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    LOC123477719 Sharpr-MPRA regulatory region 2944 [ Homo sapiens (human) ]

    Gene ID: 123477719, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC123477719
    Gene description
    Sharpr-MPRA regulatory region 2944
    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 human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K4me1 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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2023]
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    Genomic context

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    See LOC123477719 in Genome Data Viewer
    Location:
    4p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (26372370..26372961)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (26357370..26357961)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (26374289..26374583)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene recombination signal binding protein for immunoglobulin kappa J region Neighboring gene uncharacterized LOC124900690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21391 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:26206221-26206722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21392 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:26239970-26240520 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:26240521-26241069 Neighboring gene uncharacterized LOC105374542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21393 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15334 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:26301633-26302396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21396 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:26323092-26324013 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15336 Neighboring gene Sharpr-MPRA regulatory region 12863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:26353747-26354248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:26354249-26354748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21397 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:26407341-26408540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:26454493-26455031 Neighboring gene cholecystokinin A receptor Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:26569763-26570962 Neighboring gene Sharpr-MPRA regulatory region 5841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21398 Neighboring gene TBC1 domain family member 19 Neighboring gene Sharpr-MPRA regulatory region 1278 Neighboring gene small nucleolar RNA SNORD74

    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

    • NANOG-H3K4me1 hESC enhancer GRCh37_chr4:26373992-26374492

    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_077523.2 

      Range
      101..692
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      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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      26372370..26372961
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      26357370..26357961
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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