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LOC122094841 Sharpr-MPRA regulatory region 13784 [ Homo sapiens (human) ]

Gene ID: 122094841, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122094841
Gene description
Sharpr-MPRA regulatory region 13784
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 associates with the OCT4 and NANOG transcription factors. 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 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC122094841 in Genome Data Viewer
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (63774918..63775641)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (63650742..63651465)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (64240589..64240883)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene phosphoglucomutase 1 Neighboring gene uncharacterized LOC105378771 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:64140637-64141138 Neighboring gene RNA, 7SL, cytoplasmic 130, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr1:64179745-64180246 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:64187597-64188096 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:64197420-64197975 Neighboring gene Sharpr-MPRA regulatory region 14006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 952 Neighboring gene Sharpr-MPRA regulatory region 321 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:64246221-64246776 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:64260455-64261114 Neighboring gene ribosomal protein L19 pseudogene 3 Neighboring gene receptor tyrosine kinase like orphan receptor 1 Neighboring gene cofilin 1 pseudogene 3

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

  • OCT4-NANOG hESC enhancer GRCh37_chr1:64240749-64241312

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_076355.2 

    Range
    101..824
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    63774918..63775641
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    63650742..63651465
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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