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LOC124646389 Sharpr-MPRA regulatory region 7724 [ Homo sapiens (human) ]

Gene ID: 124646389, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124646389
Gene description
Sharpr-MPRA regulatory region 7724
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 16:ElonW, transcriptional elongation, weaker H3K36me3). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (100296231..100296525)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (100257654..100257948)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6854 Neighboring gene Sharpr-MPRA regulatory region 7946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:100595701-100596388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:100596389-100597074 Neighboring gene actin related protein 6 Neighboring gene DEP domain containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4765 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6858 Neighboring gene MPRA-validated peak1911 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:100688535-100689176 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:100689177-100689817 Neighboring gene SCY1 like pseudokinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6859 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:100724514-100724735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:100750302-100750802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:100750803-100751303 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr12:100766477-100767226 Neighboring gene solute carrier family 17 member 8 Neighboring gene small nucleolar RNA U13 Neighboring gene MPRA-validated peak1912 silencer Neighboring gene nuclear receptor subfamily 1 group H member 4 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22518 Neighboring gene MPRA-validated peak1913 silencer

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_079797.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    100296231..100296525
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    100257654..100257948
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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