U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    LOC124416900 Sharpr-MPRA regulatory region 15659 [ Homo sapiens (human) ]

    Gene ID: 124416900, updated on 10-Oct-2023

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC124416900
    Gene description
    Sharpr-MPRA regulatory region 15659
    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 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Feb 2022]
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See LOC124416900 in Genome Data Viewer
    Location:
    10q
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (110032151..110032445)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (110916006..110916300)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (111791909..111792203)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene X-prolyl aminopeptidase 1 Neighboring gene RNA, U4 small nuclear 5, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3997 Neighboring gene NANOG hESC enhancer GRCh37_chr10:111672994-111673649 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3999 Neighboring gene ADD3 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr10:111747103-111747604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:111766387-111766942 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:111766943-111767496 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4000 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:111774137-111774942 Neighboring gene adducin 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4004 Neighboring gene Sharpr-MPRA regulatory region 905 Neighboring gene uncharacterized LOC105378479 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:111910896-111911890 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 12

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See Variation Viewer (GRCh37.p13)

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_079115.1 

      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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      110032151..110032445
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      110916006..110916300
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Other Literature Sources
    Molecular Biology Databases