U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC125146364 Sharpr-MPRA regulatory region 1749 [ Homo sapiens (human) ]

Gene ID: 125146364, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC125146364
Gene description
Sharpr-MPRA regulatory region 1749
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 2:TssF, active promoter, flanking TSS/CpG islands). [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:
15q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (98663160..98663454)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (96427524..96427818)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene zinc finger CCHC-type containing 9 pseudogene Neighboring gene protein FAM169B Neighboring gene ReSE screen-validated silencer GRCh37_chr15:99031875-99032074 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:99056319-99056501 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99122390-99122890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99122891-99123391 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99135615-99136114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99143721-99144221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99143220-99143720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99148269-99148769 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:99189870-99190491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6854 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6855 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6857 Neighboring gene Sharpr-MPRA regulatory region 7544 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99204502-99205312 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:99211661-99212860 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:99213965-99214690 Neighboring gene IGF1R antisense imprinted non-protein coding RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99243457-99243958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:99243959-99244458 Neighboring gene insulin like growth factor 1 receptor Neighboring gene ReSE screen-validated silencer GRCh37_chr15:99247546-99247726 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99256117-99256819 Neighboring gene VISTA enhancer hs1932 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:99277618-99278148 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:99301249-99301750 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:99301751-99302250 Neighboring gene uncharacterized LOC124903560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99316261-99316843 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99316844-99317425 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99319525-99320432 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:99320433-99321339 Neighboring gene microRNA 4714

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_080294.1 

    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    98663160..98663454
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    96427524..96427818
    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