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LOC125387257 Sharpr-MPRA regulatory region 13573 [ Homo sapiens (human) ]

Gene ID: 125387257, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125387257
Gene description
Sharpr-MPRA regulatory region 13573
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 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, May 2022]
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Genomic context

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Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (32711387..32711681)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (34440054..34440349)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr20:31226322-31226509 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31226763-31227262 Neighboring gene chromosome 20 open reading frame 203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31235460-31235960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31235961-31236461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17719 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12805 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31252264-31252832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31252833-31253400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31254622-31255122 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31259991-31260490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31263362-31264064 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31266424-31267023 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31267024-31267622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31267623-31268222 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr20:31268822-31269421 and GRCh37_chr20:31269422-31270020 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31271401-31271902 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31271903-31272402 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31274017-31274656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31277881-31278443 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:31290694-31291210 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31293307-31294054 Neighboring gene BCL2 antagonist/killer 1 pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31296664-31297170 Neighboring gene COMM domain containing 7 Neighboring gene OCT4 hESC enhancer GRCh37_chr20:31310141-31310642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31310711-31311220 Neighboring gene Sharpr-MPRA regulatory region 10337 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31320600-31321468 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31321469-31322336 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31324911-31325766 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:31326137-31326302 Neighboring gene OCT4 hESC enhancer GRCh37_chr20:31328938-31329439 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:31329890-31330064 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31330109-31330936 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12807 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr20:31331824-31332768 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr20:31334657-31335599 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31336541-31337182 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31337183-31337824 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31337825-31338466 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31338467-31339107 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:31339333-31339906 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31339907-31340480 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31340481-31341054 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31343273-31344259 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31344260-31345245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31347799-31348347 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31348348-31348895 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31349119-31349784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12808 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12809 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:31351780-31352445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31353111-31353775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31353776-31354439 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31355267-31355868 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31355869-31356470 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31358045-31358546 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31361516-31362222 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31362928-31363633 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31365281-31365829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31365865-31366366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31366868-31367368 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31367369-31367869 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31367870-31368371 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31368372-31368872 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31368873-31369873 Neighboring gene DNA methyltransferase 3 beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31374779-31375450 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:31375451-31376121 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31377111-31378042 Neighboring gene OCT4-H3K27ac hESC enhancer GRCh37_chr20:31378043-31378972 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:31385992-31387191 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31388345-31389148 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31389149-31389952 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31391821-31392634 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31394723-31395522 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31395523-31396320 Neighboring gene OCT4 hESC enhancer GRCh37_chr20:31397487-31397988 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12810 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31408139-31408808 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:31408809-31409478 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:31420386-31420886 Neighboring gene microtubule associated protein RP/EB family member 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:31428835-31429334

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_080933.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    32711387..32711681
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    34440054..34440349
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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