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    LINC00685 long intergenic non-protein coding RNA 685 [ Homo sapiens (human) ]

    Gene ID: 283981, updated on 27-Aug-2024

    Summary

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    Official Symbol
    LINC00685provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 685provided by HGNC
    Primary source
    HGNC:HGNC:27560
    See related
    AllianceGenome:HGNC:27560
    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
    CXYorf10; NCRNA00107; PPP2R3B-AS1
    Expression
    Ubiquitous expression in skin (RPKM 2.1), spleen (RPKM 1.5) and 23 other tissues See more
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    Genomic context

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    Location:
    X;Y
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (319145..321332)
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (319145..321332)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (150200..152387)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (149286..151470)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (281385..282067)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (231385..232067)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol specific phospholipase C X domain containing 1 Neighboring gene GTP binding protein 6 (putative) Neighboring gene protein phosphatase 2 regulatory subunit B''beta Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chrX:323668-324173 and GRCh37_chrY:273658-274173 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrY:274174-274688 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:333708-333890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:335885-336775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:357819-358704 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:389565-389736 Neighboring gene uncharacterized LOC102724521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:396687-397186 Neighboring gene OCT4-NANOG hESC enhancers GRCh37_chrX:406609-407442 and GRCh37_chrY:356916-357447 Neighboring gene CNE-5 enhancer upstream of SHOX

    Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene vegetative cell wall protein gp1-like Neighboring gene phosphatidylinositol specific phospholipase C X domain containing 1 Neighboring gene GTP binding protein 6 (putative) Neighboring gene protein phosphatase 2 regulatory subunit B''beta Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chrX:323668-324173 and GRCh37_chrY:273658-274173 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrY:274174-274688 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:333708-333890 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:335885-336775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:357819-358704 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:389565-389736 Neighboring gene uncharacterized LOC102724521 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:396687-397186 Neighboring gene OCT4-NANOG hESC enhancers GRCh37_chrX:406609-407442 and GRCh37_chrY:356916-357447 Neighboring gene CNE-5 enhancer upstream of SHOX

    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 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. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, 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)

    See Variation Viewer (GRCh38)

    General gene information

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    Other Names

    • PPP2R3B antisense RNA 1 (non-protein coding)

    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_027231.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an internal segment, compared to variant 1.
      Source sequence(s)
      AK023454, BC041934, DA066179

    2. NR_027232.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer, unspliced transcript.
      Source sequence(s)
      AK023454, BC041934, DA521837

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      319145..321332
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

      Range
      319145..321332
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187634.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      1..1995
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      150200..152387
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060948.1 Alternate T2T-CHM13v2.0

      Range
      149286..151470
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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