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LOC123620098 Sharpr-MPRA regulatory region 10771 [ Homo sapiens (human) ]

Gene ID: 123620098, updated on 10-Oct-2023

Summary

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Gene symbol
LOC123620098
Gene description
Sharpr-MPRA regulatory region 10771
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Dec 2021]
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Genomic context

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Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (36239832..36240126)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (36060123..36060417)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (36207609..36207903)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:36098441-36099044 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36106471-36106971 Neighboring gene mitogen-activated protein kinase 13 Neighboring gene BRPF3 antisense RNA 1 Neighboring gene MPRA-validated peak5782 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24421 Neighboring gene bromodomain and PHD finger containing 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36203227-36203772 Neighboring gene uncharacterized LOC105375036 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17111 Neighboring gene patatin like phospholipase domain containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36235945-36236531 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:36253718-36253903 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:36269917-36270417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24423 Neighboring gene BCL2 interacting protein 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_078082.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    36239832..36240126
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    36060123..36060417
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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