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    LINC02476 long intergenic non-protein coding RNA 2476 [ Homo sapiens (human) ]

    Gene ID: 105375475, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LINC02476provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 2476provided by HGNC
    Primary source
    HGNC:HGNC:53419
    See related
    Ensembl:ENSG00000225546 AllianceGenome:HGNC:53419
    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
    LVCAT5; lnc-TSPAN12
    Expression
    Low expression observed in reference dataset See more
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    Genomic context

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    See LINC02476 in Genome Data Viewer
    Location:
    7q31.31
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (119619430..119907375, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (120934798..121222805, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (119259484..119547429, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak6703 silencer Neighboring gene eukaryotic translation initiation factor 3 subunit I pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:118740781-118741369 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:118850550-118851050 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:118851051-118851551 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:118947178-118947344 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:119067491-119067992 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:119067993-119068492 Neighboring gene uncharacterized LOC124901816 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:119184748-119185947 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:119227009-119227606 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:119234686-119235611 Neighboring gene NANOG hESC enhancer GRCh37_chr7:119260780-119261325 Neighboring gene uncharacterized LOC107986840 Neighboring gene Sharpr-MPRA regulatory region 12085 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:119591422-119591565 Neighboring gene NANOG hESC enhancer GRCh37_chr7:119649136-119649637 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:119654116-119654794 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:119654795-119655473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26549 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:119709548-119709749 Neighboring gene RNA, U1 small nuclear 29, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:119807553-119808172 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:119829996-119830611 Neighboring gene uncharacterized LOC105375477

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. RNA sequencing reveals the long noncoding RNA and mRNA profiles and identifies long non-coding RNA TSPAN12 as a potential microvascular invasion-related biomarker in hepatocellular carcinoma. Lu J, et al. Biomed Pharmacother, 2020 Jun. PMID 32222644
    2. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
    3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, 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)

    General gene information

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    Other Names

    • liver cancer-associated transcript 5

    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_131960.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript.
      Source sequence(s)
      AC073090, AC078848, AC091320

    2. NR_131961.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two exons and contains an alternate 3' terminal exon, compared to variant 1.
      Source sequence(s)
      AC073090, AC078848
      Related
      ENST00000426413.2

    3. NR_131962.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks three exons and contains an alternate 3' terminal exon, compared to variant 1.
      Source sequence(s)
      AC073090, AC078848, AC099648
      Related
      ENST00000431071.5

    4. NR_131963.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks three exons and contains an alternate 3' terminal exon, compared to variant 1.
      Source sequence(s)
      AC073090, AC078848

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      119619430..119907375 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      120934798..121222805 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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    Research Materials