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LOC125316775 Sharpr-MPRA regulatory region 12581 [ Homo sapiens (human) ]

Gene ID: 125316775, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125316775
Gene description
Sharpr-MPRA regulatory region 12581
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, May 2022]
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Genomic context

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Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (66467011..66467305)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (67336757..67337051)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene protein kinase C alpha Neighboring gene MPRA-validated peak2943 silencer Neighboring gene RNA, 7SL, cytoplasmic 735, pseudogene Neighboring gene Sharpr-MPRA regulatory region 12714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:64412459-64412958 Neighboring gene PRKCA antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:64429852-64430049 Neighboring gene MPRA-validated peak2944 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12613 Neighboring gene Sharpr-MPRA regulatory region 4299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12614 Neighboring gene Sharpr-MPRA regulatory region 12401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:64529308-64529848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8864 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:64544955-64545137 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:64547106-64547989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:64573678-64574638 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:64597839-64598492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:64598493-64599144 Neighboring gene RNA, U6 small nuclear 928, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 445

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_080594.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    66467011..66467305
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    67336757..67337051
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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