U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC125387303 Sharpr-MPRA regulatory region 1604 [ Homo sapiens (human) ]

Gene ID: 125387303, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC125387303
Gene description
Sharpr-MPRA regulatory region 1604
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 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, May 2022]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC125387303 in Genome Data Viewer
Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (53176270..53176564)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (54947536..54947830)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904932 Neighboring gene teashirt zinc finger homeobox 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:51664301-51665500 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:51681690-51682889 Neighboring gene NANOG hESC enhancer GRCh37_chr20:51683526-51684027 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:51705255-51705481 Neighboring gene RN7SK pseudogene 184 Neighboring gene MPRA-validated peak4263 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13046 Neighboring gene Sharpr-MPRA regulatory region 9561 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:51898656-51899211 Neighboring gene NANOG hESC enhancer GRCh37_chr20:51899474-51900080 Neighboring gene Sharpr-MPRA regulatory region 12391 Neighboring gene uncharacterized LOC105372670 Neighboring gene Sharpr-MPRA regulatory region 11508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13047 Neighboring gene peptidylprolyl isomerase A pseudogene 10

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_080978.1 

    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
    53176270..53176564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    54947536..54947830
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases