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LOC125371514 Sharpr-MPRA regulatory region 11111 [ Homo sapiens (human) ]

Gene ID: 125371514, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371514
Gene description
Sharpr-MPRA regulatory region 11111
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 DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, May 2022]
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Genomic context

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Location:
19q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (39078629..39078923)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (41882582..41882876)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14608 Neighboring gene F-box protein 27 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14610 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:39521986-39522168 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39522284-39523076 Neighboring gene uncharacterized LOC124904801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14611 Neighboring gene NANOG hESC enhancer GRCh37_chr19:39549145-39549646 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:39564087-39565286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39574861-39575361 Neighboring gene acid phosphatase 7, tartrate resistant (putative) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14612 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39622545-39623126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39623127-39623707 Neighboring gene uncharacterized LOC124904714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39625781-39626526 Neighboring gene p21 (RAC1) activated kinase 4

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_080815.1 

    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
    39078629..39078923
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    41882582..41882876
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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