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    LINC02197 long intergenic non-protein coding RNA 2197 [ Homo sapiens (human) ]

    Gene ID: 102724392, updated on 10-Oct-2023

    Summary

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    Official Symbol
    LINC02197provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 2197provided by HGNC
    Primary source
    HGNC:HGNC:53063
    See related
    AllianceGenome:HGNC:53063
    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 liver (RPKM 1.1), testis (RPKM 0.3) and 8 other tissues See more
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    Genomic context

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    Location:
    5q13.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (71321031..71446756, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (71802345..71928080, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (70616858..70742583, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900993 Neighboring gene GUSB pseudogene 17 Neighboring gene POM121 membrane glycoprotein (rat) pseudogene Neighboring gene uncharacterized LOC105379016 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:70584717-70585542 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:70585543-70586368 Neighboring gene uncharacterized LOC105379025 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:70694085-70694716 Neighboring gene pro-melanin concentrating hormone like 2 (pseudogene) Neighboring gene uncharacterized LOC107987420 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:70750413-70751339 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:70751340-70752265 Neighboring gene sterol carrier protein 2 pseudogene Neighboring gene Sharpr-MPRA regulatory region 10712 Neighboring gene B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB Neighboring gene MPRA-validated peak5278 silencer Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 12

    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. 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
    2. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

    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)

    Genotypes

    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_134268.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AC145141, AK310013

    2. NR_134269.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' and 3' exons, resulting in a shorter transcript than variant 1.
      Source sequence(s)
      AC146949, CF141492, DA795384

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      71321031..71446756 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791777.1 Reference GRCh38.p14 PATCHES

      Range
      411606..1172838 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003315917.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      1319530..1445241 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_187651.1 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      851012..976753 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      71802345..71928080 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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