U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC125138302 Sharpr-MPRA regulatory region 7683 [ Homo sapiens (human) ]

Gene ID: 125138302, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC125138302
Gene description
Sharpr-MPRA regulatory region 7683
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 22:ReprW, weaker Polycomb repression). [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
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (85652498..85652792)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (83404503..83404797)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:85958383-85958882 Neighboring gene A-kinase anchoring protein 13 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:85977313-85978117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10012 Neighboring gene fatty acid binding protein 5 pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10014 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:85996962-85997509 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:85997510-85998056 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6781 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10017 Neighboring gene Sharpr-MPRA regulatory region 6632 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_42228 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_42230 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6783 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6784 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_42240 Neighboring gene NANOG hESC enhancer GRCh37_chr15:86171542-86172083 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_42264 Neighboring gene RNA, U6 small nuclear 1280, pseudogene Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_42301 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_42317 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10018 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10019 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10022 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_42385 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10024 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:86269598-86270797 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:86303833-86304334 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:86305151-86305884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:86306619-86307352 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:86307353-86308085 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:86311017-86311791 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:86311792-86312565 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:86312566-86313340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:86313341-86314113 Neighboring gene long intergenic non-protein coding RNA 2883 Neighboring gene kelch like family member 25 Neighboring gene microRNA 1276

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_080274.1 

    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
    85652498..85652792
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    83404503..83404797
    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