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    LOC121740681 Sharpr-MPRA regulatory region 2385 [ Homo sapiens (human) ]

    Gene ID: 121740681, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC121740681
    Gene description
    Sharpr-MPRA regulatory region 2385
    Gene type
    biological region
    Feature type(s)
    regulatory: enhancer
    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 an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2023]
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    Genomic context

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    See LOC121740681 in Genome Data Viewer
    Location:
    7p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (46215751..46216345)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (46377468..46378062)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (46255649..46255943)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375264 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:46054530-46055300 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:46055301-46056071 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:46073125-46073624 Neighboring gene tetratricopeptide repeat domain 4 pseudogene 1 Neighboring gene MPRA-validated peak6509 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25973 Neighboring gene Sharpr-MPRA regulatory region 10400 Neighboring gene zinc finger protein 619 pseudogene 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr7:46245952-46247151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25974 Neighboring gene Sharpr-MPRA regulatory region 15376 Neighboring gene uncharacterized LOC105375266 Neighboring gene ZNF619P1-HMGN1P19 intergenic nontranscribed chromatin-defined enhancer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:46574043-46574599 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:46574600-46575155 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:46576337-46576836 Neighboring gene NANOG hESC enhancer GRCh37_chr7:46666250-46666778 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 19

    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_chr7:46255349-46255850

    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_075743.2 

      Range
      101..695
      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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      46215751..46216345
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      46377468..46378062
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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