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LOC125387326 Sharpr-MPRA regulatory region 10595 [ Homo sapiens (human) ]

Gene ID: 125387326, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125387326
Gene description
Sharpr-MPRA regulatory region 10595
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125387326 in Genome Data Viewer
Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (15122308..15122602)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (13477771..13478065)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61697 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61707 Neighboring gene nuclear receptor interacting protein 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:16377340-16378275 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_61740 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:16403577-16404776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18291 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13217 Neighboring gene long intergenic non-protein coding RNA 2920 Neighboring gene uncharacterized LOC107985483 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:16493536-16494052 Neighboring gene Sharpr-MPRA regulatory region 10306 Neighboring gene uncharacterized LOC124905047 Neighboring gene CRISPRi-validated cis-regulatory element chr21.79 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:16594333-16594922 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:16614113-16614728 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:16614729-16615343 Neighboring gene uncharacterized LOC105369292

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_081063.1 

    Range
    101..395
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    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    15122308..15122602
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    13477771..13478065
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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