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LOC113939959 Sharpr-MPRA regulatory region 7669 [ Homo sapiens (human) ]

Gene ID: 113939959, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113939959
Gene description
Sharpr-MPRA regulatory region 7669
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. 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 unmatched - State 5:Enh, candidate strong enhancer, open chromatin). This region also displayed enhancer activity by Sharpr-MRPA in HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 6:EnhF, candidate strong enhancer, flanking open chromatin, and K562 Repressive DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2021]
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Genomic context

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Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (29663231..29663525)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (30606120..30606414)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (27990249..27990543)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 11433 Neighboring gene uncharacterized LOC107984990 Neighboring gene Sharpr-MPRA regulatory region 3347 Neighboring gene RNA, U6 small nuclear 920, pseudogene Neighboring gene slingshot protein phosphatase 2 Neighboring gene VISTA enhancer hs1675 Neighboring gene MPRA-validated peak2783 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:28040137-28040766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8386 Neighboring gene ribosomal protein L21 pseudogene 123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11985 Neighboring gene RNA terminal phosphate cyclase like 1 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)

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_063742.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    29663231..29663525
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    30606120..30606414
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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