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LOC111413011 GATA motif-containing MPRA enhancer 137 [ Homo sapiens (human) ]

Gene ID: 111413011, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111413011
Gene description
GATA motif-containing MPRA enhancer 137
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. A sub-region 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 a GATA activator, and mutation of the motif results in reduced enhancer activity. This genomic region was also validated as a functional enhancer by the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using MPRAs) in K562 cells (group: K562 Activating DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). [provided by RefSeq, May 2018]
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Genomic context

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Location:
16q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (89004161..89004455)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (95082430..95082724)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (89070569..89070863)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene CBFA2/RUNX1 partner transcriptional co-repressor 3 Neighboring gene uncharacterized LOC107984871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11377 Neighboring gene uncharacterized LOC100129697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7885 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7886 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7887 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7889 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:89023211-89023356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11378 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11379 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89035421-89036276 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11380 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11382 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89041740-89042284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11384 Neighboring gene uncharacterized LOC124903756 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:89048580-89048782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89049867-89050367 Neighboring gene VISTA enhancer hs1854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89067412-89067972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11386 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11388 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7891 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11390 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89100847-89101733 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89103856-89104363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11391 Neighboring gene uncharacterized LOC105371411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11392 Neighboring gene uncharacterized LOC105371412

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. 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

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

  • GATA activator MPRA enhancer 137
  • Sharpr-MPRA regulatory region 15211
  • massively parallel reporter assay enhancer 137

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_055844.2 

    Range
    101..395
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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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    89004161..89004455
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    95082430..95082724
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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