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    LOC124403966 Sharpr-MPRA regulatory region 5662 [ Homo sapiens (human) ]

    Gene ID: 124403966, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC124403966
    Gene description
    Sharpr-MPRA regulatory region 5662
    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 14:Gen5', transcription transition, highly expressed genes towards 5' end). [provided by RefSeq, Feb 2022]
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    Genomic context

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    Location:
    10q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (63588809..63589103)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (64446940..64447234)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (65348569..65348863)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene jumonji domain containing 1C Neighboring gene JMJD1C antisense RNA 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:65224969-65225758 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3440 Neighboring gene JMJD1C antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3441 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2409 Neighboring gene receptor accessory protein 3 Neighboring gene uncharacterized LOC105378329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2410 Neighboring gene mitochondrial ribosomal protein L35 pseudogene 2

    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_079043.1 

      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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      63588809..63589103
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      64446940..64447234
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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