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LOC125138291 Sharpr-MPRA regulatory region 3592 [ Homo sapiens (human) ]

Gene ID: 125138291, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125138291
Gene description
Sharpr-MPRA regulatory region 3592
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. A subregion 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 12:CtcfO, distal CTCF/candidate insulator with open chromatin) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 12:CtcfO). 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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See LOC125138291 in Genome Data Viewer
Location:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (76139417..76139722)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (74010304..74010609)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene neuregulin 4 Neighboring gene uncharacterized LOC124903616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76311273-76311774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9868 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6687 Neighboring gene transmembrane protein 266 Neighboring gene uncharacterized LOC124903531 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76432149-76432982 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:76442422-76442685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76442959-76443537 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:76444006-76444636 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9873 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76453363-76454200 Neighboring gene uncharacterized LOC101929439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9874 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9875 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:76482438-76482591 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9876 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76488419-76488980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76488981-76489540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76489541-76490100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76491300-76491944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:76491945-76492588 Neighboring gene NANOG hESC enhancer GRCh37_chr15:76526655-76527344 Neighboring gene electron transfer flavoprotein subunit alpha Neighboring gene TYRO3P protein tyrosine kinase pseudogene

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 9871

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_080262.2 

    Range
    101..406
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    76139417..76139722
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    74010304..74010609
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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