U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC125138290 Sharpr-MPRA regulatory region 4583 [ Homo sapiens (human) ]

Gene ID: 125138290, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC125138290
Gene description
Sharpr-MPRA regulatory region 4583
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive human embryonic stem cells, where it is marked by the H3K4me1 histone modification. Another subregion was validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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 (75694328..75695110)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (73565045..73565827)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6676 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:75940037-75940728 Neighboring gene IMP U3 small nucleolar ribonucleoprotein 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75943426-75944362 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75945327-75945879 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75945880-75946431 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75949231-75949732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75949733-75950232 Neighboring gene sorting nexin 33 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75952205-75952778 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:75953927-75954500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75966659-75967446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75974798-75975642 Neighboring gene chondroitin sulfate proteoglycan 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75978522-75979027 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75979028-75979532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75985202-75985952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75989701-75990450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75990451-75991198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6678 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6679 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:75993083-75993582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75993590-75994515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76019661-76020161 Neighboring gene ciliary microtubule associated protein 1C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76023672-76024603 Neighboring gene dynamin 1 pseudogene 35 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76028296-76028816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6680 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6681 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9864 Neighboring gene peptidylprolyl isomerase A pseudogene 47

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

General gene information

Go to the top of the page Help

Other Names

  • ATAC-STARR-seq lymphoblastoid active region 9861
  • H3K4me1 hESC enhancer GRCh37_chr15:75986702-75987451

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_080261.2 

    Range
    101..883
    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
    75694328..75695110
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    73565045..73565827
    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