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    LOC112272560 Sharpr-MPRA regulatory region 7209 [ Homo sapiens (human) ]

    Gene ID: 112272560, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC112272560
    Gene description
    Sharpr-MPRA regulatory region 7209
    Gene type
    biological region
    Feature type(s)
    regulatory: enhancer, 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 enhancer 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 Activating non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). It also displayed weak repressive activity by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies). [provided by RefSeq, Mar 2018]
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    Genomic context

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    See LOC112272560 in Genome Data Viewer
    Location:
    14q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (78627106..78627400)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (72835664..72835958)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (79093449..79093743)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene tRNA suppressor (anticodon CTA) 3-1 Neighboring gene ribosomal protein S26 pseudogene 48 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:78793548-78794747 Neighboring gene neurexin 3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_36858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8817 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_36905 Neighboring gene MPRA-validated peak2214 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5982 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_36943 Neighboring gene uncharacterized LOC105370589 Neighboring gene MPRA-validated peak2216 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:79358917-79359500 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:79359501-79360083 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:79400229-79400386 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:79451802-79452322 Neighboring gene uncharacterized LOC124903353

    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_056698.1 

      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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      78627106..78627400
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      72835664..72835958
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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