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LOC125387267 Sharpr-MPRA regulatory region 9458 [ Homo sapiens (human) ]

Gene ID: 125387267, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125387267
Gene description
Sharpr-MPRA regulatory region 9458
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase unmatched - State 25:Art, potential CNV or repetitive artifacts) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 25:Art). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125387267 in Genome Data Viewer
Location:
20q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (37192306..37192600)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (38916371..38916665)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RB transcriptional corepressor like 1 Neighboring gene RPS27A pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17827 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35724092-35724768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17829 Neighboring gene maestro heat like repeat family member 8 Neighboring gene ribosomal protein L13 pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35807291-35807850 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35807851-35808408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35821940-35822774 Neighboring gene ribophorin II Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35858877-35859417 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:35886402-35886635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12886 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12887 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35896280-35896826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35896827-35897374 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12888 Neighboring gene growth hormone releasing hormone Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17833 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:35918028-35918932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17834 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35943167-35944074 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:35944075-35944984 Neighboring gene mannosidase beta like

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_080943.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    37192306..37192600
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791812.1 Reference GRCh38.p14 PATCHES

    Range
    101808..102102
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    38916371..38916665
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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