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LOC124629422 Sharpr-MPRA regulatory region 9787 [ Homo sapiens (human) ]

Gene ID: 124629422, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124629422
Gene description
Sharpr-MPRA regulatory region 9787
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Mar 2022]
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Genomic context

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See LOC124629422 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (83818950..83819244)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (83797593..83797887)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:83591168-83591841 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:83604635-83605269 Neighboring gene ribosomal protein L6 pseudogene 25 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:83694145-83694645 Neighboring gene NANOG hESC enhancer GRCh37_chr12:83726841-83727342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:83826060-83826560 Neighboring gene uncharacterized LOC105369874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:83977974-83978474 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:84189628-84190827 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:84264433-84264934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:84264935-84265434 Neighboring gene uncharacterized LOC107984536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:84405381-84405881 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:84436768-84436958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:84521790-84522315 Neighboring gene uncharacterized LOC124900326 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:84664122-84664844 Neighboring gene uncharacterized LOC124902976

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_079781.1 

    Range
    101..395
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    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
    83818950..83819244
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    83797593..83797887
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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