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LOC125368553 Sharpr-MPRA regulatory region 1453 [ Homo sapiens (human) ]

Gene ID: 125368553, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125368553
Gene description
Sharpr-MPRA regulatory region 1453
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 non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125368553 in Genome Data Viewer
Location:
18p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (13377550..13377844)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (13540430..13540724)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904255 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9331 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9333 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13239687-13240321 Neighboring gene low density lipoprotein receptor class A domain containing 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:13262681-13263619 Neighboring gene chromosome 18 putative open reading frame 15 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13265910-13266472 Neighboring gene Sharpr-MPRA regulatory region 6698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13272589-13273088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13114 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:13280210-13280710 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:13280711-13281211 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:13286315-13286868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13291758-13292268 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:13302309-13302494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13303607-13304108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13304109-13304608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13318811-13319312 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:13320779-13321278 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr18:13366195-13366842 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:13375117-13376316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13379815-13380316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13380317-13380816 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13381508-13382132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13116 Neighboring gene LDLRAD4 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13425961-13426523 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:13446323-13447026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:13447027-13447730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13454951-13455594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:13455595-13456240 Neighboring gene microRNA 5190

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_080668.1 

    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
    13377550..13377844
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    13540430..13540724
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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