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    LOC125371521 Sharpr-MPRA regulatory regions 2264 and 10656 [ Homo sapiens (human) ]

    Gene ID: 125371521, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC125371521
    Gene description
    Sharpr-MPRA regulatory regions 2264 and 10656
    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. Two adjacent subregions were validated as functional repressive elements by Sharpr-MPRA (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 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, May 2022]
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    Genomic context

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    See LOC125371521 in Genome Data Viewer
    Location:
    19q
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (41321724..41322398)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (44142582..44143256)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (41827629..41828303)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene heterogeneous nuclear ribonucleoprotein U like 1 Neighboring gene RNA, 7SL, cytoplasmic 34, pseudogene Neighboring gene Sharpr-MPRA regulatory region 15507 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:41806393-41807592 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14672 Neighboring gene uncharacterized LOC105372401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14674 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41825837-41826574 Neighboring gene coiled-coil domain containing 97 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:41828472-41828958 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41829057-41829826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41830597-41831366 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41831367-41832136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14675 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10658 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41833547-41834068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14676 Neighboring gene transforming growth factor beta 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14677 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10663 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:41860203-41860704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14679 Neighboring gene B9 domain containing 2 Neighboring gene transmembrane protein 91

    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)

    General gene information

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    Other Names

    • Sharpr-MPRA regulatory region 10656
    • Sharpr-MPRA regulatory region 2264

    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_080822.1 

      Range
      101..775
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      41321724..41322398
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      44142582..44143256
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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