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    LINC01090 long intergenic non-protein coding RNA 1090 [ Homo sapiens (human) ]

    Gene ID: 104355152, updated on 3-Mar-2026
    Official Symbol
    LINC01090provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 1090provided by HGNC
    Primary source
    HGNC:HGNC:49201
    See related
    Ensembl:ENSG00000231689 AllianceGenome:HGNC:49201
    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
    Try the new Gene page
    Try the new Transcripts and proteins table
    See LINC01090 in Genome Data Viewer
    Location:
    2q32.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (188035596..188287691, complement)
    RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (188524427..188776463, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (188900323..189152418, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373788 Neighboring gene MPRA-validated peak3989 silencer Neighboring gene ST13, Hsp70 interacting protein pseudogene 2 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:188897853-188898830 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:188988476-188989065 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:189038945-189039601 Neighboring gene uncharacterized LOC124907927 Neighboring gene MPRA-validated peak3993 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16845 Neighboring gene MPRA-validated peak3994 silencer Neighboring gene arkadia (RNF111) N-terminal like PKA signaling regulator 2N pseudogene Neighboring gene Sharpr-MPRA regulatory region 8723 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:189143651-189144345 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:189158453-189159336 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:189163339-189164538 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:189167937-189168854 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:189168855-189169772 Neighboring gene RNA, 5S ribosomal pseudogene 114 Neighboring gene microRNA 561 Neighboring gene GULP PTB domain containing engulfment adaptor 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:189260185-189260684 Neighboring gene uncharacterized LOC124906107

    Go to nucleotide: Graphics FASTA GenBank

    • 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

    Related articles in PubMed

    1. Genome-wide association study implicates a novel RNA gene, the lincRNA AC068718.1, as a risk factor for post-traumatic stress disorder in women. Guffanti G, et al. Psychoneuroendocrinology, 2013 Dec. PMID 24080187, Free PMC Article
    2. 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

    What's a GeneRIF?
    1. AC068718.1 is a designator for the locus represented in HGNC as LINC01090
      Title: Genome-wide association study implicates a novel RNA gene, the lincRNA AC068718.1, as a risk factor for post-traumatic stress disorder in women.
    2. findings implicate a novel RNA gene, lincRNA AC068718.1, as risk factor for post-traumatic stress disorder in women [lincRNA AC068718.1]
      Title: Genome-wide association study implicates a novel RNA gene, the lincRNA AC068718.1, as a risk factor for post-traumatic stress disorder in women.
    Submit: New GeneRIF Correction

    Review eQTL and phenotype association data in this region using PheGenI

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    NEW Try the new Transcript table

    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_126396.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC013445, AC092649, AC104131
      Related
      ENST00000434418.2

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

    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
      188035596..188287691 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      188524427..188776463 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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