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LOC124629365 Sharpr-MPRA regulatory region 13987 [ Homo sapiens (human) ]

Gene ID: 124629365, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124629365
Gene description
Sharpr-MPRA regulatory region 13987
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 DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [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 (53219645..53219939)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (53185244..53185538)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53552337-53552837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:53553211-53553838 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:53559172-53559335 Neighboring gene cysteine sulfinic acid decarboxylase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53565297-53565796 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr12:53568663-53569598 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:53573975-53574533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4496 Neighboring gene Sharpr-MPRA regulatory region 11900 Neighboring gene zinc finger protein 740 Neighboring gene Sharpr-MPRA regulatory region 11320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6403 Neighboring gene integrin subunit beta 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6404 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:53609063-53609836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53610051-53610664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4497 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4498 Neighboring gene retinoic acid receptor gamma Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4499 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:53635595-53636507 Neighboring gene uncharacterized LOC122455340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6405 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:53645725-53646396 Neighboring gene major facilitator superfamily domain containing 5

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_079735.1 

    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
    53219645..53219939
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    53185244..53185538
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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