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LOC111365185 GATA motif-containing MPRA enhancer 41 [ Homo sapiens (human) ]

Gene ID: 111365185, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111365185
Gene description
GATA motif-containing MPRA enhancer 41
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. The major subregion was validated as an active enhancer by the ChIP-STARR-seq massively parallel reporter assay in naive human embryonic stem cells, where it associates with the OCT4 and NANOG transcription factors and is marked by the H3K4me1 histone modification. Another subregion was also validated as an enhancer by high-throughput massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. That enhancer contains a conserved motif for a GATA activator, and mutation of the motif results in reduced enhancer activity. An overlapping subregion was also validated as a functional enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 cells (group: K562 Activating DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). In addition, a subregion was validated as a high-confidence cis-regulatory element for the GFI1B (growth factor independent 1B transcriptional repressor) gene on chromosome 9 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Jan 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 (133003226..133004778)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (145219172..145220724)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (135879214..135880165)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene growth factor independent 1B transcriptional repressor Neighboring gene ribosomal protein L39 pseudogene 24 Neighboring gene RNA, U7 small nuclear 21 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135869188-135869748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:135869749-135870309 Neighboring gene CRISPRi-validated cis-regulatory element chr9.3630 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135876277-135876777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:135880361-135881232 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:135894502-135895194 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:135895195-135895887 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 5 Neighboring gene small nucleolar RNA, C/D box 141A Neighboring gene uncharacterized LOC105376306 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29226

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. A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. Gasperini M, et al. Cell, 2019 Jan 10. PMID 30612741, Free PMC Article
  4. An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium. Nature, 2012 Sep 6. PMID 22955616, Free PMC Article
  5. The accessible chromatin landscape of the human genome. Thurman RE, et al. Nature, 2012 Sep 6. PMID 22955617, Free PMC Article

See all (7) citations in PubMed

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

  • CRISPRi-validated cis-regulatory element chr9.3633
  • GATA activator MPRA enhancer 41
  • OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:135878613-135879486
  • Sharpr-MPRA regulatory region 4600
  • massively parallel reporter assay enhancer

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_055798.3 

    Range
    101..1653
    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
    133003226..133004778
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    145219172..145220724
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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