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    LOC125384563 Sharpr-MPRA regulatory region 9456 [ Homo sapiens (human) ]

    Gene ID: 125384563, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC125384563
    Gene description
    Sharpr-MPRA regulatory region 9456
    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 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, May 2022]
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    Genomic context

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    See LOC125384563 in Genome Data Viewer
    Location:
    20p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (2771883..2772177)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (2802348..2802642)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372507 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2674597-2675581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2678055-2678598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2681405-2682133 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr20:2682134-2682861 Neighboring gene EBF family member 4 Neighboring gene VISTA enhancer hs632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2731029-2731709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:2731778-2732289 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12606 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2739980-2740630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17471 Neighboring gene ribosomal protein L19 pseudogene 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2778855-2779842 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2779843-2780830 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:2780831-2781816 Neighboring gene carboxypeptidase X, M14 family member 1

    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

    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_080886.1 

      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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      2771883..2772177
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      2802348..2802642
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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