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LOC125387313 Sharpr-MPRA regulatory region 1887 [ Homo sapiens (human) ]

Gene ID: 125387313, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125387313
Gene description
Sharpr-MPRA regulatory region 1887
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 21:Repr, strong Polycomb repression). [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 (61361753..61362047)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (63149484..63149778)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:59676211-59677410 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59688891-59689390 Neighboring gene long intergenic non-protein coding RNA 1718 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:59698201-59698846 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:59738200-59739399 Neighboring gene uncharacterized LOC105372701 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:59794837-59796036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59829421-59830113 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59837300-59837811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59842714-59843244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59843245-59843775 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr20:59881901-59882407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59892319-59893194 Neighboring gene cadherin 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59928779-59929522 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:59964898-59966097 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59966867-59967466 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59971133-59971634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59971635-59972134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59981242-59981742 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59981743-59982243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:59999531-60000423 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60000424-60001315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60009149-60009738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60008559-60009148 Neighboring gene uncharacterized LOC105372703 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:60011920-60013119 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60023738-60024298 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60024299-60024857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60073706-60074206 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:60075832-60077031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60088606-60089115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60106507-60107008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60113444-60114423 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60131355-60131856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60131857-60132356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60137997-60138897 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60164799-60165300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60173673-60174405 Neighboring gene MPRA-validated peak4296 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr20:60193522-60194023 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60203424-60204083 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60204084-60204742 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:60231445-60231625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60237181-60237694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60237695-60238208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60263433-60263932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60274679-60275179 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:60284281-60284449 Neighboring gene uncharacterized LOC100128310

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_081038.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    61361753..61362047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    63149484..63149778
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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