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    LOC122757938 Sharpr-MPRA regulatory region 1309 [ Homo sapiens (human) ]

    Gene ID: 122757938, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC122757938
    Gene description
    Sharpr-MPRA regulatory region 1309
    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 23:Low, low signal proximal to active elements). [provided by RefSeq, Sep 2021]
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    Genomic context

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    See LOC122757938 in Genome Data Viewer
    Location:
    2p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (47593130..47593424)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (47598137..47598431)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (47820269..47820563)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15732 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:47630036-47630746 Neighboring gene epithelial cell adhesion molecule Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:47630747-47631455 Neighboring gene microRNA 559 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:47653397-47653896 Neighboring gene mutS homolog 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:47699841-47700005 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15734 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11464 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:47761774-47762289 Neighboring gene potassium two pore domain channel subfamily K member 12 Neighboring gene MSH2 overlapping transcript 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:47796495-47797364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:47798518-47799048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:47799049-47799577 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15735 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15736 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:47891127-47891628 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:47891629-47892128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:47918101-47918767 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:47921671-47922214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11466 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:47923304-47923848 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:47923849-47924392 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:47925482-47926026 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:47928206-47928749 Neighboring gene ribosomal protein L18a pseudogene 6 Neighboring gene NME2 pseudogene 2

    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_076930.1 

      Range
      101..395
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      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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      47593130..47593424
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      47598137..47598431
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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