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Aliases for MALAT1 Gene

Subcategory (RNA class) for MALAT1 Gene


Quality Score for this RNA gene is


Aliases for MALAT1 Gene

  • Metastasis Associated Lung Adenocarcinoma Transcript 1 (Non-Protein Coding) 2 3
  • 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
  • MALAT1-Associated Small Cytoplasmic RNA 3
  • Non-Protein Coding RNA 47 2
  • NCRNA00047 3
  • LINC00047 3
  • PRO2853 3
  • MascRNA 3
  • PRO1073 6
  • 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 (Non-Protein Coding)) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with MALAT1 include undifferentiated embryonal sarcoma of the liver and adenocarcinoma.

Gene Wiki entry for MALAT1 Gene

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

Genomics for MALAT1 Gene

Regulatory Elements for MALAT1 Gene

Genomic Location for MALAT1 Gene

65,497,762 bp from pter
65,506,516 bp from pter
8,755 bases
Plus strand

Genomic View for MALAT1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for MALAT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MALAT1 Gene

Proteins for MALAT1 Gene

  • Protein details for MALAT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Metastasis-associated lung adenocarcinoma transcript 1
    Protein Accession:
    Secondary Accessions:

    Protein attributes for MALAT1 Gene

    57 amino acids
    Molecular mass:
    6289 Da
    Quaternary structure:
    No Data Available

neXtProt entry for MALAT1 Gene

Proteomics data for MALAT1 Gene at MOPED

Post-translational modifications for MALAT1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for MALAT1 Gene

Domains for MALAT1 Gene

Gene Families for MALAT1 Gene

Protein Domains 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 UniProtKB/Swiss-Prot for MALAT1 Gene

Function for MALAT1 Gene

Phenotypes for MALAT1 Gene

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

Animal Models for MALAT1 Gene

MGI Knock Outs for MALAT1:

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , miRNA , Transcription Factor Targeting and HOMER Transcription for MALAT1 Gene

Localization for MALAT1 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS and Gene Ontology (GO) - Cellular Components for MALAT1 Gene

Pathways 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 for MALAT1 Gene

Transcripts for MALAT1 Gene

mRNA/cDNA for MALAT1 Gene

(18) Additional mRNA sequences :
(19) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for MALAT1 Gene

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

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 for MALAT1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

SOURCE GeneReport for Unigene cluster for MALAT1 Gene Hs.621695

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

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

In Situ Assay Products

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , mRNA Expression by UniProt/SwissProt and Expression partners for MALAT1 Gene

Orthologs for MALAT1 Gene

This gene was present in the common ancestor of human and mouse.

Orthologs for MALAT1 Gene

Organism Taxonomy Gene Similarity Type Details
(Mus musculus)
Mammalia Malat1 16
Species with no ortholog for MALAT1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for MALAT1 Gene

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

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 Sequence Context AA Info Type MAF
rs591291 -- 65,497,011(+) GGTTC(C/T)AAAGA upstream-variant-2KB
rs619586 -- 65,498,698(+) TACCT(A/G)CTGTC nc-transcript-variant
rs643125 -- 65,506,143(+) TGGTT(C/T)CCAGG nc-transcript-variant
rs650324 -- 65,500,998(+) ATGGC(A/C)AGTTT nc-transcript-variant
rs656605 -- 65,506,800(+) TTGAG(A/G)CAGTC downstream-variant-500B

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

Variant ID Type Subtype PubMed ID
dgv1175n71 CNV Loss 21882294
nsv897717 CNV Loss 21882294
nsv897718 CNV Loss 21882294
nsv897719 CNV Loss 21882294
nsv897720 CNV Loss 21882294
esv23728 CNV Loss 19812545
nsv825951 CNV Gain 20364138
nsv820139 CNV Loss 19587683

Relevant External Links for MALAT1 Gene

HapMap Linkage Disequilibrium report

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

Disorders for MALAT1 Gene

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

No data available for OMIM , UniProtKB/Swiss-Prot , University of Copenhagen DISEASES , Novoseek inferred disease relationships , Genatlas and External Links for MALAT1 Gene

Publications for MALAT1 Gene

  1. 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 2012) 2 3
  2. 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. … MA1ller-Tidow C. (Oncogene 2003) 2 3
  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. (PMID: 10843802) van Asseldonk M. … Geurts van Kessel A. (Genomics 2000) 3 4
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 3
  5. Upregulation of the transcription factor TFEB in t(6;11)(p21;q13)- positive renal cell carcinomas due to promoter substitution. (PMID: 12837690) Kuiper R.P. … Geurts van Kessel A. (Hum. Mol. Genet. 2003) 3

Products for MALAT1 Gene

Sources for MALAT1 Gene

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