U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC125424386 Sharpr-MPRA regulatory region 15144 [ Homo sapiens (human) ]

Gene ID: 125424386, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC125424386
Gene description
Sharpr-MPRA regulatory region 15144
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 22:ReprW, weaker Polycomb repression). [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
Location:
22q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (19619686..19619980)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (19996541..19996835)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19509616-19510548 Neighboring gene claudin 5 Neighboring gene MPRA-validated peak4453 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19531837-19532336 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19542168-19542870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19542871-19543573 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19554961-19555296 Neighboring gene long intergenic non-protein coding RNA 895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19583904-19584446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19585482-19585982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19585983-19586483 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19592881-19593448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:19593449-19594016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19594499-19595072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19604675-19605254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19605255-19605833 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:19607854-19608615 Neighboring gene CRISPRi-validated cis-regulatory element chr22.250 Neighboring gene chromosome 3 open reading frame 38 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr22:19640940-19641163 Neighboring gene uncharacterized LOC100420103

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_081121.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    19619686..19619980
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    19996541..19996835
    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