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LOC125371502 Sharpr-MPRA regulatory region 12624 [ Homo sapiens (human) ]

Gene ID: 125371502, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125371502
Gene description
Sharpr-MPRA regulatory region 12624
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 matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, May 2022]
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Genomic context

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See LOC125371502 in Genome Data Viewer
Location:
19q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (28526082..28526376)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (31056034..31056328)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2987 Neighboring gene zinc finger protein 709 pseudogene Neighboring gene uncharacterized LOC105372346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14404 Neighboring gene NANOG hESC enhancer GRCh37_chr19:28621443-28621988 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:28659458-28660167 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:28660168-28660878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:28727181-28727891 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:28726469-28727180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:28760939-28761439 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr19:28781600-28782131 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr19:28794338-28794874 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:28804274-28805473 Neighboring gene MPRA-validated peak3419 silencer Neighboring gene MPRA-validated peak3420 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr19:28881947-28882183 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:28891469-28892122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:28890814-28891468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:28893490-28894450 Neighboring gene MPRA-validated peak3422 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:28913828-28914513 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:28916721-28917240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:28917241-28917759 Neighboring gene Sharpr-MPRA regulatory region 924 Neighboring gene SHC binding and spindle associated 1 pseudogene Neighboring gene uncharacterized LOC105372349 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:28936697-28937404 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:29036304-29036510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:29080318-29080960 Neighboring gene uncharacterized LOC124904681 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:29096818-29098017 Neighboring gene uncharacterized LOC102724908 Neighboring gene Sharpr-MPRA regulatory region 736 Neighboring gene Sharpr-MPRA regulatory region 5210 Neighboring gene uncharacterized LOC124904679

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

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_080803.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    28526082..28526376
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    31056034..31056328
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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