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    LOC125024496 Sharpr-MPRA regulatory region 5996 [ Homo sapiens (human) ]

    Gene ID: 125024496, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC125024496
    Gene description
    Sharpr-MPRA regulatory region 5996
    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 non-DNase unmatched - State 3:PromF, promoter flanking). [provided by RefSeq, Apr 2022]
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    Genomic context

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    See LOC125024496 in Genome Data Viewer
    Location:
    14q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (60977771..60978065)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (55184311..55184605)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene MNAT1 component of CDK activating kinase Neighboring gene Sharpr-MPRA regulatory region 12651 Neighboring gene Sharpr-MPRA regulatory region 14697 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8484 Neighboring gene SRM pseudogene 2 Neighboring gene RNA, U6 small nuclear 398, pseudogene Neighboring gene uncharacterized LOC101927756 Neighboring gene solute carrier family 38 member 6 Neighboring gene tRNA methyltransferase 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:61555743-61556244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8485 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:61567888-61568804 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:61570068-61571267 Neighboring gene Sharpr-MPRA regulatory region 14232 Neighboring gene NANOG hESC enhancer GRCh37_chr14:61641010-61641511 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:61644371-61644872 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:61644987-61646186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8486 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:61721487-61722686 Neighboring gene protein kinase C eta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61736629-61737128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:61746518-61747481 Neighboring gene transmembrane protein 30B

    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_080108.1 

      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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      60977771..60978065
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      55184311..55184605
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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