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    LINC00299 long intergenic non-protein coding RNA 299 [ Homo sapiens (human) ]

    Gene ID: 339789, updated on 10-Oct-2023

    Summary

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    Official Symbol
    LINC00299provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 299provided by HGNC
    Primary source
    HGNC:HGNC:27940
    See related
    Ensembl:ENSG00000236790 AllianceGenome:HGNC:27940
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    C2orf46; NCRNA00299
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    Location:
    2p25.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (8007771..8328419, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (8031814..8352337, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (8147901..8468549, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373409 Neighboring gene uncharacterized LOC101929551 Neighboring gene long intergenic non-protein coding RNA 298 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:8098775-8098955 Neighboring gene uncharacterized LOC124907727 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8160164-8160664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8160665-8161165 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8168595-8169096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8169097-8169596 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:8226605-8227804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8289994-8290494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8290495-8290995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8299141-8299642 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:8299609-8299785 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8329342-8329842 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:8333701-8334276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15252 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8393901-8394772 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:8403947-8404533 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8417861-8418362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8421562-8422062 Neighboring gene NANOG hESC enhancer GRCh37_chr2:8440800-8441356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15255 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8532754-8533299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8580531-8581030 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:8587230-8588429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8635675-8636175 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15260 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11124 Neighboring gene CRISPRi-validated cis-regulatory element chr2.183 Neighboring gene CRISPRi-validated cis-regulatory element chr2.184 Neighboring gene CRISPRi-validated cis-regulatory element chr2.185 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8683848-8684354 Neighboring gene Sharpr-MPRA regulatory region 11674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15268 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8684355-8684861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15265 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8712051-8712630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15272 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8723860-8724539 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:8724540-8725218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:8727462-8728114 Neighboring gene long intergenic non-protein coding RNA 1814 Neighboring gene uncharacterized LOC105373411 Neighboring gene SNRPE pseudogene 5

    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 intergenic noncoding RNA 299 methylation in peripheral blood is a biomarker for triple-negative breast cancer. Bermejo JL, et al. Epigenomics, 2019 Jan. PMID 30208740
    2. Disruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities. Talkowski ME, et al. Am J Hum Genet, 2012 Dec 7. PMID 23217328, Free PMC Article
    3. Long non-coding RNA LINC00299 knockdown inhibits ox-LDL-induced T/G HA-VSMC injury by regulating miR-135a-5p/XBP1 axis in atherosclerosis. Chang M, et al. Panminerva Med, 2022 Mar. PMID 32700888
    4. Linc00299/miR-490-3p/AURKA axis regulates cell growth and migration in atherosclerosis. Liu Y, et al. Heart Vessels, 2019 Aug. PMID 30734057
    5. A genome-wide association study of plasma total IgE concentrations in the Framingham Heart Study. Granada M, et al. J Allergy Clin Immunol, 2012 Mar. PMID 22075330, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Long non-coding RNA LINC00299 knockdown inhibits ox-LDL-induced T/G HA-VSMC injury by regulating miR-135a-5p/XBP1 axis in atherosclerosis.
      Title: Long non-coding RNA LINC00299 knockdown inhibits ox-LDL-induced T/G HA-VSMC injury by regulating miR-135a-5p/XBP1 axis in atherosclerosis.
    2. Expressions of Linc00299 and miR-490-3p were upregulated and downregulated in atherosclerosis patients, respectively.
      Title: Linc00299/miR-490-3p/AURKA axis regulates cell growth and migration in atherosclerosis.
    3. Hypermethylation of LINC00299 in peripheral blood may constitute a useful circulating biomarker for TNBC.
      Title: Long intergenic noncoding RNA 299 methylation in peripheral blood is a biomarker for triple-negative breast cancer.
    4. Disruption of LINC00299 in subjects with neurodevelopmental disabilities implicate this particular noncoding RNA in brain development and raise the possibility that, as a class, abnormalities of lincRNAs may play a significant role in human developmental disorders.
      Title: Disruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.
    EBI GWAS Catalog
    A genome-wide association study of plasma total IgE concentrations in the Framingham Heart Study.
    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

    Clone Names

    • FLJ45673

    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_034135.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC007464, AC092177
      Related
      ENST00000430192.5

    2. NR_152741.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC092177, U91324
      Related
      ENST00000442956.1

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      8007771..8328419 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      8031814..8352337 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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