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LOC125110355 Sharpr-MPRA regulatory region 14876 [ Homo sapiens (human) ]

Gene ID: 125110355, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125110355
Gene description
Sharpr-MPRA regulatory region 14876
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 3:PromF, promoter flanking). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125110355 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (71610050..71610344)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (69429097..69429391)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene thrombospondin type 1 domain containing 4 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:71655547-71656054 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:71656055-71656562 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:71656563-71657070 Neighboring gene ribosomal protein L17 pseudogene 39 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:71678327-71678861 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:71678925-71679818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71684826-71685326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71685327-71685827 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:71757823-71758514 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6614 Neighboring gene uncharacterized LOC107984716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6615 Neighboring gene Sharpr-MPRA regulatory region 7020 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:71947880-71949079 Neighboring gene THSD4 antisense RNA 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:72053567-72054766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9705 Neighboring gene Sharpr-MPRA regulatory region 1602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9706 Neighboring gene nuclear receptor subfamily 2 group E member 3

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

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_080256.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    71610050..71610344
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    69429097..69429391
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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