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LOC125316784 Sharpr-MPRA regulatory region 13674 [ Homo sapiens (human) ]

Gene ID: 125316784, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125316784
Gene description
Sharpr-MPRA regulatory region 13674
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 22:ReprW, weaker Polycomb repression). [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 (68628168..68628462)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (69505031..69505325)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene arylsulfatase G Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:66432181-66432681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8900 Neighboring gene protein kinase cAMP-dependent type I regulatory subunit alpha Neighboring gene ReSE screen-validated silencer GRCh37_chr17:66453793-66454079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8902 Neighboring gene microRNA 635 Neighboring gene WD repeat domain, phosphoinositide interacting 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:66494688-66494871 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66508045-66508618 Neighboring gene Sharpr-MPRA regulatory region 15560 Neighboring gene FAM20A golgi associated secretory pathway pseudokinase Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66627729-66628228 Neighboring gene long intergenic non-protein coding RNA 1482 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66682485-66682986 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:66682987-66683486 Neighboring gene uncharacterized LOC124904049 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66728411-66728992 Neighboring gene Sharpr-MPRA regulatory region 8583 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12651 Neighboring gene uncharacterized LOC105371874 Neighboring gene uncharacterized LOC124904050

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_080603.1 

    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
    68628168..68628462
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    69505031..69505325
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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