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LOC125371432 Sharpr-MPRA regulatory region 1890 [ Homo sapiens (human) ]

Gene ID: 125371432, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371432
Gene description
Sharpr-MPRA regulatory region 1890
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 24:Quies, heterochromatin/dead zone). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125371432 in Genome Data Viewer
Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (59311757..59312051)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (59513244..59513538)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:56886610-56887224 Neighboring gene MPRA-validated peak3170 silencer Neighboring gene gastrin releasing peptide Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:56936011-56936521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9492 Neighboring gene retina and anterior neural fold homeobox Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9493 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9495 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9494 Neighboring gene complexin 4 Neighboring gene lectin, mannose binding 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13414 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13415 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9496 Neighboring gene uncharacterized LOC107985156 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:57053866-57054862

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_080702.1 

    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    59311757..59312051
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    59513244..59513538
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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