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    LOC123775399 Sharpr-MPRA regulatory region 11560 [ Homo sapiens (human) ]

    Gene ID: 123775399, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC123775399
    Gene description
    Sharpr-MPRA regulatory region 11560
    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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 19:H4K20, transcription, primarily H4K20me1, more intronic). [provided by RefSeq, Jan 2022]
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    Genomic context

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    See LOC123775399 in Genome Data Viewer
    Location:
    6q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (108673646..108673940)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (109850996..109851290)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (108994849..108995143)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901372 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17453 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17454 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:108882597-108883097 Neighboring gene Sharpr-MPRA regulatory region 14072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24915 Neighboring gene forkhead box O3 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:108908380-108908581 Neighboring gene SUMO2 pseudogene 8 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:108960200-108960701 Neighboring gene Sharpr-MPRA regulatory region 11562 Neighboring gene MPRA-validated peak6015 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:109019778-109020977 Neighboring gene Sharpr-MPRA regulatory region 15105 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:109051727-109052654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109052989-109053781 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109053782-109054573 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:109057555-109058224 Neighboring gene uncharacterized LOC107986629 Neighboring gene long intergenic non-protein coding RNA 222

    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_078168.1 

      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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      108673646..108673940
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      109850996..109851290
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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