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LOC124416912 Sharpr-MPRA regulatory region 959 [ Homo sapiens (human) ]

Gene ID: 124416912, updated on 12-Sep-2024

Summary

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Gene symbol
LOC124416912
Gene description
Sharpr-MPRA regulatory region 959
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 13:Ctcf, distal CTCF/candidate insulator without open chromatin). [provided by RefSeq, Feb 2022]
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Genomic context

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See LOC124416912 in Genome Data Viewer
Location:
10q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (113611010..113611304)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (114502651..114502945)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (115370769..115371063)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902504 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:115317286-115317966 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:115317967-115318647 Neighboring gene Sharpr-MPRA regulatory region 9721 Neighboring gene hyaluronan binding protein 2 Neighboring gene MPRA-validated peak1095 silencer Neighboring gene OCT4 hESC enhancer GRCh37_chr10:115376450-115376951 Neighboring gene nebulin related anchoring protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4071 Neighboring gene caspase 7 Neighboring gene uncharacterized LOC124902505 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:115479382-115479555 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:115480728-115481927 Neighboring gene pleckstrin homology domain containing S1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:115532373-115533572 Neighboring gene microRNA 4483

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_079128.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    113611010..113611304
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    114502651..114502945
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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