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LOC122861289 Sharpr-MPRA regulatory region 10603 [ Homo sapiens (human) ]

Gene ID: 122861289, updated on 10-Oct-2023

Summary

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Gene symbol
LOC122861289
Gene description
Sharpr-MPRA regulatory region 10603
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 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [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 (215420546..215420840)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (215905584..215905878)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (216285269..216285563)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124907975 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:216176486-216177136 Neighboring gene 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:216240057-216241256 Neighboring gene fibronectin 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:216255920-216257119 Neighboring gene Sharpr-MPRA regulatory region 14446 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:216288045-216289244 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:216298103-216299302 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12299 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12300 Neighboring gene FN1 divergent transcript Neighboring gene uncharacterized LOC102724849

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_077104.1 

    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
    215420546..215420840
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    215905584..215905878
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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