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LOC124625873 Sharpr-MPRA regulatory region 14910 [ Homo sapiens (human) ]

Gene ID: 124625873, updated on 10-Oct-2023

Summary

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Gene symbol
LOC124625873
Gene description
Sharpr-MPRA regulatory region 14910
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone). [provided by RefSeq, Mar 2022]
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Genomic context

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Location:
11q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (131839455..131839749)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (131876746..131877040)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene neurotrimin Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:131533266-131533822 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:131540246-131540746 Neighboring gene Sharpr-MPRA regulatory region 15285 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:131547556-131548159 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:131549985-131550486 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:131550487-131550986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:131551806-131552306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:131552307-131552807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4083 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:131560563-131561086 Neighboring gene NTM antisense RNA 1 Neighboring gene GPN-loop GTPase 1 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:131707168-131707668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:131707669-131708169 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:131735724-131736230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:131737835-131738360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:131738361-131738886 Neighboring gene uncharacterized LOC107984413 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:131758747-131759640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4084 Neighboring gene Sharpr-MPRA regulatory region 6145 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:131801564-131801730 Neighboring gene NANOG hESC enhancer GRCh37_chr11:131824673-131825174 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:131847321-131847831 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:131851053-131852006 Neighboring gene VISTA enhancer hs335 Neighboring gene uncharacterized LOC124902795

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_079473.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    131839455..131839749
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    131876746..131877040
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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