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    LINC00642 long intergenic non-protein coding RNA 642 [ Homo sapiens (human) ]

    Gene ID: 400238, updated on 17-Sep-2024

    Summary

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    Official Symbol
    LINC00642provided by HGNC
    Official Full Name
    long intergenic non-protein coding RNA 642provided by HGNC
    Primary source
    HGNC:HGNC:44293
    See related
    Ensembl:ENSG00000233208 AllianceGenome:HGNC:44293
    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 1.8) See more
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    Genomic context

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    See LINC00642 in Genome Data Viewer
    Location:
    14q32.11
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (90455230..90458905)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (84679941..84683616)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (90921574..90925249)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 5900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8880 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6009 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6010 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8881 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:90870785-90871984 Neighboring gene calmodulin 1 Neighboring gene MPRA-validated peak2228 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:90905675-90906438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8882 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr14:90920205-90920822 and GRCh37_chr14:90920823-90921440 Neighboring gene long intergenic non-protein coding RNA 2317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:90953133-90953634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:90962117-90962616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:90967372-90968082 Neighboring gene uncharacterized LOC124903359 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:90975958-90976791 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:90978459-90979291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:90979510-90980022 Neighboring gene Sharpr-MPRA regulatory region 509 Neighboring gene uncharacterized LOC105370619

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

    • FLJ35947, AL096869.5

    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_033986.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      BC036259, BX101323
      Related
      ENST00000442515.5

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      90455230..90458905
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      84679941..84683616
      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.

    Chemical Information
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