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

Gene ID: 378938, updated on 16-Apr-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
Ensembl:ENSG00000251562 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
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Genomic context

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Location:
11q13.1
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (65497738..65506516)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65491042..65499820)
105.20220307 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
  • 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. Long noncoding RNA MALAT1 is dynamically regulated in leader cells during collective cancer invasion. Zhu N, et al. Proc Natl Acad Sci U S A, 2023 Jul 4. PMID 37364126, Free PMC Article
  2. Long Noncoding RNA Metastasis-Associated Lung Adenocarcinoma Transcript 1 Promotes HIV-1 Replication through Modulating microRNAs in Macrophages. Yuan Z, et al. J Virol, 2023 Jun 29. PMID 37255470, Free PMC Article
  3. Deconstructing the role of MALAT1 in MAPK-signaling in melanoma: insights from antisense oligonucleotide treatment. Feichtenschlager V, et al. Oncotarget, 2023 May 26. PMID 37235843, Free PMC Article
  4. Haplotype-GGGT in long non-coding RNA MALAT1 inhibits brain metastatic lung cancer and lymph nodes of lung cancer via the MALAT1/miR-328/KATNB1. Liu T, et al. Aging (Albany NY), 2023 Mar 2. PMID 36934373, Free PMC Article
  5. LncRNA-MALAT1: A Key Participant in the Occurrence and Development of Cancer. Hao L, et al. Molecules, 2023 Feb 24. PMID 36903369, Free PMC Article

See all (637) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Evaluation of the clinical significance of long non-coding RNA MALAT1 genetic variants in human lung adenocarcinoma.
    Title: Evaluation of the clinical significance of long non-coding RNA MALAT1 genetic variants in human lung adenocarcinoma.
  2. MALAT1 DEREPRESSES MIR-433-3P-MEDIATED RPTOR SUPPRESSION TO IMPAIR AUTOPHAGY AND DRIVE PYROPTOSIS IN ENDOTOXEMIA.
    Title: MALAT1 DEREPRESSES MIR-433-3P-MEDIATED RPTOR SUPPRESSION TO IMPAIR AUTOPHAGY AND DRIVE PYROPTOSIS IN ENDOTOXEMIA.
  3. Long noncoding RNA Malat1 protects against osteoporosis and bone metastasis.
    Title: Long noncoding RNA Malat1 protects against osteoporosis and bone metastasis.
  4. Expression and diagnostic value of lncRNA MALAT1 and NLRP3 in lower limb atherosclerosis in diabetes.
    Title: Expression and diagnostic value of lncRNA MALAT1 and NLRP3 in lower limb atherosclerosis in diabetes.
  5. MALAT1 expression in granulosa cells in PCOS patients with different phenotypes.
    Title: MALAT1 expression in granulosa cells in PCOS patients with different phenotypes.
  6. Suppression of MALAT1 promotes human synovial mesenchymal stem cells enhance chondrogenic differentiation and prevent osteoarthritis of the knee in a rat model via regulating miR-212-5p/MyD88 axis.
    Title: Suppression of MALAT1 promotes human synovial mesenchymal stem cells enhance chondrogenic differentiation and prevent osteoarthritis of the knee in a rat model via regulating miR-212-5p/MyD88 axis.
  7. The lncRNAs Gas5, MALAT1 and SNHG8 as diagnostic biomarkers for epithelial malignant pleural mesothelioma in Egyptian patients.
    Title: The lncRNAs Gas5, MALAT1 and SNHG8 as diagnostic biomarkers for epithelial malignant pleural mesothelioma in Egyptian patients.
  8. Effects of the lncRNA MALAT1 gene region rs664589 site mutation on acute myocardial infarction in Chinese Han.
    Title: Effects of the lncRNA MALAT1 gene region rs664589 site mutation on acute myocardial infarction in Chinese Han.
  9. Mechanistic actions of long non-coding RNA MALAT1 within the ovary and at the feto-maternal interface.
    Title: Mechanistic actions of long non-coding RNA MALAT1 within the ovary and at the feto-maternal interface.
  10. Pleomorphic adenoma with extensive squamous and mucinous metaplasia and a novel MALAT1::PLAG1 fusion gene.
    Title: Pleomorphic adenoma with extensive squamous and mucinous metaplasia and a novel MALAT1::PLAG1 fusion gene.
Submit: New GeneRIF Correction See all GeneRIFs (637)

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 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 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_002819.4 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the unspliced, longest transcript.
    Source sequence(s)
    AI805768, CA394984, EF177381
    Related
    ENST00000534336.3

  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_2023_10

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

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Chemical Information
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Research Materials