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LOC113875033 Sharpr-MPRA regulatory region 5919 [ Homo sapiens (human) ]

Gene ID: 113875033, updated on 10-Oct-2023

Summary

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Gene symbol
LOC113875033
Gene description
Sharpr-MPRA regulatory region 5919
Gene type
biological region
Feature type(s)
regulatory: enhancer
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. A subregion was validated as a functional enhancer 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 Activating non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating DNase unmatched - State 1:Tss). This locus also includes two accessible chromatin subregions that were validated as enhancers based on their 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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See LOC113875033 in Genome Data Viewer
Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (53225089..53225601)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (52511353..52511865)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (53254489..53254783)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene lysine demethylase 5C Neighboring gene microRNA 6895 Neighboring gene microRNA 6894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29656 Neighboring gene IQ motif and Sec7 domain ArfGEF 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:53285843-53286438 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:53309250-53309449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:53310370-53311197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:53317293-53318184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20858 Neighboring gene ribosomal protein SA pseudogene 62

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

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 29657
  • ATAC-STARR-seq lymphoblastoid active region 29658

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_063221.2 

    Range
    101..613
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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
    53225089..53225601
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    52511353..52511865
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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