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LOC125467764 Sharpr-MPRA regulatory region 2135 [ Homo sapiens (human) ]

Gene ID: 125467764, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125467764
Gene description
Sharpr-MPRA regulatory region 2135
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. It was validated as a functional 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 DNase matched - State 4:PromP, inactive/poised promoter, highly conserved) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 4:PromP). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
Xq
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (72306899..72307193)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (70739795..70740089)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29756 Neighboring gene peptidylprolyl cis/trans isomerase, NIMA-interacting 4 Neighboring gene ERCC excision repair 6 like, spindle assembly checkpoint helicase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29757 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29758 Neighboring gene uncharacterized LOC105373250 Neighboring gene NANOG hESC enhancer GRCh37_chrX:71528736-71529237 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:71532082-71532582 Neighboring gene ribosomal protein S4 X-linked Neighboring gene Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29761 Neighboring gene histone deacetylase 8 Neighboring gene RNA, U2 small nuclear 68, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:71773892-71775091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29762 Neighboring gene phosphorylase kinase regulatory subunit alpha 1 Neighboring gene MATR3 pseudogene 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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, 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

  • ATAC-STARR-seq lymphoblastoid active region 29759

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_081234.1 

    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    72306899..72307193
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    70739795..70740089
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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