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LOC113939988 Sharpr-MPRA regulatory region 13643 [ Homo sapiens (human) ]

Gene ID: 113939988, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113939988
Gene description
Sharpr-MPRA regulatory region 13643
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 primed 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 20:ReprD, Polycomb repression with Duke DNase/promoter and conservation enriched). [provided by RefSeq, Jan 2023]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (29312829..29313431)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (29155483..29156085)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (29639649..29639943)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:29482895-29483396 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29490994-29491614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29504446-29504946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 553 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 554 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29508465-29509102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29509103-29509740 Neighboring gene serine and arginine rich splicing factor 4 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29513125-29513770 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29513771-29514415 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29524789-29525289 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 555 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:29535731-29536232 Neighboring gene mitochondrial trans-2-enoyl-CoA reductase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 610 Neighboring gene uncharacterized LOC124903887 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:29556822-29557322 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:29557323-29557823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29569846-29570346 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29570347-29570847 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29571433-29571934 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29575791-29576456 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29576457-29577122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29577907-29578624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29581288-29581806 Neighboring gene protein tyrosine phosphatase receptor type U Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29609955-29610695 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29610696-29611435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29617387-29617889 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:29637206-29637706 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:29637707-29638207 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29638763-29639340 Neighboring gene Sharpr-MPRA regulatory region 8387 Neighboring gene long intergenic non-protein coding RNA 1756 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:29685237-29685910 Neighboring gene Sharpr-MPRA regulatory region 1590 Neighboring gene MPRA-validated peak141 silencer Neighboring gene uncharacterized LOC107984933 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29779419-29779919 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29781005-29781983 Neighboring gene MPRA-validated peak142 silencer Neighboring gene MPRA-validated peak143 silencer Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:29798359-29798929 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29814305-29814937 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:29814938-29815569 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29826683-29827364 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29827365-29828046 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:29828047-29828728

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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • H3K4me1 hESC enhancer GRCh37_chr1:29639341-29639916

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_063767.2 

    Range
    101..703
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    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    29312829..29313431
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    29155483..29156085
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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