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LOC125177455 Sharpr-MPRA regulatory region 6529 [ Homo sapiens (human) ]

Gene ID: 125177455, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177455
Gene description
Sharpr-MPRA regulatory region 6529
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 non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Apr 2022]
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Genomic context

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See LOC125177455 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (31754270..31754564)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (32700098..32700392)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903975 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:29998466-29998650 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:30005071-30005572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:30022898-30023398 Neighboring gene RNA, U6 small nuclear 1134, pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:30088656-30089855 Neighboring gene GPR160 pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:30114922-30115422 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:30127927-30128120 Neighboring gene Sharpr-MPRA regulatory region 4911 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:30185250-30185924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8414 Neighboring gene coordinator of PRMT5 and differentiation stimulator

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_080510.1 

    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
    31754270..31754564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    32700098..32700392
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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