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LOC122861240 Sharpr-MPRA regulatory region 126 [ Homo sapiens (human) ]

Gene ID: 122861240, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122861240
Gene description
Sharpr-MPRA regulatory region 126
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 21:Repr, strong Polycomb repression). [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 (173761661..173761955)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (174247964..174248258)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (174626389..174626683)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene peptidylprolyl isomerase A pseudogene 66 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:174397206-174397786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:174397787-174398367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12116 Neighboring gene heat shock protein 90 alpha family class B member 1 pseudogene Neighboring gene MPRA-validated peak3928 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:174505321-174505869 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:174611449-174611950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:174611951-174612450 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:174662067-174662806 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:174662807-174663544 Neighboring gene uncharacterized LOC105373745 Neighboring gene ribosomal protein L5 pseudogene 7

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_077056.1 

    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
    173761661..173761955
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    174247964..174248258
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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