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LOC125024505 Sharpr-MPRA regulatory region 13095 [ Homo sapiens (human) ]

Gene ID: 125024505, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125024505
Gene description
Sharpr-MPRA regulatory region 13095
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 DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Apr 2022]
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Genomic context

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Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (65551091..65551385)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (59755852..59756146)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene fucosyltransferase 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8567 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:65973464-65974162 Neighboring gene microRNA 625 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:66004186-66004695 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:66004696-66005204 Neighboring gene EIF1AX pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:66061145-66061679 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:66130864-66131624 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_35248 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:66158244-66158806 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:66159369-66159930 Neighboring gene NANOG hESC enhancer GRCh37_chr14:66212022-66212983 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_35265 Neighboring gene uncharacterized LOC107984641 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:66280257-66280852 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:66280853-66281448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:66297664-66298182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:66305153-66305654 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:66317337-66317512 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_35314 Neighboring gene nuclear receptor coactivator 4 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_080117.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    65551091..65551385
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    59755852..59756146
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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