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LOC125467745 Sharpr-MPRA regulatory region 5754 [ Homo sapiens (human) ]

Gene ID: 125467745, updated on 10-Oct-2023

Summary

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Gene symbol
LOC125467745
Gene description
Sharpr-MPRA regulatory region 5754
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 18:Pol2, Pol2 specific locations, majority in genes but substantial portion in intergenic locations). [provided by RefSeq, Jun 2022]
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Genomic context

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See LOC125467745 in Genome Data Viewer
Location:
Xp
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (47587290..47587584)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (46997180..46997474)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20807 Neighboring gene Sharpr-MPRA regulatory region 4668 Neighboring gene A-Raf proto-oncogene, serine/threonine kinase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:47434199-47434706 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:47434707-47435213 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:47435306-47435806 Neighboring gene Sharpr-MPRA regulatory region 5152 Neighboring gene CRISPRi-FlowFISH-validated HDAC6 regulatory element 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20808 Neighboring gene synapsin I Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20809 Neighboring gene TIMP metallopeptidase inhibitor 1 Neighboring gene microRNA 4769 Neighboring gene Sharpr-MPRA regulatory region 11481 Neighboring gene complement factor properdin Neighboring gene ETS transcription factor ELK1 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 2

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_081218.1 

    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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    47587290..47587584
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    46997180..46997474
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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