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LOC125371464 Sharpr-MPRA regulatory region 3427 [ Homo sapiens (human) ]

Gene ID: 125371464, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371464
Gene description
Sharpr-MPRA regulatory region 3427
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 matched - State 10:DNaseD, primarily Duke DNase, candidate regulatory elements in more likely repressive locations) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, May 2022]
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Genomic context

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Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (6232998..6233292)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (6221180..6221474)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene regulatory factor X2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6074378-6075171 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:6086791-6087292 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:6087293-6087792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6092583-6093288 Neighboring gene ribosomal protein L32 pseudogene 37 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6109025-6109525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9944 Neighboring gene uncharacterized LOC105372255 Neighboring gene Sharpr-MPRA regulatory region 9390 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:6134642-6135545 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:6135546-6136448 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9945 Neighboring gene acyl-CoA synthetase bubblegum family member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6198732-6199335 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr19:6199336-6199938 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13821 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6216753-6217667 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6227079-6227744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6239861-6240362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6243510-6244224 Neighboring gene MLLT1 super elongation complex subunit Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6263545-6264044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6263043-6263544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6273107-6273706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6276605-6277105 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9947 Neighboring gene alkaline ceramidase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6362217-6363174 Neighboring gene caseinolytic mitochondrial matrix peptidase proteolytic subunit

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_080734.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    6232998..6233292
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    6221180..6221474
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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