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    LOC125446235 Sharpr-MPRA regulatory region 1576 [ Homo sapiens (human) ]

    Gene ID: 125446235, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC125446235
    Gene description
    Sharpr-MPRA regulatory region 1576
    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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Jun 2022]
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    Genomic context

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    See LOC125446235 in Genome Data Viewer
    Location:
    22q
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (39384784..39385078)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39855408..39855702)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39780789..39781083)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39712838-39713726 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39714617-39715506 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39715507-39716396 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39716397-39717285 Neighboring gene small nucleolar RNA, C/D box 139 Neighboring gene Sharpr-MPRA regulatory region 3662 Neighboring gene small nucleolar RNA, C/D box 43 Neighboring gene ribosomal protein L3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19045 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39753396-39753924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39755840-39756638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39757867-39758453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39758454-39759039 Neighboring gene synaptogyrin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39769919-39770434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19046 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39811177-39811678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39811679-39812178 Neighboring gene TGF-beta activated kinase 1 (MAP3K7) binding protein 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39824885-39825527 Neighboring gene uncharacterized LOC100506472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39829518-39830236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39830237-39830954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19048 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39843664-39843855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39844165-39845073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19050 Neighboring gene CRISPRi-validated cis-regulatory element chr22.2018 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13753 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19054 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19055 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39866163-39867092 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39869361-39869718 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39869884-39870813 Neighboring gene beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase Neighboring gene MGAT3 antisense RNA 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_081174.1 

      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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      39384784..39385078
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      39855408..39855702
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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