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LOC125467786 Sharpr-MPRA regulatory region 6850 [ Homo sapiens (human) ]

Gene ID: 125467786, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125467786
Gene description
Sharpr-MPRA regulatory region 6850
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 is marked by the H3K4me1 histone modification. 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 both HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC125467786 in Genome Data Viewer
Location:
Xq
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (134908419..134909147)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (133233528..133234256)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene placenta enriched 1 Neighboring gene RNA, U4 small nuclear 44, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21013 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21014 Neighboring gene PABIR family member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29977 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:133942169-133943125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21015 Neighboring gene PABIR family member 3 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:133966100-133966314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21016 Neighboring gene motile sperm domain containing 1 Neighboring gene MPRA-validated peak7431 silencer Neighboring gene RNA, U6 small nuclear 616, pseudogene Neighboring gene long intergenic non-protein coding RNA 2243

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

General gene information

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Other Names

  • H3K4me1 hESC enhancer GRCh37_chrX:134042634-134043177

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_081255.2 

    Range
    101..829
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    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    134908419..134909147
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    133233528..133234256
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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