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LOC122056875 Sharpr-MPRA regulatory region 4702 [ Homo sapiens (human) ]

Gene ID: 122056875, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122056875
Gene description
Sharpr-MPRA regulatory region 4702
Gene type
biological region
Feature type(s)
regulatory: 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. It was validated as a functional repressive element by the Sharpr-MPRA technique (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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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See LOC122056875 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 (52910057..52910351)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (52791577..52791871)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (53375729..53376023)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene zyg-11 family member B, cell cycle regulator Neighboring gene RNA, U6 small nuclear 969, pseudogene Neighboring gene Sharpr-MPRA regulatory region 11599 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:53297677-53298444 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53301449-53302130 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53302131-53302812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53309013-53309606 Neighboring gene zyg-11 family member A, cell cycle regulator Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53334860-53335744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53335745-53336627 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53370741-53371532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53372219-53372718 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:53377381-53377881 Neighboring gene enoyl-CoA hydratase domain containing 2 Neighboring gene translation machinery-associated protein 7-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:53387115-53387797 Neighboring gene ATP synthase membrane subunit j pseudogene

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

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)

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_076331.1 

    Range
    101..395
    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
    52910057..52910351
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    52791577..52791871
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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