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LOC125138293 Sharpr-MPRA regulatory region 2017 [ Homo sapiens (human) ]

Gene ID: 125138293, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125138293
Gene description
Sharpr-MPRA regulatory region 2017
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 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 non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC125138293 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 (78944167..78944777)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (76807837..76808447)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6717 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6718 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:79165819-79166450 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:79168309-79168910 Neighboring gene mortality factor 4 like 1 Neighboring gene RNA, U6 small nuclear 415, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:79237120-79237658 Neighboring gene cathepsin H Neighboring gene Ras protein specific guanine nucleotide releasing factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9928 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9929 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9930 Neighboring gene uncharacterized LOC100129540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:79288791-79289564 Neighboring gene uncharacterized LOC105370917 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:79296069-79297268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:79298197-79299032 Neighboring gene Sharpr-MPRA regulatory region 5581

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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. 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

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

General gene information

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Other Names

  • H3K4me1 hESC enhancer GRCh37_chr15:79236581-79237119

NCBI Reference Sequences (RefSeq)

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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_080265.2 

    Range
    101..711
    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
    78944167..78944777
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    76807837..76808447
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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