U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC125078040 Sharpr-MPRA regulatory region 9666 [ Homo sapiens (human) ]

Gene ID: 125078040, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC125078040
Gene description
Sharpr-MPRA regulatory region 9666
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 15:Elon, transcription elongation, stronger H3K36me3, more exonic). [provided by RefSeq, Apr 2022]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
14q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (102050632..102050926)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (96286242..96286536)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene protein phosphatase 2 regulatory subunit B'gamma Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9054 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9055 Neighboring gene nucleophosmin 1 pseudogene 20 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6104 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9057 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr14:102383507-102384162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:102394927-102395427 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:102394426-102394926 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr14:102411293-102411954 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr14:102411955-102412614 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102413937-102414598 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9059 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:102427622-102427798 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9061 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102430647-102431257 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102431258-102431867 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:102436952-102437452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9064 Neighboring gene dynein cytoplasmic 1 heavy chain 1 Neighboring gene NANOG hESC enhancer GRCh37_chr14:102474230-102474777 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:102493659-102494858 Neighboring gene uncharacterized LOC107984661 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:102515797-102516781 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102523379-102524082 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:102522673-102523378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:102530418-102531305 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:102550057-102551256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6107 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6108 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6109 Neighboring gene RNA, 7SL, cytoplasmic 472, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6110 Neighboring gene heat shock protein 90 alpha family class A member 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:102605474-102605669 Neighboring gene WD repeat domain 20

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the pageHelp

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

Go to the top of the page Help

Review eQTL and phenotype association data in this region using PheGenI

Variation

Go to the top of the page Help

See variants in ClinVar

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_080176.1 

    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    102050632..102050926
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    96286242..96286536
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Molecular Biology Databases