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LOC125387249 Sharpr-MPRA regulatory region 9809 [ Homo sapiens (human) ]

Gene ID: 125387249, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125387249
Gene description
Sharpr-MPRA regulatory region 9809
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [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 (31569606..31569900)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (33293831..33294125)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12757 Neighboring gene CD24 molecule pseudogene 3 Neighboring gene histocompatibility minor 13 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:30134937-30136136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30137639-30138140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30138141-30138640 Neighboring gene MCTS family member 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:30142553-30143052 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:30148388-30149587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30153591-30154466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30154467-30155342 Neighboring gene HM13 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:30160423-30160964 Neighboring gene uncharacterized LOC107985416 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:30162848-30163017 Neighboring gene RNA, U6 small nuclear 384, pseudogene

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_080926.1 

    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
    31569606..31569900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    33293831..33294125
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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