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    LOC125138294 Sharpr-MPRA regulatory region 5581 [ Homo sapiens (human) ]

    Gene ID: 125138294, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC125138294
    Gene description
    Sharpr-MPRA regulatory region 5581
    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 K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Apr 2022]
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    Genomic context

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    Location:
    15q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (79007127..79007421)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (76870784..76871078)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9927 Neighboring gene Sharpr-MPRA regulatory region 2017 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:79237120-79237658 Neighboring gene cathepsin H Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9930 Neighboring gene uncharacterized LOC100129540 Neighboring gene Ras protein specific guanine nucleotide releasing factor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:79288791-79289564 Neighboring gene uncharacterized LOC105370917 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:79296069-79297268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:79298197-79299032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:79327280-79327780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:79339175-79339674 Neighboring gene uncharacterized LOC107984750 Neighboring gene ANKRD34C antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:79489533-79490066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:79497097-79497660 Neighboring gene microRNA 184

    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_080266.1 

      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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      79007127..79007421
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      76870784..76871078
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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