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    LOC123477793 Sharpr-MPRA regulatory region 8198 [ Homo sapiens (human) ]

    Gene ID: 123477793, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC123477793
    Gene description
    Sharpr-MPRA regulatory region 8198
    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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive and primed human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K27ac histone modification. Another subregion was validated as a repressive element by Sharpr-MPRA (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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Jan 2023]
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    Genomic context

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    See LOC123477793 in Genome Data Viewer
    Location:
    4q
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (101031726..101032266)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (104346980..104347520)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (101952883..101953423)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1217 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:101731907-101732751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21746 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71492 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_71505 Neighboring gene long intergenic non-protein coding RNA 1218 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:101887592-101888092 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:101907345-101907846 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15589 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21747 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:101961837-101962456 Neighboring gene protein phosphatase 3 catalytic subunit alpha Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:102035867-102036688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15590 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21748 Neighboring gene NANOG hESC enhancer GRCh37_chr4:102076410-102076911 Neighboring gene Sharpr-MPRA regulatory region 422 Neighboring gene microRNA 8066 Neighboring gene Sharpr-MPRA regulatory region 14793 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:102225920-102226503 Neighboring gene microRNA 1255a

    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
    2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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)

    General gene information

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    Other Names

    • OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:101952883-101953417

    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_077596.2 

      Range
      101..641
      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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      101031726..101032266
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      104346980..104347520
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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