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LOC125048428 Sharpr-MPRA regulatory region 12367 [ Homo sapiens (human) ]

Gene ID: 125048428, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125048428
Gene description
Sharpr-MPRA regulatory region 12367
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 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125048428 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 (69133392..69133686)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (63346498..63346792)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:69504114-69504810 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:69504811-69505508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:69515530-69516030 Neighboring gene ribosomal protein S29 pseudogene 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:69521614-69522813 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:69522944-69523511 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8633 Neighboring gene DDB1 and CUL4 associated factor 5 Neighboring gene Sharpr-MPRA regulatory region 2739 Neighboring gene DEAD-box helicase 18 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 6895 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5877 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5878 Neighboring gene GALNT16 and EXD2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5879 Neighboring gene exonuclease 3'-5' domain containing 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:69705439-69706063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5880 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 16 Neighboring gene uncharacterized LOC105370549

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_080124.1 

    Range
    101..395
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    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
    69133392..69133686
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    63346498..63346792
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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