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LOC125384574 Sharpr-MPRA regulatory region 13354 [ Homo sapiens (human) ]

Gene ID: 125384574, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125384574
Gene description
Sharpr-MPRA regulatory region 13354
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 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 12:CtcfO). [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 (8043702..8043996)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (8085700..8085994)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:7964803-7965420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12666 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12667 Neighboring gene TMX4 antisense RNA 1 Neighboring gene thioredoxin related transmembrane protein 4 Neighboring gene Sharpr-MPRA regulatory region 6433 Neighboring gene 20p12 distal LINE-mediated recombination region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12668 Neighboring gene HNF1, HNF4 and FOXA motif-containing MPRA enhancers 45, 51 and 106/107 Neighboring gene phosphorylase kinase regulatory subunit beta pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17536 Neighboring gene phospholipase C beta 1 Neighboring gene PLCB1 intronic transcript 1

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_080897.1 

    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
    8043702..8043996
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    8085700..8085994
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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