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LOC125418055 Sharpr-MPRA regulatory region 7516 [ Homo sapiens (human) ]

Gene ID: 125418055, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125418055
Gene description
Sharpr-MPRA regulatory region 7516
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 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125418055 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 (28742607..28742901)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (27105775..27106069)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1697 Neighboring gene long intergenic non-protein coding RNA 1695 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:29697851-29698465 Neighboring gene long intergenic non-protein coding RNA 161 Neighboring gene N-6 adenine-specific DNA methyltransferase 1 Neighboring gene uncharacterized LOC124905067 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18322 Neighboring gene MPRA-validated peak4395 silencer Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:30206496-30207695 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:30228725-30229226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:30229227-30229726 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr21:30256988-30257547 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr21:30257548-30258106 Neighboring gene heat shock protein family D (Hsp60) member 1 pseudogene 7

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_081081.1 

    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    28742607..28742901
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    27105775..27106069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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