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    LOC122889029 Sharpr-MPRA regulatory region 13942 [ Homo sapiens (human) ]

    Gene ID: 122889029, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC122889029
    Gene description
    Sharpr-MPRA regulatory region 13942
    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 unmatched - State 4:PromP, inactive/poised promoter, highly conserved). [provided by RefSeq, Oct 2021]
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    Genomic context

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    See LOC122889029 in Genome Data Viewer
    Location:
    3p
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (9862685..9862979)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (9854693..9854987)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (9904369..9904663)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene RNA pseudouridine synthase D3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19411 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:9890179-9891039 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:9895593-9896262 Neighboring gene MARK2 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:9901011-9901551 Neighboring gene Sharpr-MPRA regulatory region 9891 Neighboring gene cell death inducing DFFA like effector c Neighboring gene jagunal homolog 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_077161.1 

      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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      9862685..9862979
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      9854693..9854987
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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