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

Gene ID: 105375475, updated on 10-Oct-2023

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_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (119619430..119907375, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (120934798..121222805, complement)
105.20220307 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: 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. 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)

Genotypes

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_2023_10

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

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