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    LOC125316789 Sharpr-MPRA regulatory region 3335 [ Homo sapiens (human) ]

    Gene ID: 125316789, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC125316789
    Gene description
    Sharpr-MPRA regulatory region 3335
    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 DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, May 2022]
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    Genomic context

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    Location:
    17q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (72859050..72859344)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (73732415..73732709)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:70662937-70663580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70663581-70664223 Neighboring gene solute carrier family 39 member 11 Neighboring gene RN7SK pseudogene 180 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:70682597-70683097 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70715406-70716084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70716085-70716762 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:70717445-70717660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12682 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8917 Neighboring gene Sharpr-MPRA regulatory region 3582 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70738945-70739482 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70739483-70740019 Neighboring gene small Cajal body-specific RNA 24 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:70943638-70944837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70947920-70948848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70948849-70949777 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70950549-70951109 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:70949987-70950548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:70974043-70974543 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12684 Neighboring gene Sharpr-MPRA regulatory region 7306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71085784-71086284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71086285-71086785 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:71087756-71087987 Neighboring gene autophagy related 12 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:71128061-71128610 Neighboring gene MPRA-validated peak2987 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12687 Neighboring gene RNA polymerase III subunit K 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

    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_080608.1 

      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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      72859050..72859344
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_019805501.1 Reference GRCh38.p14 PATCHES

      Range
      25720..26014
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187616.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      25717..26011
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      73732415..73732709
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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