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LOC111429620 GATA motif-containing MPRA enhancer 217 [ Homo sapiens (human) ]

Gene ID: 111429620, updated on 17-Sep-2024

Summary

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Gene symbol
LOC111429620
Gene description
GATA motif-containing MPRA enhancer 217
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 subregion was validated as a functional enhancer by high-throughput massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. The enhancer contains a conserved motif for a GATA activator, and mutation of the motif results in reduced enhancer activity. In addition, this genomic region was validated as a high-confidence cis-regulatory element for the RHAG (Rh associated glycoprotein) gene on chromosome 6 based on multiplex CRISPR/Cas9-mediated perturbation in K562 cells. [provided by RefSeq, Oct 2019]
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Genomic context

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See LOC111429620 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (49646128..49646757)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (49488140..49488769)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (49613841..49614470)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 6456 Neighboring gene cytochrome P450 family 2 subfamily AC member 1, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr6:49553494-49553995 Neighboring gene MPRA-validated peak5837 silencer Neighboring gene Rh associated glycoprotein Neighboring gene Sharpr-MPRA regulatory region 4614 Neighboring gene cysteine rich secretory protein 2 Neighboring gene MPRA-validated peak5838 silencer Neighboring gene MPRA-validated peak5839 silencer Neighboring gene cysteine rich secretory protein 3

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

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 chr6.3307
  • GATA activator MPRA enhancer 217
  • massively parallel reporter assay enhancer 217

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_055895.2 

    Range
    101..730
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    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    49646128..49646757
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    49488140..49488769
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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