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    LOC125384555 Sharpr-MPRA regulatory region 12860 [ Homo sapiens (human) ]

    Gene ID: 125384555, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC125384555
    Gene description
    Sharpr-MPRA regulatory region 12860
    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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, May 2022]
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    Genomic context

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    See LOC125384555 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 (301205..301499)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (344387..344681)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene chromosome 20 open reading frame 96 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17433 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12560 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12561 Neighboring gene zinc finger CCHC-type containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17435 Neighboring gene NRSN2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12562 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12563 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12566 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12568 Neighboring gene SRY-box transcription factor 12

    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_080878.1 

      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
      301205..301499
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      344387..344681
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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