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LOC113939919 Sharpr-MPRA regulatory region 8002 [ Homo sapiens (human) ]

Gene ID: 113939919, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113939919
Gene description
Sharpr-MPRA regulatory region 8002
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. A subregion was validated as a functional repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations), with weaker repression in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 10:DNaseD). An overlapping subregion was also identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. That subregion was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq MPRAs in K562 cells. [provided by RefSeq, Apr 2023]
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Genomic context

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Location:
11q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (116379432..116379739)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (116393507..116393814)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (116250149..116250443)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107984393 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116001721-116002220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116038545-116039045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116038044-116038544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116047950-116048450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116048451-116048951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116051365-116051866 Neighboring gene Sharpr-MPRA regulatory region 5427 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:116105565-116106066 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:116106067-116106566 Neighboring gene Sharpr-MPRA regulatory region 931 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116136339-116136840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116136841-116137340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116146332-116147282 Neighboring gene uncharacterized LOC107987166 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116201553-116202053 Neighboring gene Sharpr-MPRA regulatory region 3214 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116228067-116228930 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116228931-116229794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116230668-116231168 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:116237776-116238513 Neighboring gene Sharpr-MPRA regulatory region 10278 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:116314992-116315809 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:116315810-116316626 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:116316627-116317444 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:116320808-116321353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116329609-116330153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116369918-116370610 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116375709-116376258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116377349-116377849 Neighboring gene long intergenic non-protein coding RNA 2151 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116406562-116407062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116407063-116407563 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:116451429-116452038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116452039-116452648 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:116452758-116452938 Neighboring gene uncharacterized LOC107984372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:116507034-116507534

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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, Free PMC Article
  2. 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • MPRA-validated peak1479 silencer

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_063705.2 

    Range
    101..408
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    116379432..116379739
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    116393507..116393814
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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