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LOC122861297 Sharpr-MPRA regulatory region 7025 [ Homo sapiens (human) ]

Gene ID: 122861297, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122861297
Gene description
Sharpr-MPRA regulatory region 7025
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 non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Oct 2021]
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Genomic context

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Location:
2q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (222734090..222734384)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (223219208..223219502)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (223598809..223599103)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene monoacylglycerol O-acyltransferase 1 Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory regions 6546 and 9925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17169 Neighboring gene uncharacterized LOC105373903 Neighboring gene ribosomal protein L31 pseudogene 17 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:223659282-223660204 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:223660205-223661127 Neighboring gene Sharpr-MPRA regulatory region 2575 Neighboring gene Sharpr-MPRA regulatory region 9896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12374 Neighboring gene NANOG hESC enhancer GRCh37_chr2:223730990-223731491 Neighboring gene acyl-CoA synthetase long chain family member 3 Neighboring gene MPRA-validated peak4046 silencer Neighboring gene autophagy related 12 pseudogene 2

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_077112.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    222734090..222734384
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    223219208..223219502
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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