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    LOC121466695 Sharpr-MPRA regulatory region 11040 [ Homo sapiens (human) ]

    Gene ID: 121466695, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC121466695
    Gene description
    Sharpr-MPRA regulatory region 11040
    Gene type
    biological region
    Feature type(s)
    regulatory: enhancer, 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 enhancer 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 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, May 2021]
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    Genomic context

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    See LOC121466695 in Genome Data Viewer
    Location:
    12q
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (48859606..48859900)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (48821801..48822095)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (49253389..49253683)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927241 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:49208339-49208840 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:49208841-49209340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4413 Neighboring gene calcium voltage-gated channel auxiliary subunit beta 3 Neighboring gene DEAD-box helicase 23 Neighboring gene uncharacterized LOC105369755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6293 Neighboring gene Rho family GTPase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6294 Neighboring gene RNA, U6 small nuclear 600, pseudogene Neighboring gene MPRA-validated peak1724 silencer Neighboring gene ribosomal protein L32 pseudogene 27

    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_074626.1 

      Range
      101..395
      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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      48859606..48859900
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      48821801..48822095
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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