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LOC125048424 Sharpr-MPRA regulatory region 10624 [ Homo sapiens (human) ]

Gene ID: 125048424, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125048424
Gene description
Sharpr-MPRA regulatory region 10624
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 LOC125048424 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 (68294852..68295146)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (62501288..62501582)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene RAD51 paralog B Neighboring gene uncharacterized LOC105370546 Neighboring gene VISTA enhancer hs1392 Neighboring gene RNA, 7SL, cytoplasmic 706, pseudogene Neighboring gene Sharpr-MPRA regulatory region 3110 Neighboring gene MPRA-validated peak2183 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8589 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8590 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:68698864-68700063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8592 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8593 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8594 Neighboring gene RNA, 7SL, cytoplasmic 108, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8595 Neighboring gene Sharpr-MPRA regulatory region 2611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8596 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8597 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8598 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8599 Neighboring gene Sharpr-MPRA regulatory region 2571 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8606 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:68810048-68810732 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5867 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:68830720-68831247 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:68831248-68831776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8607 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:68838900-68839755 Neighboring gene VISTA enhancer hs1688 Neighboring gene uncharacterized LOC101927971 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:68863880-68864606 Neighboring gene ribosomal protein L7a pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8608

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_080120.1 

    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
    68294852..68295146
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    62501288..62501582
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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