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LOC125384566 Sharpr-MPRA regulatory region 6416 [ Homo sapiens (human) ]

Gene ID: 125384566, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125384566
Gene description
Sharpr-MPRA regulatory region 6416
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 non-DNase unmatched - State 14:Gen5', transcription transition, highly expressed genes towards 5' end) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 14:Gen5'). [provided by RefSeq, May 2022]
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Genomic context

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Location:
20p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (3896302..3896596)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (3927236..3927530)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12633 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:3831491-3831992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3838319-3838818 Neighboring gene mitochondrial antiviral signaling protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3846659-3847160 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:3869109-3869660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12635 Neighboring gene PANK2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17488 Neighboring gene pantothenate kinase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:3886163-3886663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17489 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60114 Neighboring gene microRNA 103a-2 Neighboring gene microRNA 103b-2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17490 Neighboring gene ring finger protein 24 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:3996195-3997127

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_080889.1 

    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
    3896302..3896596
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    3927236..3927530
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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