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LOC121366066 Sharpr-MPRA regulatory region 2866 [ Homo sapiens (human) ]

Gene ID: 121366066, updated on 10-Oct-2023

Summary

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Gene symbol
LOC121366066
Gene description
Sharpr-MPRA regulatory region 2866
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF). [provided by RefSeq, May 2021]
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Genomic context

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Location:
10q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (77947151..77947445)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (78816188..78816483)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (79706909..79707203)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene discs large MAGUK scaffold protein 5 Neighboring gene Sharpr-MPRA regulatory region 2984 Neighboring gene RNA, 7SL, cytoplasmic 284, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr10:79688206-79688382 Neighboring gene DLG5 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:79707975-79708512 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr10:79708513-79709050 and GRCh37_chr10:79709051-79709588 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:79730866-79731376 Neighboring gene H2A.Z histone pseudogene 5 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:79743812-79745011 Neighboring gene RNA polymerase III subunit A Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:79784551-79785750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3612

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_074416.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    77947151..77947445
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    78816188..78816483
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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