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LOC125177387 Sharpr-MPRA regulatory region 159 [ Homo sapiens (human) ]

Gene ID: 125177387, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177387
Gene description
Sharpr-MPRA regulatory region 159
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 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (86732943..86733237)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (92801113..92801407)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:86613015-86613636 Neighboring gene forkhead box L1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:86643521-86644020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:86644136-86644702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:86655227-86655748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:86679869-86680369 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:86697509-86698708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7832 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:86733288-86733475 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:86733737-86734644 Neighboring gene long intergenic non-protein coding RNA 2189 Neighboring gene long intergenic non-protein coding RNA 2188 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr16:86775893-86776639 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:86780915-86781458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:86782557-86783058 Neighboring gene Sharpr-MPRA regulatory region 6377 Neighboring gene uncharacterized LOC105371392 Neighboring gene uncharacterized LOC107984819 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:86806242-86806760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:86806761-86807277

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_080444.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    86732943..86733237
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    92801113..92801407
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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