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    LOC124310616 Sharpr-MPRA regulatory region 7300 [ Homo sapiens (human) ]

    Gene ID: 124310616, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC124310616
    Gene description
    Sharpr-MPRA regulatory region 7300
    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 non-DNase unmatched - State 23:Low, low signal proximal to active elements) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low). [provided by RefSeq, Feb 2022]
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    Genomic context

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    Location:
    9q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (100455607..100455901)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (112627270..112627564)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (103217889..103218183)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:103114917-103115551 Neighboring gene uncharacterized LOC105376177 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:103131616-103131808 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:103155294-103155664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20136 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20137 Neighboring gene MSANTD3-TMEFF1 readthrough Neighboring gene Myb/SANT DNA binding domain containing 3 Neighboring gene uncharacterized LOC124902237 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20139 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:103254247-103254747 Neighboring gene transmembrane protein with EGF like and two follistatin like domains 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:103276664-103277164 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:103277165-103277665 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:103289773-103290326 Neighboring gene caveolae associated protein 4

    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_078898.1 

      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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      100455607..100455901
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      112627270..112627564
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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