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    LOC124625871 Sharpr-MPRA regulatory region 10235 [ Homo sapiens (human) ]

    Gene ID: 124625871, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC124625871
    Gene description
    Sharpr-MPRA regulatory region 10235
    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 matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Mar 2022]
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    Genomic context

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    See LOC124625871 in Genome Data Viewer
    Location:
    11q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (130145494..130145788)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (130181163..130181457)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene amyloid beta precursor like protein 2 Neighboring gene ribosomal protein L34 pseudogene 21 Neighboring gene MPRA-validated peak1513 silencer Neighboring gene uncharacterized LOC124902850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:129993119-129993620 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:129993621-129994120 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:130015754-130016953 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4078 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4079 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:130030913-130031412 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5752 Neighboring gene ST14 transmembrane serine protease matriptase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:130068001-130068502 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:130079505-130080004 Neighboring gene zinc finger and BTB domain containing 44 Neighboring gene NDUFAF2 pseudogene 2

    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

    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_079471.1 

      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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      130145494..130145788
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      130181163..130181457
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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