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    LOC123480942 Sharpr-MPRA regulatory region 8632 [ Homo sapiens (human) ]

    Gene ID: 123480942, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC123480942
    Gene description
    Sharpr-MPRA regulatory region 8632
    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 21:Repr, strong Polycomb repression). [provided by RefSeq, Nov 2021]
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    Genomic context

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    Location:
    4q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (140219115..140219409)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (143538875..143539169)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (141140269..141140563)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene mastermind like transcriptional coactivator 3 Neighboring gene uncharacterized LOC124900783 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:140969917-140970453 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:140970454-140970989 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr4:140999743-141000242 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:141013378-141014229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21933 Neighboring gene uncharacterized LOC101927516 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:141071212-141072056 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:141072057-141072899 Neighboring gene uncharacterized LOC124900784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15708 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:141187913-141189112 Neighboring gene uncharacterized LOC124900785 Neighboring gene SCOC antisense RNA 1 Neighboring gene short coiled-coil protein

    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_077636.1 

      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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      140219115..140219409
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      143538875..143539169
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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