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LOC125418088 Sharpr-MPRA regulatory region 3768 [ Homo sapiens (human) ]

Gene ID: 125418088, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125418088
Gene description
Sharpr-MPRA regulatory region 3768
Gene type
biological region
Feature type(s)
regulatory: enhancer, silencer
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This genomic sequence was predicted to be a transcriptional regulatory region 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 is marked by the H3K4me1 histone modification. Another subregion was validated as a repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 17:Gen3', transcription 3' end of genes, highly expressed, more exonic) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 7:EnhWF, candidate poised/weak enhancer, flanking open chromatin of candidate enhancers). [provided by RefSeq, Jan 2023]
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Genomic context

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See LOC125418088 in Genome Data Viewer
Location:
21q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (46141942..46142509)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (44520349..44520916)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene COL6A2 divergent transcript Neighboring gene Sharpr-MPRA regulatory region 12001 Neighboring gene collagen type VI alpha 2 chain Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr21:47527125-47527884 Neighboring gene uncharacterized LOC124905043 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47551971-47552475 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47556247-47557020 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:47560109-47560298 Neighboring gene formimidoyltransferase cyclodeaminase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47571745-47572448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47572449-47573154 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47573155-47573858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47573859-47574562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47574563-47575266 Neighboring gene FTCD antisense RNA 1 Neighboring gene spermatogenesis and centriole associated 1 like Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47590104-47590604 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47590605-47591105 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47600015-47600618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47602435-47603038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47603039-47603642

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. 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
  2. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

General gene information

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Other Names

  • H3K4me1 hESC enhancer GRCh37_chr21:47561856-47562376

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_081114.2 

    Range
    101..668
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    46141942..46142509
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187626.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    1001..1568
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    44520349..44520916
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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