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    LNCATV lncRNA negative regulator of antiviral signaling [ Homo sapiens (human) ]

    Gene ID: 101927851, updated on 10-Oct-2023

    Summary

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    Official Symbol
    LNCATVprovided by HGNC
    Official Full Name
    lncRNA negative regulator of antiviral signalingprovided by HGNC
    Primary source
    HGNC:HGNC:54478
    See related
    Ensembl:ENSG00000238005
    Gene type
    ncRNA
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See LNCATV in Genome Data Viewer
    Location:
    1q42.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (234957342..234963999, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (234348042..234354701, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (235093089..235099746, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985365 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2771 Neighboring gene Sharpr-MPRA regulatory region 4610 Neighboring gene Sharpr-MPRA regulatory region 12865 Neighboring gene RNY4 pseudogene 16 Neighboring gene GATA motif-containing MPRA enhancer 94/95 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:235017825-235017961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2772 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235034177-235035114 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:235048721-235049466 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:235049467-235050211 Neighboring gene RNA, 7SL, cytoplasmic 668, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235053443-235054122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:235056123-235056622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:235067947-235068447 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:235098512-235099711 Neighboring gene long intergenic non-protein coding RNA 2971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2779 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:235115282-235115785 Neighboring gene long intergenic non-protein coding RNA 3108 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:235122747-235123286 and GRCh37_chr1:235122207-235122746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:235123287-235123826 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:235133684-235134883 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2780 Neighboring gene Sharpr-MPRA regulatory region 4658 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2788 Neighboring gene Sharpr-MPRA regulatory region 5019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:235191005-235191504 Neighboring gene long intergenic non-protein coding RNA 1348

    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. A Human Long Non-coding RNA LncATV Promotes Virus Replication Through Restricting RIG-I-Mediated Innate Immunity. Fan J, et al. Front Immunol, 2019. PMID 31379885, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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

    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_125945.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BC016972
      Related
      ENST00000418557.1

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      234957342..234963999 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      234348042..234354701 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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