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    LOC123477754 Sharpr-MPRA regulatory region 2882 [ Homo sapiens (human) ]

    Gene ID: 123477754, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC123477754
    Gene description
    Sharpr-MPRA regulatory region 2882
    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 DNase matched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Nov 2021]
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    Genomic context

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    See LOC123477754 in Genome Data Viewer
    Location:
    4q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (70914632..70914926)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (74257071..74257365)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (71780349..71780643)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 891, pseudogene Neighboring gene uncharacterized LOC124900711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15473 Neighboring gene MOB kinase activator 1B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21603 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:71869952-71870648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21605 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:71883900-71884096 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:71894495-71894995 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:71924658-71925260 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:71925261-71925861 Neighboring gene deoxycytidine kinase Neighboring gene solute carrier family 4 member 4 Neighboring gene uncharacterized LOC124900712

    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_077557.1 

      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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      70914632..70914926
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      74257071..74257365
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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