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LOC125146438 Sharpr-MPRA regulatory region 8859 [ Homo sapiens (human) ]

Gene ID: 125146438, updated on 12-Sep-2024

Summary

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Gene symbol
LOC125146438
Gene description
Sharpr-MPRA regulatory region 8859
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 K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125146438 in Genome Data Viewer
Location:
16p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (29202608..29202902)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (29483910..29484204)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (29213929..29214223)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene RRN3 pseudogene 2 Neighboring gene uncharacterized LOC101928215 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29126448-29126996 Neighboring gene uncharacterized LOC124903671 Neighboring gene uncharacterized LOC100129184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29141163-29141951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29145325-29145825 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29155082-29155768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29155769-29156455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29163489-29164159 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:29166386-29167585 Neighboring gene Sharpr-MPRA regulatory region 414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29177699-29178199 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:29196056-29197255 Neighboring gene RRN3P2-SNX29P2 intergenic nontranscribed DNase I hypersensitive site-defined enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29203636-29204362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:29209784-29210284 Neighboring gene uncharacterized LOC101928188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:29232263-29232832 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:29233140-29233640 Neighboring gene uncharacterized LOC102723708

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_080364.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    29202608..29202902
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    29483910..29484204
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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