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LOC124909512 Sharpr-MPRA regulatory region 4273 [ Homo sapiens (human) ]

Gene ID: 124909512, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124909512
Gene description
Sharpr-MPRA regulatory region 4273
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 matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC124909512 in Genome Data Viewer
Location:
13q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (95754095..95754389)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (94958653..94958947)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5448 Neighboring gene MT-ND6 pseudogene 18 Neighboring gene MT-CYB pseudogene 3 Neighboring gene DnaJ heat shock protein family (Hsp40) member C3 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 24 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:96558977-96559478 Neighboring gene UDP-glucose glycoprotein glucosyltransferase 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:96606253-96607155 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:96611347-96611848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:96611849-96612348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:96666836-96667336 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:96693792-96694381 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:96705417-96705916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:96741684-96742184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:96742185-96742685 Neighboring gene heparan sulfate 6-O-sulfotransferase 3 Neighboring gene RNA, 7SL, cytoplasmic 164, pseudogene

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_080023.1 

    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    95754095..95754389
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    94958653..94958947
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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