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    LOC123522803 Sharpr-MPRA regulatory region 11914 [ Homo sapiens (human) ]

    Gene ID: 123522803, updated on 10-Oct-2023

    Summary

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    Gene symbol
    LOC123522803
    Gene description
    Sharpr-MPRA regulatory region 11914
    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 DNase matched - State 2:TssF, active promoter, flanking TSS/CpG islands). [provided by RefSeq, Dec 2021]
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    Genomic context

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    See LOC123522803 in Genome Data Viewer
    Location:
    5q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (139481024..139481318)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (140006089..140006383)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (138860609..138860903)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene endothelial cell surface expressed chemotaxis and apoptosis regulator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23233 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138840510-138841099 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138841100-138841688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138842278-138842865 Neighboring gene Sharpr-MPRA regulatory region 4960 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138852141-138852662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138854227-138854748 Neighboring gene small integral membrane protein 33 Neighboring gene stimulator of interferon response cGAMP interactor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23236 Neighboring gene cancer-related nucleoside-triphosphatase-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138864368-138864868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138865995-138866495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23237 Neighboring gene nuclear receptor coactivator 4 pseudogene 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_077832.1 

      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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      139481024..139481318
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_021159996.1 Reference GRCh38.p14 PATCHES

      Range
      70819..71113
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      140006089..140006383
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      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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