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LOC111429628 GATA motif-containing MPRA enhancer 228 [ Homo sapiens (human) ]

Gene ID: 111429628, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111429628
Gene description
GATA motif-containing MPRA enhancer 228
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 a GATA activator. Mutation of this motif results in reduced enhancer activity. [provided by RefSeq, Nov 2017]
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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 (105647629..105647773)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (117822309..117822453)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (108409910..108410054)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene fibronectin type III and SPRY domain containing 1 like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28742 Neighboring gene RALGAPA1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28744 Neighboring gene FKTN antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr9:108355386-108355925 Neighboring gene fukutin Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:108413980-108414542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20154 Neighboring gene TAL bHLH transcription factor 2 Neighboring gene uncharacterized LOC107987107 Neighboring gene serine and arginine rich splicing factor 10 pseudogene Neighboring gene transmembrane protein 38B

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

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 228
  • massively parallel reporter assay enhancer 228

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_055900.1 

    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
    105647629..105647773
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    117822309..117822453
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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