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Aliases for MALAT1 Gene

Subcategory (RNA class) for MALAT1 Gene

non-coding RNA

Quality Score for this RNA gene is


Aliases for MALAT1 Gene

  • Metastasis Associated Lung Adenocarcinoma Transcript 1 2 3
  • Metastasis Associated Lung Adenocarcinoma Transcript 1 (Non-Protein Coding) 2 3 5
  • Nuclear Paraspeckle Assembly Transcript 2 (Non-Protein Coding) 2 3
  • Long Intergenic Non-Protein Coding RNA 47 2 3
  • Nuclear Enriched Abundant Transcript 2 2 3
  • Hepcarcin 2 3
  • Metastasis Associated In Lung Adenocarcinoma Transcript 1 2
  • Non-Protein Coding RNA 47 2
  • NCRNA00047 3
  • LINC00047 3
  • PRO2853 3
  • NEAT2 3
  • HCN 3

External Ids for MALAT1 Gene

Previous GeneCards Identifiers for MALAT1 Gene

  • GC11P065032
  • GC11U900628
  • GC11P065266
  • GC11P061592

Summaries for MALAT1 Gene

Entrez Gene Summary for MALAT1 Gene

  • This gene produces a precursor transcript from which a long non-coding RNA is derived by RNase P cleavage of a tRNA-like small ncRNA (known as mascRNA) from its 3' end. The resultant mature transcript lacks a canonical poly(A) tail but is instead stabilized by a 3' triple helical structure. This transcript is retained in the nucleus where it is thought to form molecular scaffolds for ribonucleoprotein complexes. It may act as a transcriptional regulator for numerous genes, including some genes involved in cancer metastasis and cell migration, and it is involved in cell cycle regulation. Its upregulation in multiple cancerous tissues has been associated with the proliferation and metastasis of tumor cells. [provided by RefSeq, Mar 2015]

GeneCards Summary for MALAT1 Gene

MALAT1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) is an RNA Gene, and is affiliated with the non-coding RNA class. Diseases associated with MALAT1 include Tongue Cancer and Leukemia, Acute Monocytic.

Gene Wiki entry for MALAT1 Gene

Additional gene information for MALAT1 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for MALAT1 Gene

Genomics for MALAT1 Gene

GeneHancer (GH) Regulatory Elements for MALAT1 Gene

Promoters and enhancers for MALAT1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J065567 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 19.5 +76.0 75986 12 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 SSSCA1 EHBP1L1 FAM89B SF1 POLA2 LOC105369352 PCNX3 EIF1AD KAT5 MUS81
GH11J065470 Promoter/Enhancer 2.9 VISTA FANTOM5 Ensembl ENCODE dbSUPER 10.3 -7.6 -7604 40 CLOCK MLX ZFP64 FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 LOC105369346 SF1 POLA2 PCNX3 ZFPL1 EIF1AD SART1 LOC105369352 MUS81 KAT5
GH11J065377 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10 -115.2 -115206 10.3 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 ZNF143 ZNF263 SP3 FRMD8 SLC25A45 SF1 PCNX3 MUS81 POLA2 SART1 ZFPL1 ENSG00000255320 EIF1AD
GH11J065886 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.9 +397.8 397770 18.4 CLOCK ZFP64 FEZF1 DMAP1 YY1 SLC30A9 E2F8 ZNF143 ZNF263 SP3 FOSL1 FIBP DRAP1 RBM14 ENSG00000258297 KAT5 MUS81 SART1 SF3B2 RBM4
GH11J066342 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.9 +850.9 850857 11.8 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 LOC102724064 B4GAT1 TRS-GCT3-1 RBM14 ENSG00000258297 LOC105369352 RBM4 EIF1AD RIN1 ENSG00000255320
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MALAT1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the MALAT1 gene promoter:
  • Nkx2-5
  • deltaCREB
  • CREB
  • SREBP-1a
  • SREBP-1c
  • SREBP-1b
  • CBF(2)
  • NF-Y
  • FOXO1
  • FOXO1a

Genomic Locations for MALAT1 Gene

Genomic Locations for MALAT1 Gene
8,829 bases
Plus strand
8,708 bases
Plus strand

Genomic View for MALAT1 Gene

Genes around MALAT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MALAT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MALAT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MALAT1 Gene

Proteins for MALAT1 Gene

Post-translational modifications for MALAT1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for MALAT1 Gene

Domains & Families for MALAT1 Gene

Gene Families for MALAT1 Gene

Suggested Antigen Peptide Sequences for MALAT1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with MALAT1: view

No data available for Protein Domains and UniProtKB/Swiss-Prot for MALAT1 Gene

Function for MALAT1 Gene

Phenotypes From GWAS Catalog for MALAT1 Gene

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MALAT1

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for MALAT1 Gene

Localization for MALAT1 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for MALAT1 gene
Compartment Confidence
plasma membrane 2
extracellular 2
nucleus 2
cytosol 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for MALAT1 Gene

Pathways & Interactions for MALAT1 Gene

SuperPathways for MALAT1 Gene

No Data Available

Interacting Proteins for MALAT1 Gene

Gene Ontology (GO) - Biological Process for MALAT1 Gene


No data available for Pathways by source and SIGNOR curated interactions for MALAT1 Gene

Drugs & Compounds for MALAT1 Gene

(1) Drugs for MALAT1 Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Platinum compounds Pharma 0
genes like me logo Genes that share compounds with MALAT1: view

Transcripts for MALAT1 Gene

mRNA/cDNA for MALAT1 Gene

(18) Additional mRNA sequences :
(17) Ensembl transcripts including schematic representations, and UCSC links where relevant :
(20) RNA Central transcripts :

Unigene Clusters for MALAT1 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MALAT1

Alternative Splicing Database (ASD) splice patterns (SP) for MALAT1 Gene

No ASD Table

Relevant External Links for MALAT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for MALAT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for MALAT1 Gene

NURSA nuclear receptor signaling pathways regulating expression of MALAT1 Gene:


SOURCE GeneReport for Unigene cluster for MALAT1 Gene:


Evidence on tissue expression from TISSUES for MALAT1 Gene

  • Nervous system(2.2)
  • Heart(2.1)
genes like me logo Genes that share expression patterns with MALAT1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for MALAT1 Gene

Orthologs for MALAT1 Gene

Evolution for MALAT1 Gene

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

No data available for Orthologs for MALAT1 Gene

Paralogs for MALAT1 Gene

No data available for Paralogs for MALAT1 Gene

Variants for MALAT1 Gene

Sequence variations from dbSNP and Humsavar for MALAT1 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000379526 -- 65,499,088(+) G/A non_coding_transcript_variant
rs1000567968 -- 65,499,663(+) A/G non_coding_transcript_variant
rs1000803626 -- 65,503,861(+) G/A non_coding_transcript_variant
rs1001077875 -- 65,504,195(+) CC/C non_coding_transcript_variant
rs1001130007 -- 65,504,084(+) A/G non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for MALAT1 Gene

Variant ID Type Subtype PubMed ID
esv23728 CNV loss 19812545
nsv555210 CNV gain 21841781
nsv555211 CNV loss 21841781
nsv820139 CNV loss 19587683
nsv825951 CNV gain 20364138

Additional Variant Information for MALAT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for MALAT1 Gene

Disorders for MALAT1 Gene

MalaCards: The human disease database

(74) MalaCards diseases for MALAT1 Gene - From: LncRNADisease, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
tongue cancer
  • malignant neoplasm of anterior 2/3 of tongue
leukemia, acute monocytic
  • acute monocytic leukemia
uterine corpus endometrial stromal sarcoma
  • uterine corpus endometrial stromal tumor
histiocytoid hemangioma
  • angiolymphoid hyperplasia with eosinophilia
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for MALAT1

genes like me logo Genes that share disorders with MALAT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MALAT1 Gene

Publications for MALAT1 Gene

  1. Disrupting MALAT1/miR-200c sponge decreases invasion and migration in endometrioid endometrial carcinoma. (PMID: 27693631) Li Q … Jiang Q (Cancer letters 2016) 2 3 58
  2. MALAT-1, a non protein-coding RNA is upregulated in the cerebellum, hippocampus and brain stem of human alcoholics. (PMID: 22560368) Kryger R … Jaquet V (Alcohol (Fayetteville, N.Y.) 2012) 2 3 58
  3. MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. (PMID: 12970751) Ji P … Müller-Tidow C (Oncogene 2003) 2 3 58
  4. Long non-coding RNA MALAT1 promotes oral squamous cell carcinoma development via microRNA-125b/STAT3 axis. (PMID: 28926115) Chang SM … Hu WW (Journal of cellular physiology 2018) 3 58
  5. Association analyses of genetic variants in long non-coding RNA MALAT1 with breast cancer susceptibility and mRNA expression of MALAT1 in Chinese Han population. (PMID: 29146194) Peng R … Song C (Gene 2018) 3 58

Products for MALAT1 Gene

Sources for MALAT1 Gene

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