U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC125138300 Sharpr-MPRA regulatory region 10787 [ Homo sapiens (human) ]

Gene ID: 125138300, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC125138300
Gene description
Sharpr-MPRA regulatory region 10787
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 DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Apr 2022]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC125138300 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (84992598..84992892)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (82744840..82745134)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 28 member 1 Neighboring gene RNA, U6 small nuclear 796, pseudogene Neighboring gene high mobility group box 1 pseudogene 43 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41947 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:85522585-85523086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:85523087-85523586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6775 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85524736-85525268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9997 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6777 Neighboring gene phosphodiesterase 8A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10001 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41972 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_42025 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:85668261-85668811 Neighboring gene uncharacterized LOC124903545 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_42032 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:85708039-85708575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6778 Neighboring gene NIFK pseudogene 8

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_080272.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    84992598..84992892
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    82744840..82745134
    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