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Malat1 Gene Detail
Summary
  • Symbol
    Malat1
  • Name
    metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA)
  • Synonyms
    2210401K01Rik, 9430072K23Rik, NEAT2
  • Feature Type
    lncRNA gene
  • IDs
    MGI:1919539
    NCBI Gene: 72289
  • Alliance
  • Transcription Start Sites
    55 TSS
Location &
Maps
more
  • Sequence Map
    Chr19:5845718-5852700 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
  • Genetic Map
    Chromosome 19, 4.34 cM
  • Mapping Data
    2 experiments
Strain
Comparison
more
  • SNPs within 2kb
    200 from dbSNP Build 142
  • Strain Annotations
    19
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1919539
lncRNA gene Chr19:5845717-5853602 (-)
129S1/SvImJ ENSMUSG00200053393
lncRNA gene Chr19:2608061-2615048 (-)
A/J ENSMUSG00195053958
lncRNA gene Chr19:3003448-3010435 (-)
AKR/J ENSMUSG00220050842
lncRNA gene Chr19:2776571-2783558 (-)
BALB/cJ ENSMUSG00180051598
lncRNA gene Chr19:3378156-3385143 (-)
C3H/HeJ ENSMUSG00175014708
lncRNA gene Chr19:2628353-2635340 (-)
C57BL/6NJ ENSMUSG00215047205
lncRNA gene Chr19:2846274-2853261 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0005280
lincRNA gene Chr19:2542262-2549261 (-)
CAST/EiJ ENSTCUG00005043968
lncRNA gene Chr19:2765012-2772005 (-)
CBA/J ENSMUSG00210050645
lncRNA gene Chr19:2631128-2638115 (-)
DBA/2J ENSMUSG00185053434
lncRNA gene Chr19:3007612-3014599 (-)
FVB/NJ ENSMUSG00205053257
lncRNA gene Chr19:3013839-3020827 (-)
JF1/MsJ ENSUMUG00000056958
lncRNA gene Chr19:2983678-2990650 (-)
LP/J ENSMUSG00230054303
lncRNA gene Chr19:3914960-3921947 (-)
NOD/ShiLtJ ENSMUSG00190051894
lncRNA gene Chr19:2537956-2544943 (-)
NZO/HlLtJ ENSMUSG00225026834
lncRNA gene Chr19:7623706-7630693 (-)
PWK/PhJ ENSLUMG00010008196
lncRNA gene Chr19:2749896-2756877 (-)
SPRET/EiJ ENSMSPG00010050690
lncRNA gene Chr19:2739904-2746893 (-)
WSB/EiJ ENSIUOG00005051913
lncRNA gene Chr19:2646020-2653007 (-)



Homology
more
  • Human Ortholog
    MALAT1, metastasis associated lung adenocarcinoma transcript 1
  • Vertebrate Orthologs
    1
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    MALAT1, metastasis associated lung adenocarcinoma transcript 1
  • Synonyms
    HCN, LINC00047, miPEP-52, NCRNA00047, NEAT2, PRO2853
  • Links
    NCBI Gene ID: 378938

  • Chr Location
    11q13.1; chr11:65497606-65508073 (+)  GRCh38

Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    6 phenotypes from 1 allele in 2 genetic backgrounds
    35 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Mice homozygous for a knock-out allele exhibit increased susceptibility to ischemic brain injury with increased cerebral infarction size, worse neurological scores and sensorimotor dysfunction, and increased expression of proapoptotic and proinflammatory factors in brain than wild-type controls.
Expression
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Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
  • Tissues
  • cDNA Data
  • Literature Summary
  • Comparison Matrix
  • Sequences &
    Gene Models
    less
    • All Sequences
    • RefSeq
    • UniProt
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 72289 NCBI Gene Model | MGI Sequence Detail 6983 C57BL/6J ±  kb
    transcript NR_002847 RefSeq | MGI Sequence Detail 6983 C57BL/6  
    polypeptide B0LAE7 UniProt | EBI | MGI Sequence Detail 10 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      1 Sequence
    Molecular
    Reagents
    less
    • All nucleic 25
      cDNA 17
      Primer pair 3
      Other 5

      Microarray probesets 6
    Other
    Accession IDs
    less
    MGI:1924542, MGI:2147588
    References
    more
    • Summaries
      All 88
      Developmental Gene Expression 14
      Phenotypes 35
    • Earliest
      J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
    • Latest
      J:378425 Sueblinvong V, et al., Long Non-Coding RNA MALAT1 Regulates HMOX1 in Sickle Cell Disease-Associated Pulmonary Hypertension. Cells. 2026 Jan 15;15(2)

    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
    Citing These Resources
    Funding Information
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    last database update
    09/01/2026
    MGI 6.24
    The Jackson Laboratory