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LOC125177519 Sharpr-MPRA regulatory region 2303 [ Homo sapiens (human) ]

Gene ID: 125177519, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177519
Gene description
Sharpr-MPRA regulatory region 2303
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 H3K27ac and H3K4me1 histone modifications. 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 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (57898968..57899865)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (58772251..58773148)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RN7SK pseudogene 94 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:55887988-55888874 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:55910113-55910624 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:55910625-55911135 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:55911304-55911804 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55923593-55924200 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:55927391-55927900 Neighboring gene mitochondrial ribosomal protein S23 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:55937722-55938572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:55938573-55939422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:55939423-55940272 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:55945275-55946474 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55951125-55951765 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55951766-55952407 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55953049-55953690 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55953691-55954331 Neighboring gene CUE domain containing 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:55956376-55956928 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55958036-55958588 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55958589-55959141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:55962626-55963126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55969929-55970670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55977227-55977897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12452 Neighboring gene uncharacterized LOC107985065 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:55991179-55991679 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr17:56004573-56005088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12454 Neighboring gene Sharpr-MPRA regulatory region 4150 Neighboring gene Sharpr-MPRA regulatory region 6256 Neighboring gene NANOG hESC enhancer GRCh37_chr17:56029838-56030339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8753 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:56043109-56043617 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:56046907-56047067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8754 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8755 Neighboring gene uncharacterized LOC101929185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8756 Neighboring gene vascular endothelial zinc finger 1

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

  • H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:55976555-55977226

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_080574.2 

    Range
    101..998
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    57898968..57899865
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    58772251..58773148
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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