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    LINC03099 long intergenic non-protein coding RNA 3099 [ Homo sapiens (human) ]

    Gene ID: 101927476, updated on 19-Aug-2025
    Official Symbol
    LINC03099provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 3099provided by HGNC
    Primary source
    HGNC:HGNC:56750
    See related
    Ensembl:ENSG00000236393 AllianceGenome:HGNC:56750
    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
    Biased expression in adrenal (RPKM 6.8), placenta (RPKM 3.0) and 2 other tissues See more
    NEW
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    See LINC03099 in Genome Data Viewer
    Location:
    Xp11.4
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2025_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (40262917..40287721)
    RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (39664490..39689298)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (40122170..40146974)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39871294-39872017 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20740 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:39873755-39874254 Neighboring gene long intergenic non-protein coding RNA 3053 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39918103-39918602 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:39932994-39934193 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20741 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:39950161-39950788 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:39952045-39952671 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29534 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20747 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39959601-39960121 Neighboring gene translation initiation factor IF-2-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39961792-39962382 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29535 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20751 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39966379-39967135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20753 Neighboring gene BCL6 corepressor Neighboring gene ReSE screen-validated silencer GRCh37_chrX:39971030-39971309 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:39999891-40000415 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:40007775-40008318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20754 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:40015867-40016606 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:40016607-40017346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20756 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:40028374-40029064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:40029065-40029755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20757 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29537 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20759 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:40041386-40041565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20762 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:40070301-40070852 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:40097124-40097650 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29539 Neighboring gene Sharpr-MPRA regulatory region 4836 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29540 Neighboring gene uncharacterized LOC105373182 Neighboring gene inosine monophosphate dehydrogenase 1 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29541 Neighboring gene Sharpr-MPRA regulatory region 9554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:40350139-40350639 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:40377714-40378214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:40378215-40378715 Neighboring gene RNA, U7 small nuclear 164 pseudogene

    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

    GeneRIFs: Gene References Into Functions

    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)

    See Variation Viewer (GRCh38)

    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_110386.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC091806
      Related
      ENST00000452690.1

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      40262917..40287721
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      39664490..39689298
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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