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LOC125387277 Sharpr-MPRA regulatory region 6194 [ Homo sapiens (human) ]

Gene ID: 125387277, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125387277
Gene description
Sharpr-MPRA regulatory region 6194
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 23:Low, low signal proximal to active elements). [provided by RefSeq, May 2022]
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Genomic context

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Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (45781290..45781584)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (47517823..47518117)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904915 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44391506-44392438 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:44393372-44394304 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:44394305-44395236 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:44399706-44400299 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:44400300-44400892 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60389 Neighboring gene Sharpr-MPRA regulatory region 12827 Neighboring gene RNA, U6atac small nuclear 38, pseudogene Neighboring gene WAP four-disulfide core domain 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44408579-44409079 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60411 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12961 Neighboring gene deoxynucleotidyltransferase terminal interacting protein 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60428 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12962 Neighboring gene ubiquitin conjugating enzyme E2 C

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_080953.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    45781290..45781584
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    47517823..47518117
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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