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LOC125177467 Sharpr-MPRA regulatory region 1854 [ Homo sapiens (human) ]

Gene ID: 125177467, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125177467
Gene description
Sharpr-MPRA regulatory region 1854
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 non-DNase unmatched - State 21:Repr, strong Polycomb repression). [provided by RefSeq, Apr 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 (39600016..39600310)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (40463582..40463876)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37730809-37731383 Neighboring gene uncharacterized LOC105371771 Neighboring gene neuronal differentiation 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8458 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8459 Neighboring gene VISTA enhancer hs627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:37775157-37775657 Neighboring gene uncharacterized LOC124903997 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12099

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_080522.1 

    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
    39600016..39600310
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    40463582..40463876
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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