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LOC125146429 Sharpr-MPRA regulatory region 8546 [ Homo sapiens (human) ]

Gene ID: 125146429, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125146429
Gene description
Sharpr-MPRA regulatory region 8546
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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See LOC125146429 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (23223448..23223742)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (23499491..23499785)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23079291-23079792 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:23104917-23105463 Neighboring gene ubiquitin specific peptidase 31 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7271 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7273 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23183549-23184050 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7275 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23197073-23197574 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23197575-23198074 Neighboring gene sodium channel epithelial 1 subunit gamma Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:23291226-23291748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23312821-23313338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23313339-23313855 Neighboring gene sodium channel epithelial 1 subunit beta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23359541-23360042 Neighboring gene Sharpr-MPRA regulatory region 1348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23391379-23391880 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:23410440-23411363 Neighboring gene component of oligomeric golgi complex 7 Neighboring gene RN7SK pseudogene 23

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_080355.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    23223448..23223742
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    23499491..23499785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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