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LOC122094906 Sharpr-MPRA regulatory region 2420 [ Homo sapiens (human) ]

Gene ID: 122094906, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122094906
Gene description
Sharpr-MPRA regulatory region 2420
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 25:Art, potential CNV or repetitive artifacts). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (114453507..114453801)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (114465182..114465476)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (114996129..114996423)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L57 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114888268-114888768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:114891333-114891833 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:114895122-114895622 and GRCh37_chr1:114895623-114896123 Neighboring gene trafficking kinesin protein 2 pseudogene Neighboring gene MPRA-validated peak378 silencer Neighboring gene tripartite motif containing 33 Neighboring gene Sharpr-MPRA regulatory region 2597 Neighboring gene ribosomal protein L26 pseudogene 10 Neighboring gene eukaryotic translation initiation factor 2 subunit 2 beta pseudogene 5

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_076420.1 

    Range
    101..395
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    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
    114453507..114453801
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    114465182..114465476
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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