U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    LOC122756685 Sharpr-MPRA regulatory region 12598 [ Homo sapiens (human) ]

    Gene ID: 122756685, updated on 10-Oct-2023

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC122756685
    Gene description
    Sharpr-MPRA regulatory region 12598
    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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Sep 2021]
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    2p
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (30193023..30193317)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (30237283..30237577)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (30415889..30416183)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11321 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11323 Neighboring gene yippee like 5 Neighboring gene uncharacterized LOC105374414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:30413091-30413789 Neighboring gene uncharacterized LOC124907749 Neighboring gene small nucleolar RNA, H/ACA box 10B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30416411-30416970 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:30431474-30431698 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:30440807-30442006 Neighboring gene H3 histone pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15534 Neighboring gene Sharpr-MPRA regulatory region 4877 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30453066-30453581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:30453582-30454096 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11327 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11328 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:30459095-30459302 Neighboring gene LBH regulator of WNT signaling pathway

    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_076901.1 

      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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      30193023..30193317
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      30237283..30237577
      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.

    Molecular Biology Databases