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    MALAT1 metastasis associated lung adenocarcinoma transcript 1 [ Homo sapiens (human) ]

    Gene ID: 378938, updated on 5-Nov-2024

    Summary

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    Official Symbol
    MALAT1provided by HGNC
    Official Full Name
    metastasis associated lung adenocarcinoma transcript 1provided by HGNC
    Primary source
    HGNC:HGNC:29665
    See related
    MIM:607924; AllianceGenome:HGNC:29665
    Gene type
    ncRNA
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HCN; NEAT2; PRO2853; LINC00047; NCRNA00047
    Summary
    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]
    Expression
    Ubiquitous expression in bone marrow (RPKM 137.2), thyroid (RPKM 115.3) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See MALAT1 in Genome Data Viewer
    Location:
    11q13.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (65497738..65506516)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65491042..65499820)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (65265209..65273987)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene NEAT1-MALAT1 intergenic CAGE-defined high expression enhancer Neighboring gene CRISPRi-validated cis-regulatory element chr11.3247 Neighboring gene NEAT1-MALAT1 intergenic CAGE-defined low expression enhancer Neighboring gene enhancer lncRNA neighbor of NEAT1 and MALAT1 Neighboring gene VISTA enhancer hs1759 Neighboring gene long intergenic non-protein coding RNA 2736 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:65259133-65259634 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65260440-65260950 Neighboring gene Sharpr-MPRA regulatory region 14387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4977 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:65264508-65265707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4983 Neighboring gene TALAM1 transcript, MALAT1 antisense RNA Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4984 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:65274865-65275546 Neighboring gene MALAT1-associated small cytoplasmic RNA Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 19 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3529 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:65297753-65297921 Neighboring gene SCY1 like pseudokinase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65305475-65305979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65305980-65306483 Neighboring gene latent transforming growth factor beta binding protein 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Inhibition of MALAT1 reduces tumor growth and metastasis and promotes drug sensitivity in colorectal cancer. Tang D, et al. Cell Signal, 2019 May. PMID 30716387
    2. MALAT1-miR663a negative feedback loop in colon cancer cell functions through direct miRNA-lncRNA binding. Tian W, et al. Cell Death Dis, 2018 Aug 28. PMID 30154407, Free PMC Article
    3. Downregulated MALAT1 relates to recurrent pregnancy loss via sponging miRNAs. Wang Y, et al. Kaohsiung J Med Sci, 2018 Sep. PMID 30173780
    4. [Long chain non-coding RNA MALAT-1 gene knockdown inhibits growth and migration and promotes apoptosis of human laryngeal squamous cell carcinoma Hep-2 cells in vitro]. Han Y, et al. Nan Fang Yi Ke Da Xue Xue Bao, 2018 Jul 30. PMID 30187883, Free PMC Article
    5. Long non-coding RNA MALAT1 mediates hypoxia-induced pro-survival autophagy of endometrial stromal cells in endometriosis. Liu H, et al. J Cell Mol Med, 2019 Jan. PMID 30324652, Free PMC Article

    See all (683) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association between IL-6, miRNA-146a, MALAT1 genetic polymorphisms and risk of rheumatoid arthritis.
      Title: Association between IL-6, miRNA-146a, MALAT1 genetic polymorphisms and risk of rheumatoid arthritis.
    2. MALAT1/miR-7-5p/TCF4 Axis Regulating Menstrual Blood Mesenchymal Stem Cells Improve Thin Endometrium Fertility by the Wnt Signaling Pathway.
      Title: MALAT1/miR-7-5p/TCF4 Axis Regulating Menstrual Blood Mesenchymal Stem Cells Improve Thin Endometrium Fertility by the Wnt Signaling Pathway.
    3. Relationship between lncRNA MALAT1 and Chemo-radiotherapy Resistance of Cancer Cells: Uncovered Truths.
      Title: Relationship between lncRNA MALAT1 and Chemo-radiotherapy Resistance of Cancer Cells: Uncovered Truths.
    4. Silencing the long noncoding RNA MALAT1 inhibits vitreous-induced epithelial-mesenchymal transition in RPE cells by regulating the PDGFRs/AKT axis.
      Title: Silencing the long noncoding RNA MALAT1 inhibits vitreous-induced epithelial-mesenchymal transition in RPE cells by regulating the PDGFRs/AKT axis.
    5. LncRNA MALAT1 regulates cigarette smoke induced airway inflammation by modulating miR-30a-5p/JNK signaling pathway.
      Title: LncRNA MALAT1 regulates cigarette smoke induced airway inflammation by modulating miR-30a-5p/JNK signaling pathway.
    6. LncRNA MALAT1 Expression Regulates Breast Cancer Progression via PI3K/AKT/mTOR Pathway Modulation.
      Title: LncRNA MALAT1 Expression Regulates Breast Cancer Progression via PI3K/AKT/mTOR Pathway Modulation.
    7. LncRNA MALAT1 promotes osteogenic differentiation through the miR-93-5p/SMAD5 axis.
      Title: LncRNA MALAT1 promotes osteogenic differentiation through the miR-93-5p/SMAD5 axis.
    8. The Long Non-Coding RNA MALAT1 Modulates NR4A1 Expression through a Downstream Regulatory Element in Specific Cancer Cell Types.
      Title: The Long Non-Coding RNA MALAT1 Modulates NR4A1 Expression through a Downstream Regulatory Element in Specific Cancer Cell Types.
    9. Long Non-Coding RNA MALAT1 Protects Against Spinal Cord Injury via Suppressing microRNA-125b-5p Mediated Microglial M1 Polarization, Neuroinflammation, and Neural Apoptosis.
      Title: Long Non-Coding RNA MALAT1 Protects Against Spinal Cord Injury via Suppressing microRNA-125b-5p Mediated Microglial M1 Polarization, Neuroinflammation, and Neural Apoptosis.
    10. M2 Tumor-Associated Macrophages-Derived Exosomal MALAT1 Promotes Glycolysis and Gastric Cancer Progression.
      Title: M2 Tumor-Associated Macrophages-Derived Exosomal MALAT1 Promotes Glycolysis and Gastric Cancer Progression.
    Submit: New GeneRIF Correction See all GeneRIFs (648)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Other Names

    • hepcarcin
    • long intergenic non-protein coding RNA 47
    • metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)
    • nuclear enriched abundant transcript 2
    • nuclear paraspeckle assembly transcript 2 (non-protein coding)

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin-protein adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables miRNA inhibitor activity via base-pairing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to hypoxia IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lncRNA-mediated post-transcriptional gene silencing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of cardiac muscle myoblast proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of cell motility IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of miRNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    RNA

    1. NR_002819.5 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the unspliced transcript.
      Source sequence(s)
      AP000769

    2. NR_144567.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also known as long) lacks an alternate segment in the 5' region compared to variant 1.
      Source sequence(s)
      AI805768, BK001418, CA394984, EF177381

    3. NR_144568.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3, also known as short) lacks two alternate segments compared to variant 1.
      Source sequence(s)
      AI805768, BK001411, CA394984, EF177381

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      65497738..65506516
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      65491042..65499820
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

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    Research Materials