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LOC125371515 Sharpr-MPRA regulatory region 7883 [ Homo sapiens (human) ]

Gene ID: 125371515, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125371515
Gene description
Sharpr-MPRA regulatory region 7883
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC125371515 in Genome Data Viewer
Location:
19q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (39428053..39428763)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (42232316..42233026)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (39918693..39919403)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:39900078-39900668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14619 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10604 Neighboring gene tRNA-Ile (anticodon TAT) 1-1 Neighboring gene microRNA 4530 Neighboring gene pleckstrin homology and RhoGEF domain containing G2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14620 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39925783-39926362 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:39928026-39928794 Neighboring gene ribosomal protein S16 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:39935465-39936262 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:39936263-39937059 Neighboring gene SPT5 homolog, DSIF elongation factor subunit Neighboring gene small nucleolar RNA, C/D box 175

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
  2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:39918693-39919338

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_080816.2 

    Range
    101..811
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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
    39428053..39428763
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    42232316..42233026
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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