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LOC111365192 GATA motif-containing MPRA enhancer 55/56 [ Homo sapiens (human) ]

Gene ID: 111365192, updated on 10-Oct-2023

Summary

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Gene symbol
LOC111365192
Gene description
GATA motif-containing MPRA enhancer 55/56
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 the Sharpr-MPRA technique (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Activating DNase matched - State 5:Enh). A sub-region also functioned as an enhancer by high-throughput massively parallel reporter assays (MPRAs) in K562 cells. The sub-region contains a conserved motif for a GATA activator, and mutation of the motif results in reduced enhancer activity. [provided by RefSeq, Dec 2018]
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Genomic context

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Location:
7p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (22434030..22434324)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (22569937..22570231)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (22473649..22473943)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene dynein axonemal heavy chain 11 Neighboring gene NANOG hESC enhancer GRCh37_chr7:21981192-21981812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:21985471-21986181 Neighboring gene cell division cycle associated 7 like Neighboring gene VISTA enhancer hs807 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22097966 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22117733 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22118756 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22119917 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22121421 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22123422 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 7:22141595 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17999 Neighboring gene NANOG hESC enhancer GRCh37_chr7:22218362-22218864 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr7:22224198-22225096 Neighboring gene Rap guanine nucleotide exchange factor 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:22281835-22282335 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:22369304-22369804 Neighboring gene RNA, 5S ribosomal pseudogene 227 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25705 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25706 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18002 Neighboring gene HNF4 motif-containing MPRA enhancer 142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:22517166-22517666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:22517667-22518167 Neighboring gene STEAP family member 1B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:22602981-22603482 Neighboring gene STEAP1B antisense RNA 1 Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 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. Toward a complete human genome sequence. Sanger Center, et al. Genome Res, 1998 Nov. PMID 9847074
  4. 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 55/56
  • Sharpr-MPRA regulatory region 12314
  • massively parallel reporter assay enhancer 55/56

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_055807.2 

    Range
    101..395
    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    22434030..22434324
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    22569937..22570231
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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