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LOC124646388 Sharpr-MPRA regulatory region 15444 [ Homo sapiens (human) ]

Gene ID: 124646388, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124646388
Gene description
Sharpr-MPRA regulatory region 15444
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 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [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 (98955231..98955525)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (98928246..98928540)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4756 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:99038539-99039166 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:99043141-99044340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:99072005-99072576 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_31421 Neighboring gene MPRA-validated peak1909 silencer Neighboring gene apoptotic peptidase activating factor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:99187754-99187963 Neighboring gene probable ribosome biogenesis protein RLP24 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_31455 Neighboring gene ankyrin repeat and sterile alpha motif domain containing 1B Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:99250207-99250805 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:99250806-99251403 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:99254871-99255612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:99288347-99288846 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:99303485-99304033 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_31475 Neighboring gene uncharacterized LOC101928937 Neighboring gene RNA, 5S ribosomal pseudogene 366

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_079796.1 

    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
    98955231..98955525
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    98928246..98928540
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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