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LOC125316776 Sharpr-MPRA regulatory region 6976 [ Homo sapiens (human) ]

Gene ID: 125316776, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125316776
Gene description
Sharpr-MPRA regulatory region 6976
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 23:Low, low signal proximal to active elements). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125316776 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (66654391..66654685)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (67530457..67530754)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (64650509..64650803)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene protein kinase C alpha Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:64640965-64642164 Neighboring gene RNA, U6 small nuclear 928, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:64672313-64673082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:64710611-64711307 Neighboring gene NANOG hESC enhancer GRCh37_chr17:64718354-64718855 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:64726459-64727144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:64743608-64744108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:64778583-64779084 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:64803038-64803887 Neighboring gene VISTA enhancer hs2613 Neighboring gene microRNA 634 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:64874747-64874957 Neighboring gene calcium voltage-gated channel auxiliary subunit gamma 5

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_080595.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    66654391..66654685
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    67530457..67530754
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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