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NEAT1 Gene

RNA gene   GIFtS: 28
GCID: GC11P065190

Nuclear Paraspeckle Assembly Transcript 1 (Non-Protein Coding)

(Previous name: non-protein coding RNA 84)
(Previous symbol: NCRNA00084)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 3

Aliases
Nuclear Paraspeckle Assembly Transcript 1 (Non-Protein Coding)1 2     Virus Inducible Non-Coding RNA1
NCRNA000841 2 5     LINC000842
Long Intergenic Non-Protein Coding RNA 841     TncRNA2
Non-Protein Coding RNA 841     VINC2
Nuclear Enriched Abundant Transcript 11     TNCRNA5
Trophoblast Derived Non-Protein Coding RNA1     

External Ids:    HGNC: 308151   Entrez Gene: 2831312   Ensembl: ENSG000002455327   OMIM: 6127695   

Export aliases for NEAT1 gene to outside databases

Previous GC identifer: GC11U901304


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for NEAT1 Gene:
NEAT1 (nuclear paraspeckle assembly transcript 1 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class.

Gene Wiki entry for NEAT1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000011.9  NC_018922.2  NT_167190.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for NEAT1
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NEAT1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11q13.1   Ensembl cytogenetic band:  11q13.1   HGNC cytogenetic band: 11q13.1

NEAT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NEAT1 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P065190:  view genomic region     (about GC identifiers)

Start:
65,190,245 bp from pter      End:
65,213,011 bp from pter
Size:
22,767 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for NEAT1

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
LNCRNA: Long non-coding RNAs

  --

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Phenotypes:
     3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Neat1):
 cellular  digestive/alimentary  mortality/aging 

Find genes that share phenotypes with NEAT1           About GenesLikeMe

Animal Models:
     MGI mouse knock-out Neat1tm1.1Shna for NEAT1

   genOway: Develop your customized and physiologically relevant rodent model for NEAT1

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for NEAT1
Interactions:

    Search GeneGlobe Interaction Network for NEAT1

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for NEAT1



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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Unigene Cluster for NEAT1:

Nuclear paraspeckle assembly transcript 1 (non-protein coding)
Hs.523789  [show with all ESTs]
Unigene Representative Sequence: GQ859162
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000499732(lincRNA) ENST00000501122(lincRNA)(uc010rog.2) ENST00000384994(lincRNA) ENST00000601801(lincRNA)

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Additional mRNA sequence: 

AF001892.1 AF001893.1 AF080092.1 AF508303.1 AK027191.1 AL389939.1 BX647603.1 EF177379.1 
GQ859162.1 NR_028272.1 U60873.1 

Selected DOTS entries (see all 62):

DT.456041  DT.91771949  DT.100686364  DT.95309854  DT.75131871  DT.100817699  DT.100768840  DT.91683143 
DT.91766702  DT.95085140  DT.423643  DT.100817701  DT.75135835  DT.92411884  DT.120708179  DT.120708185 
DT.95309887  DT.100686370  DT.120708188  DT.91763350  DT.100686371  DT.120708187  DT.75179848  DT.100671020 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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Expression evidence for NEAT1:none

NEAT1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TACATAATTA
NEAT1 Expression
About this image


NEAT1 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 5) fully expand
 
 Kidney (Urinary System)    fully expand to see all 2 entries
         Renal Collecting Duct System
 
 Fibroblasts
         Detroit 551
 
 Epidermis (Integumentary System)
         Detroit 551
 
 Bone (Muscoskeletal System)
         Mandibular Condyle
 
 Blood (Hematopoietic System)
         Hematopoietic Stem Cells Hematopoietic Bone Marrow
NEAT1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.523789
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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and mouse.

Orthologs for NEAT1 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Neat15 nuclear paraspeckle assembly transcript 1 (non-protein more   --   19 (4.34 cM) 5824708 


ENSEMBL Gene Tree for NEAT1 (if available)
TreeFam Gene Tree for NEAT1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for NEAT1 (see all 116)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 11 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs6744001,2
C,H--65188327(-) GGCCAA/TGGTGG 1 -- us2k19Minor allele frequency- T:0.08NA WA CSA 132
rs734843731,2
C--65188375(+) AAAATG/CTACCA 1 -- us2k11Minor allele frequency- C:0.50WA 2
rs1808981971,2
C--65188429(+) AGATTC/TCGAGA 1 -- us2k10--------
rs1864325431,2
--65188903(+) CCTGCC/TTGCTG 1 -- us2k10--------
rs1911674681,2
--65189108(+) GGGCCA/GGAGCT 1 -- us2k10--------
rs1144780511,2
C,F--65189307(+) TCACCT/CTTCTC 1 -- us2k11Minor allele frequency- C:0.03WA 118
rs1816408921,2
--65189391(+) TATCTC/TGGTTT 1 -- us2k10--------
rs1116850981,2
C--65189438(+) ATCCTA/GAACAC 1 -- us2k10--------
rs610598751,2
C,F--65189512(+) CCCCTG/AGGAAG 1 -- us2k11Minor allele frequency- A:0.09WA 118
rs1868553921,2
--65189556(+) CGCGCA/GGCTCC 1 -- us2k10--------

HapMap Linkage Disequilibrium report for NEAT1 (65190245 - 65213011 bp)

Structural Variations
     Database of Genomic Variants (DGV) 6 variations for NEAT1:    About this table    
Variant IDTypeSubtypePubMed ID
esv2422285CNV Deletion17116639
nsv897717CNV Loss21882294
nsv897719CNV Loss21882294
dgv1175n71CNV Loss21882294
nsv897718CNV Loss21882294
nsv526181CNV Gain19592680

Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 612769    OMIM disorders: --


Find genes that share disorders with NEAT1           About GenesLikeMe

Genetic Association Database (GAD): NEAT1

Export disorders for NEAT1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for NEAT1 gene, integrated from 10 sources (see all 14):
(articles sorted by number of sources associating them with NEAT1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Human trophoblast noncoding RNA suppresses CIITA promoter III activity in murine B-lymphocytes. (PubMed id 12565840)1, 3 Geirsson A....Hammond G.L. (Biochem. Biophys. Res. Commun. 2003)
  2. Repression of major histocompatibility complex genes by a human trophoblast ribonucleic acid. (PubMed id 9858482)1, 3 Peyman J.A. (Biol. Reprod. 1999)
  3. A transcript map for the 2.8-Mb region containing the multiple endocrine neoplasia type 1 locus. (PubMed id 9253601)1, 3 Guru S.C.... Chandrasekharappa S.C. (Genome Res. 1997)
  4. The long non-coding RNA nuclear-enriched abundant transcript 1_2 induces paraspeckle formation in the motor neuron during the early phase of amyotrophic lateral sclerosis. (PubMed id 23835137)1 Nishimoto Y....Okano H. (Mol Brain 2013)
  5. NEAT1 long noncoding RNA and paraspeckle bodies modulate HIV-1 posttranscriptional expression. (PubMed id 23362321)1 Zhang Q....Jeang K.T. (MBio 2013)
  6. Alternative 3'-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. (PubMed id 22960638)1 Naganuma T....Hirose T. (EMBO J. 2012)
  7. Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. (PubMed id 21170033)1 Mao Y.S....Spector D.L. (Nat. Cell Biol. 2011)
  8. LSINCT5 is over expressed in breast and ovarian cancer and affects cellular proliferation. (PubMed id 21532345)1 Silva J.M....Smith D.I. (RNA Biol 2011)
  9. Highly ordered spatial organization of the structural long noncoding NEAT1 RNAs within paraspeckle nuclear bodies. (PubMed id 20881053)1 Souquere S....Pierron G. (Mol. Biol. Cell 2010)
  10. A genome-wide association study of optic disc parameters. (PubMed id 20548946)4 Ramdas W.D....van Duijn C.M. (PLoS Genet. 2010)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 283131 HGNC: 30815 Ensembl:ENSG00000245532 euGenes: HUgn283131 ECgene: NEAT1
H-InvDB: NEAT1

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for NEAT1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for NEAT1 gene:
Search GeneIP for patents involving NEAT1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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