT1 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

Stem Cell Differentiation: 1 LifeMap Cell

Name

Category

White adipocyte-like cells (Differentiation of ...)

Adipose

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Genevestigator expression for MALAT1

SOURCE GeneReport for Unigene cluster: Hs.621695

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, UniProtKB, 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

SNP ID	Valid	Clinical significance	Chr 11 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs138334156^1,2	C,	--	65263234(+)	`AAAAA-/TTAT TTACG`	1	--	us2k¹		0	--	--	--	--
rs113637620^1,2	C,	--	65263287(+)	`GGATAC/TGGGAG`	1	--	us2k¹		1		NA	2
rs112829653^1,2		--	65263484(+)	`AGATCG/CAGACC`	1	--	us2k¹		1		CSA	2
rs140829378^1,2		--	65263505(+)	`ACACGA/GTGAAA`	1	--	us2k¹		0	--	--	--	--
rs192164487^1,2		--	65263600(+)	`GTGAAC/TTGCTT`	1	--	us2k¹		0	--	--	--	--
rs78901688^1,2	C	--	65263640(+)	`CGAGAC/TCCCGC`	1	--	us2k¹		0	--	--	--	--
rs200348803^1,2	C	--	65263702(-)	`TGTTTC/TTTTTT`	1	--	us2k¹		0	--	--	--	--
rs34634035^1,2	C,	--	65263819(+)	`AGAGC-/AGAGAGT`	1	--	us2k¹		0	--	--	--	--
rs200993639^1,2		--	65263824(+)	`AGAGA-/GTACAGA`	1	--	us2k¹		0	--	--	--	--
rs4102217^1,2	C,F,A,H,	--	65263895(+)	`TGCTGG/CAGAGG`	1	--	us2k¹		10		NS EA NA WA	748

HapMap Linkage Disequilibrium report for MALAT1 (65265233 - 65273940 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 2 variations for MALAT1
2 CNVs: 58533 65973

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(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.)
About This Section

MALAT1 for disorders           About GeneDecksing

OMIM gene information: 607924
12 diseases for MALAT1:    About MalaCards

lung adenocarcinoma adenocarcinoma multiple endocrine neoplasia endometrial stromal sarcoma

renal cell carcinoma sarcoma cervical cancer cervicitis

colorectal cancer lung cancer neuroblastoma carcinoma

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 23):
(articles sorted by number of sources associating them with MALAT1)

Utopia: connect your pdf to the dynamic
world of online information

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)
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)
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)
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)
Upregulated MALAT-1 contributes to bladder cancer cell migration by inducing epithelial-to-mesenchymal transition. (PubMed id 22722759)¹ Ying L....Qiu F. (2012)
The long noncoding MALAT-1 RNA indicates a poor progno sis in non-small cell lung cancer and induces migration and tumor growth. (PubMed id 22088988)¹ Schmidt L.H....Muller-Tidow C. (2011)
MALAT-1: a long non-coding RNA and its important 3' e nd functional motif in colorectal cancer metastasis. (PubMed id 21503572)¹ Xu C....Li Z. (2011)
RNA splicing control: yet another gene regulatory role for long nuclear noncoding RNAs. (PubMed id 21941126)¹ Zong X....Prasanth K.V. (2011)
ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. (PubMed id 22078878)¹ Yang L....Rosenfeld M.G. (2011)
Inhibition of metastasis-associated lung adenocarcino ma transcript 1 in CaSki human cervical cancer cells suppresses cell proliferat ion and invasion. (PubMed id 20213048)¹ Guo F....Li G. (2010)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
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

Name	Description
PharmGKB entry for MALAT1	Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for MALAT1	Genetics and Cytogenetics in Oncology and Haematology

Intellectual Property for MALAT1 gene
(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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, 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),
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MALAT1

	Browse SwitchGear 3'UTR luciferase reporter plasmids for MALAT1
	Browse SwitchGear Promoter luciferase reporter plasmids for MALAT1

Search ThermoFisher Antibodies for MALAT1

Search Vector BioLabs for ready-to-use adenovirus/AAV for human, mouse, rat MALAT1

GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

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

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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MALAT1 Gene

metastasis associated lung adenocarcinoma transcript 1 (non-protein...

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MALAT1 Gene

metastasis associated lung adenocarcinoma transcript 1 (non-protein...

Aliasesfor MALAT1 gene

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Proteinsfor MALAT1 gene

Protein Domains /Familiesfor MALAT1 gene

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Genome Databases showing MALAT1 gene

Other Databases showing MALAT1 gene

Specialized Databases showing MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene

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for MALAT1 gene