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LOC111413024 NFE2L2 motif-containing MPRA enhancer 159 [ Homo sapiens (human) ]

Gene ID: 111413024, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111413024
Gene description
NFE2L2 motif-containing MPRA enhancer 159
Gene type
biological region
Feature type(s)
regulatory: enhancer, transcriptional_cis_regulatory_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic region was predicted to be a cell type-specific enhancer based on chromatin state analysis from the ENCODE (ENCyclopedia Of DNA Elements) project. It was validated as a functional enhancer by high-throughput massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. This enhancer contains a conserved motif for the NFE2L2 activator. Mutation of this motif results in reduced enhancer activity. 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:
9q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (124202650..124202794)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (136400748..136400892)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (126964929..126965073)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:126774959-126775531 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:126775532-126776104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:126792309-126793096 Neighboring gene uncharacterized LOC107987037 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:126803186-126803720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:126803721-126804253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:126807814-126808609 Neighboring gene LIM homeobox 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:126840763-126841962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28957 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:126893859-126894071 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28958 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28959 Neighboring gene Sharpr-MPRA regulatory region 10969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:126905749-126906322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:126906323-126906898 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:126906899-126907472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28962 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:126964420-126964620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28964 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20258 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127004798-127005314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127005315-127005831 Neighboring gene Sharpr-MPRA regulatory region 14990 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28972 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20260 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20261 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:127020845-127021790 Neighboring gene uncharacterized LOC124902268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:127026232-127026845 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20262 Neighboring gene uncharacterized LOC613206 Neighboring gene NIMA related kinase 6

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. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Kheradpour P, et al. Genome Res, 2013 May. PMID 23512712, Free PMC Article
  2. Mapping and analysis of chromatin state dynamics in nine human cell types. Ernst J, et al. Nature, 2011 May 5. PMID 21441907, Free PMC Article
  3. 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 28965
  • NFE2L2 activator MPRA enhancer 159
  • massively parallel reporter assay enhancer 159

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_055856.1 

    Range
    101..245
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    124202650..124202794
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    136400748..136400892
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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