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LOC122861294 Sharpr-MPRA regulatory region 8597 [ Homo sapiens (human) ]

Gene ID: 122861294, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122861294
Gene description
Sharpr-MPRA regulatory region 8597
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 unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [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 (219476287..219476581)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (219961007..219961301)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (220341009..220341303)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene aspartyl aminopeptidase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12356 Neighboring gene DNPEP antisense RNA 1 Neighboring gene desmin locus control region Neighboring gene VISTA enhancer hs2169 Neighboring gene desmin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220313846-220314453 Neighboring gene striated muscle enriched protein kinase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220315912-220316716 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:220317062-220318261 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:220325404-220325584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220329861-220330528 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220330529-220331194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220331442-220331984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220339972-220340679 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:220341387-220342094 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220348981-220349782 Neighboring gene ASIC4 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 15624 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220361035-220361852 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220361853-220362670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:220362671-220363488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17153 Neighboring gene SPEG neighbor Neighboring gene GDP-mannose pyrophosphorylase A

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_077109.1 

    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
    219476287..219476581
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    219961007..219961301
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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