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LOC125110357 Sharpr-MPRA regulatory region 342 [ Homo sapiens (human) ]

Gene ID: 125110357, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125110357
Gene description
Sharpr-MPRA regulatory region 342
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 21:Repr, strong Polycomb repression). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (73362928..73363222)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (71180061..71180355)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene neogenin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:73617084-73617584 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:73617585-73618085 Neighboring gene microRNA 12135 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:73622233-73623136 Neighboring gene uncharacterized LOC105370890 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:73635762-73636961 Neighboring gene MPRA-validated peak2386 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:73644210-73644710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:73644711-73645211 Neighboring gene VISTA enhancer hs2161 Neighboring gene hyperpolarization activated cyclic nucleotide gated potassium channel 4 Neighboring gene serine-aspartate repeat-containing protein I-like Neighboring gene REC114 meiotic recombination protein Neighboring gene mitochondrial ribosomal protein S15 pseudogene 1

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_080258.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    73362928..73363222
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    71180061..71180355
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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