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    LOC122819158 Sharpr-MPRA regulatory region 15464 [ Homo sapiens (human) ]

    Gene ID: 122819158, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC122819158
    Gene description
    Sharpr-MPRA regulatory region 15464
    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 12:CtcfO, distal CTCF/candidate insulator with open chromatin). [provided by RefSeq, Oct 2021]
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    Genomic context

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    Location:
    2q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (134466218..134466512)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (134905785..134906079)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (135223789..135224083)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135002234-135002734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135002735-135003235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16551 Neighboring gene RNA, 5S ribosomal pseudogene 104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16554 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16555 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16559 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16561 Neighboring gene epididymal protein 3C, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:135129934-135130438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16562 Neighboring gene Sharpr-MPRA regulatory region 6492 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135201292-135201792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135217811-135218312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135218313-135218812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135240067-135240597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135240598-135241127 Neighboring gene uncharacterized LOC124906076 Neighboring gene transmembrane protein 163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:135293574-135294074 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:135318760-135318939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16563 Neighboring gene MPRA-validated peak3868 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11977 Neighboring gene uncharacterized LOC105373629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11978 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:135478596-135479795

    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_077018.1 

      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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      134466218..134466512
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      134905785..134906079
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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