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LOC125177318 Sharpr-MPRA regulatory region 3823 [ Homo sapiens (human) ]

Gene ID: 125177318, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177318
Gene description
Sharpr-MPRA regulatory region 3823
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 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (56316537..56316831)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (62111571..62111865)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56226034-56226607 Neighboring gene GNAO1 antisense RNA 1 Neighboring gene G protein subunit alpha o1 Neighboring gene microRNA 3935 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56297649-56298217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56311207-56311706 Neighboring gene Sharpr-MPRA regulatory region 182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:56316059-56316608 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:56316609-56317156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56318360-56318881 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56322213-56322875 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_43505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56337209-56337709 Neighboring gene NANOG hESC enhancer GRCh37_chr16:56339811-56340312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56346109-56347085 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56379271-56379958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56382339-56382839 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:56389828-56389987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10848 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:56396251-56396424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:56396447-56396947 Neighboring gene autocrine motility factor receptor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10849 Neighboring gene nudix hydrolase 21

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

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_080386.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    56316537..56316831
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    62111571..62111865
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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