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    LINC02140 long intergenic non-protein coding RNA 2140 [ Homo sapiens (human) ]

    Gene ID: 100996345, updated on 10-Dec-2024

    Summary

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    Official Symbol
    LINC02140provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 2140provided by HGNC
    Primary source
    HGNC:HGNC:53000
    See related
    Ensembl:ENSG00000261803 AllianceGenome:HGNC:53000
    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
    Restricted expression toward testis (RPKM 8.5) See more
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    Genomic context

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    See LINC02140 in Genome Data Viewer
    Location:
    16q12.2
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (54366007..54370699, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (60164020..60168716, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (54399919..54404611, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2169 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:54318795-54319714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:54319715-54320634 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:54320768-54321268 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:54321269-54321769 Neighboring gene VISTA enhancer hs51 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:54325084-54325965 Neighboring gene iroquois homeobox 3 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:54364959-54365668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:54396413-54396916 Neighboring gene uncharacterized LOC105371272 Neighboring gene NANOG hESC enhancer GRCh37_chr16:54459786-54460294 Neighboring gene NANOG hESC enhancer GRCh37_chr16:54464241-54464805 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:54523058-54523261 Neighboring gene VISTA enhancer hs43 Neighboring gene long intergenic non-protein coding RNA 2183 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:54616376-54617284 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:54618909-54619453 Neighboring gene VISTA enhancer hs37 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:54658831-54659077 Neighboring gene uncharacterized LOC105371274

    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. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    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)

    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_134922.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript.
      Source sequence(s)
      AC018553, AK057319
      Related
      ENST00000566649.1

    2. NR_134923.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' terminal exon and is shorter, compared to variant 1.
      Source sequence(s)
      AC018553, AK057319, DB447763

    3. NR_134924.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' terminal exon and is shorter, compared to variant 1.
      Source sequence(s)
      AC018553, AK057319, HY020479

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      54366007..54370699 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      60164020..60168716 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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