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LOC125384571 Sharpr-MPRA regulatory region 14731 [ Homo sapiens (human) ]

Gene ID: 125384571, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125384571
Gene description
Sharpr-MPRA regulatory region 14731
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 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:
20p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (5714583..5714877)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (5754981..5755275)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5637190-5637690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5637691-5638191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5668750-5669250 Neighboring gene Sharpr-MPRA regulatory region 5332 Neighboring gene uncharacterized LOC105372514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17527 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17529 Neighboring gene shieldin complex subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:5807499-5808000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17532 Neighboring gene MPRA-validated peak4135 silencer Neighboring gene RNA, U1 small nuclear 55, 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_080894.1 

    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
    5714583..5714877
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    5754981..5755275
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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