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    LOC123000067 Sharpr-MPRA regulatory region 7664 [ Homo sapiens (human) ]

    Gene ID: 123000067, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC123000067
    Gene description
    Sharpr-MPRA regulatory region 7664
    Gene type
    biological region
    Feature type(s)
    regulatory: silencer
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This genomic sequence was predicted to be a transcriptional regulatory region based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional repressive element by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 19:H4K20, transcription, primarily H4K20me1, more intronic). [provided by RefSeq, Oct 2021]
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    Genomic context

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    Location:
    3p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (65901274..65901568)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (65945280..65945574)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (65886949..65887243)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene membrane associated guanylate kinase, WW and PDZ domain containing 1 Neighboring gene uncharacterized LOC107986018 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:65747629-65748266 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:65776724-65776896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:65854323-65854824 Neighboring gene ribosomal protein L17 pseudogene 17 Neighboring gene MAGI1 intronic transcript 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:65887567-65888467 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:65888468-65889367 Neighboring gene Sharpr-MPRA regulatory region 14829 Neighboring gene MAGI1 antisense RNA 1 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:65949459-65950658 Neighboring gene uncharacterized LOC124900543 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:65985258-65985772 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:65985773-65986287 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:65995041-65995541 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:65996456-65997048 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:66021123-66021952 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:66021953-66022780 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:66022781-66023608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14503 Neighboring gene uncharacterized LOC105377128

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions. Ernst J, et al. Nat Biotechnol, 2016 Nov. PMID 27701403, 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 Variation Viewer (GRCh37.p13)

    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.

    Genomic

    1. NG_077250.1 

      Range
      101..395
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      65901274..65901568
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      65945280..65945574
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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