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    LOC122889023 Sharpr-MPRA regulatory region 5493 [ Homo sapiens (human) ]

    Gene ID: 122889023, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC122889023
    Gene description
    Sharpr-MPRA regulatory region 5493
    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, Oct 2021]
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    Genomic context

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    See LOC122889023 in Genome Data Viewer
    Location:
    3p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (5136624..5136918)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (5130557..5130849)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (5178309..5178603)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene CD24 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14023 Neighboring gene uncharacterized LOC124906212 Neighboring gene Sharpr-MPRA regulatory region 5688 Neighboring gene ADP ribosylation factor like GTPase 8B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19376 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19379 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14024 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14025 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19380 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14027 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19383 Neighboring gene ER degradation enhancing alpha-mannosidase like protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19384 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:5255069-5255570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:5264003-5264559 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:5264560-5265115 Neighboring gene NANOG hESC enhancer GRCh37_chr3:5274159-5274668 Neighboring gene microRNA 4790

    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_077155.1 

      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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      5136624..5136918
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      5130557..5130849
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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