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LOC125371413 Sharpr-MPRA regulatory region 1203 [ Homo sapiens (human) ]

Gene ID: 125371413, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371413
Gene description
Sharpr-MPRA regulatory region 1203
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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Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (46448466..46448760)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (46639027..46639321)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene arkadia (RNF111) C-terminal like ring finger ubiquitin ligase 2C Neighboring gene uncharacterized LOC105372095 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:43972627-43973160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:43991726-43992676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:43994577-43995525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:44004729-44005693 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:44007521-44008096 Neighboring gene uncharacterized LOC124904293 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:44015273-44015773 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:44027257-44028040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:44038097-44038886 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:44044737-44045236 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:44046140-44046972 Neighboring gene MPRA-validated peak3132 silencer Neighboring gene MPRA-validated peak3133 silencer Neighboring gene lipoxygenase homology PLAT domains 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:44237431-44238380 Neighboring gene uncharacterized LOC105372096

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_080683.1 

    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
    46448466..46448760
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    46639027..46639321
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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