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    LOC122128464 Sharpr-MPRA regulatory region 1770 [ Homo sapiens (human) ]

    Gene ID: 122128464, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC122128464
    Gene description
    Sharpr-MPRA regulatory region 1770
    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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Jul 2021]
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    Genomic context

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    See LOC122128464 in Genome Data Viewer
    Location:
    1q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (164731472..164731766)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (164077713..164078007)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (164700709..164701003)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904759 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:164528003-164528502 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164559870-164560837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164561919-164562862 Neighboring gene PBX homeobox 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:164571452-164572217 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:164572218-164572982 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164578838-164579391 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164579392-164579944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:164580135-164580676 Neighboring gene hESC enhancers GRCh37_chr1:164581219-164581760 and GRCh37_chr1:164581219-164581760 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:164581761-164582300 Neighboring gene VISTA enhancer hs1202 Neighboring gene VISTA enhancer hs1235 Neighboring gene RNA, U6 small nuclear 171, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:164660437-164660937 Neighboring gene VISTA enhancer hs1144 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1496 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:164704495-164705047 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:164717166-164718365 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:164728525-164729026 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:164729027-164729526 Neighboring gene PBX1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:164769015-164769515 Neighboring gene VISTA enhancer hs1191 Neighboring gene NANOG hESC enhancer GRCh37_chr1:164807885-164808386 Neighboring gene uncharacterized LOC107985451

    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_076484.1 

      Range
      101..395
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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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      164731472..164731766
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      164077713..164078007
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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