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LOC111828490 Sharpr-MPRA regulatory regions 4336 and 10869 [ Homo sapiens (human) ]

Gene ID: 111828490, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111828490
Gene description
Sharpr-MPRA regulatory regions 4336 and 10869
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. Two overlapping sub-regions were validated as functional enhancers by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in HepG2 liver carcinoma cells (group: HepG2 Activating DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). One sub-region also displayed weak repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jan 2018]
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Genomic context

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See LOC111828490 in Genome Data Viewer
Location:
17p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (8420371..8420685)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (8326543..8326857)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (8323689..8324003)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:8285969-8286686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:8286687-8287404 Neighboring gene ribosomal protein L26 Neighboring gene Sharpr-MPRA regulatory region 12124 Neighboring gene ring finger protein 222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8183 Neighboring gene nudE neurodevelopment protein 1 like 1 Neighboring gene MPRA-validated peak2716 silencer Neighboring gene MPRA-validated peak2717 silencer Neighboring gene Sharpr-MPRA regulatory region 9669 Neighboring gene uncharacterized LOC107987245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:8390687-8391187 Neighboring gene Sharpr-MPRA regulatory region 1803 Neighboring gene myosin heavy chain 10 Neighboring gene uncharacterized LOC102724262 Neighboring gene RNA, U7 small nuclear 43 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • Sharpr-MPRA regulatory region 10869
  • Sharpr-MPRA regulatory region 4336

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_056223.1 

    Range
    101..415
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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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    8420371..8420685
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    8326543..8326857
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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