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LOC124416877 Sharpr-MPRA regulatory region 6385 [ Homo sapiens (human) ]

Gene ID: 124416877, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124416877
Gene description
Sharpr-MPRA regulatory region 6385
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 23:Low, low signal proximal to active elements). [provided by RefSeq, Feb 2022]
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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 (97422892..97423186)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (98303066..98303360)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (99182649..99182943)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2676 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:99096642-99097160 Neighboring gene ribosomal RNA processing 12 homolog Neighboring gene ReSE screen-validated silencer GRCh37_chr10:99154004-99154171 Neighboring gene ribosomal protein L34 pseudogene 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3850 Neighboring gene uncharacterized LOC644215 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2677 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:99186899-99187121 Neighboring gene phosphoglycerate mutase 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:99204892-99205472 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:99205473-99206052 Neighboring gene exosome component 1

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_079099.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    97422892..97423186
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    98303066..98303360
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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Other Literature Sources
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