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    LOC123620118 Sharpr-MPRA regulatory region 15280 [ Homo sapiens (human) ]

    Gene ID: 123620118, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC123620118
    Gene description
    Sharpr-MPRA regulatory region 15280
    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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Dec 2021]
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    Genomic context

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    See LOC123620118 in Genome Data Viewer
    Location:
    6p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (41801471..41801765)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (41630033..41630327)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (41769209..41769503)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41755120-41756119 Neighboring gene prickle planar cell polarity protein 4 Neighboring gene translocase of outer mitochondrial membrane 6 Neighboring gene ubiquitin specific peptidase 49 Neighboring gene small nucleolar RNA SNORA8 Neighboring gene MPRA-validated peak5805 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41861872-41862386 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:41862979-41863271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24529 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:41884515-41885714 Neighboring gene mediator complex subunit 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24530 Neighboring gene bystin like

    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_078102.1 

      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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      41801471..41801765
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      41630033..41630327
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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