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LOC125371436 Sharpr-MPRA regulatory region 1275 [ Homo sapiens (human) ]

Gene ID: 125371436, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371436
Gene description
Sharpr-MPRA regulatory region 1275
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 21:Repr, strong Polycomb repression) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, May 2022]
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Genomic context

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Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (62027996..62028290)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (62231173..62231467)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372159 Neighboring gene uncharacterized LOC112268209 Neighboring gene Sharpr-MPRA regulatory region 15585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9501 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_48468 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_48472 Neighboring gene ribose 5-phosphate isomerase A pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:59667958-59668797 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:59668798-59669636 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class N Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_48670 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_48690 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_48726/48728 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_48738 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_48746 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:59853791-59854003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13429 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9502 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_48887 Neighboring gene RAB11 binding and LisH domain, coiled-coil and HEAT repeat containing Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9503 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_48897 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:59957531-59957709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9504 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9505 Neighboring gene TNF receptor superfamily member 11a Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr18:60034196-60034732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9506 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr18:60041621-60042250

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_080706.1 

    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    62027996..62028290
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    62231173..62231467
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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