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LOC125371421 Sharpr-MPRA regulatory region 125 [ Homo sapiens (human) ]

Gene ID: 125371421, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371421
Gene description
Sharpr-MPRA regulatory region 125
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 2:TssF, active promoter, flanking TSS/CpG islands). [provided by RefSeq, May 2022]
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Genomic context

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Location:
18q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (51194699..51194993)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (51396463..51396757)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:48556194-48556812 Neighboring gene SMAD family member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:48636043-48636544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:48636545-48637044 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:48663303-48664282 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:48664283-48665261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13328 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:48690189-48690688 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:48694526-48695106 Neighboring gene serine and arginine rich splicing factor 10 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:48722055-48722676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9463 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9467 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9468 Neighboring gene mex-3 RNA binding family member C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9469 Neighboring gene RNA, U1 small nuclear 46, pseudogene Neighboring gene long intergenic non-protein coding RNA 1630 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:48943905-48944452 Neighboring gene SS18 like 2 pseudogene 2

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_080691.1 

    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    51194699..51194993
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    51396463..51396757
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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