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LOC125424410 Sharpr-MPRA regulatory region 9271 [ Homo sapiens (human) ]

Gene ID: 125424410, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125424410
Gene description
Sharpr-MPRA regulatory region 9271
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 23:Low, low signal proximal to active elements). [provided by RefSeq, Jun 2022]
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Genomic context

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See LOC125424410 in Genome Data Viewer
Location:
22q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (27329548..27329842)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (27790508..27790802)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (27725509..27725803)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27706583-27707357 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27707358-27708131 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:27710082-27710283 Neighboring gene long intergenic non-protein coding RNA 2554 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63191 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63195 Neighboring gene uncharacterized LOC105372979 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63206 Neighboring gene uncharacterized LOC102724900 Neighboring gene NANOG hESC enhancer GRCh37_chr22:27754348-27754896 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:27769315-27769815 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:27803625-27804177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:27828998-27829600 Neighboring gene uncharacterized LOC105372980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:27833795-27834458

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

See Variation Viewer (GRCh37.p13)

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_081145.1 

    Range
    101..395
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    27329548..27329842
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    27790508..27790802
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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