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LOC125177494 Sharpr-MPRA regulatory region 629 [ Homo sapiens (human) ]

Gene ID: 125177494, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177494
Gene description
Sharpr-MPRA regulatory region 629
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 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177494 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (47275303..47275597)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48137660..48137954)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:45266269-45266865 Neighboring gene CRISPRi-validated cis-regulatory element chr17.3215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12300 Neighboring gene myosin light chain 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12303 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12304 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8623 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:45298098-45298754 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45298755-45299410 Neighboring gene Sharpr-MPRA regulatory region 4457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12305 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45314666-45315602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45315603-45316539 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8624 Neighboring gene RNA, U7 small nuclear 186 pseudogene Neighboring gene integrin subunit beta 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45353259-45353806 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12306 Neighboring gene uncharacterized LOC107985029 Neighboring gene Sharpr-MPRA regulatory region 4923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12309 Neighboring gene Sharpr-MPRA regulatory region 4395 Neighboring gene VISTA enhancer hs2033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45369753-45370253 Neighboring gene EFCAB13 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8625

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_080549.1 

    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
    47275303..47275597
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    48137660..48137954
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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