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LOC125048431 Sharpr-MPRA regulatory region 2331 [ Homo sapiens (human) ]

Gene ID: 125048431, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125048431
Gene description
Sharpr-MPRA regulatory region 2331
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 DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125048431 in Genome Data Viewer
Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (69688312..69688606)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (63895979..63896273)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene RPL24 pseudogene 3 Neighboring gene coiled-coil domain containing 177 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:70061623-70061793 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8639 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:70088656-70089156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8641 Neighboring gene sushi domain containing 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:70104475-70104987 Neighboring gene Sharpr-MPRA regulatory region 10837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:70124416-70125196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8646 Neighboring gene Sharpr-MPRA regulatory region 930 Neighboring gene Sharpr-MPRA regulatory region 8327 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:70207027-70208226 Neighboring gene uncharacterized LOC100289511 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8648 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:70233975-70234739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8649 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:70237232-70238431 Neighboring gene serine and arginine rich splicing factor 5 Neighboring gene solute carrier family 10 member 1 Neighboring gene Sharpr-MPRA regulatory region 10266

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_080127.1 

    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
    69688312..69688606
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    63895979..63896273
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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