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LOC122847301 Sharpr-MPRA regulatory region 14614 [ Homo sapiens (human) ]

Gene ID: 122847301, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122847301
Gene description
Sharpr-MPRA regulatory region 14614
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 HepG2 liver carcinoma cells (group: HepG2 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 LOC122847301 in Genome Data Viewer
Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (159146771..159147452)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (159606561..159607241)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (160003669..160003963)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1 Neighboring gene VISTA enhancer hs2027 Neighboring gene RNA, U6 small nuclear 580, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:159920830-159921358 Neighboring gene glutathione S-transferase mu 3 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16682 Neighboring gene Sharpr-MPRA regulatory region 14439 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:159980099-159980612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:159980613-159981124 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_53540 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_53569 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_53596 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16683 Neighboring gene microRNA 6888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16684 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:160067858-160068472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:160081586-160082095 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:160082096-160082604 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_53624 Neighboring gene uncharacterized LOC105373716 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_53635 Neighboring gene WD repeat, sterile alpha motif and U-box domain containing 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • H3K4me1 hESC enhancer GRCh37_chr2:160003282-160003882

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_077036.2 

    Range
    101..782
    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    159146771..159147452
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    159606561..159607241
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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