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    LOC125371434 Sharpr-MPRA regulatory region 560 [ Homo sapiens (human) ]

    Gene ID: 125371434, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC125371434
    Gene description
    Sharpr-MPRA regulatory region 560
    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 non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, May 2022]
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    Genomic context

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    See LOC125371434 in Genome Data Viewer
    Location:
    18q
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (59864177..59864471)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (60066863..60067157)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (57531409..57531703)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13416 Neighboring gene glutamate dehydrogenase 1 pseudogene 4 Neighboring gene ribosomal protein lateral stalk subunit P0 pseudogene 12 Neighboring gene Sharpr-MPRA regulatory region 9182 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:57514626-57515543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13421 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:57566317-57567068 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13422 Neighboring gene phorbol-12-myristate-13-acetate-induced protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13423 Neighboring gene uncharacterized LOC105372151 Neighboring gene PLEKHB2 pseudogene 1

    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_080704.1 

      Range
      101..395
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      59864177..59864471
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      60066863..60067157
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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