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LOC125418081 Sharpr-MPRA regulatory region 10850 [ Homo sapiens (human) ]

Gene ID: 125418081, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125418081
Gene description
Sharpr-MPRA regulatory region 10850
Gene type
biological region
Feature type(s)
regulatory: 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. It was validated as a functional repressive element 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 Repressive DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125418081 in Genome Data Viewer
Location:
21q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (43430729..43431023)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (41785997..41786291)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (44850609..44850903)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44828891-44829414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44829939-44830462 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44830463-44830986 Neighboring gene Sharpr-MPRA regulatory region 3188 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr21:44833640-44834222 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44834223-44834804 Neighboring gene uncharacterized LOC124905029 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44853691-44854192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44854193-44854692 Neighboring gene SIK1-LINC00319 intergenic CAGE-defined high expression enhancer Neighboring gene salt inducible kinase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44865413-44866032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44866033-44866652 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:44867273-44867892 Neighboring gene uncharacterized LOC124900467 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:44874448-44875423 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44875523-44876522 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:44876822-44877032 Neighboring gene long intergenic non-protein coding RNA 319 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:44882521-44883518 Neighboring gene uncharacterized LOC102723380 Neighboring gene heat shock transcription factor 2 binding protein Neighboring gene long intergenic non-protein coding RNA 313

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

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)

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_081107.1 

    Range
    101..395
    Download
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    43430729..43431023
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    41785997..41786291
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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