U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC123775385 Sharpr-MPRA regulatory region 15648 [ Homo sapiens (human) ]

Gene ID: 123775385, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC123775385
Gene description
Sharpr-MPRA regulatory region 15648
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 24:Quies, heterochromatin/dead zone) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 24:Quies). [provided by RefSeq, Jan 2022]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC123775385 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (91473751..91474045)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (92685469..92685763)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (92183469..92183763)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986623 Neighboring gene uncharacterized LOC105377893 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:91379294-91380249 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:91380250-91381204 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:91383116-91384071 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:91384072-91385026 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:91385983-91386936 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:91388246-91389050 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:91489789-91490333 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:91617235-91618434 Neighboring gene NANOG hESC enhancer GRCh37_chr6:91624822-91625331 Neighboring gene NANOG hESC enhancer GRCh37_chr6:91867325-91867853 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:92007857-92008449 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:92008450-92009041 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:92009042-92009634 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:92009635-92010225 Neighboring gene uncharacterized LOC107986624 Neighboring gene MPRA-validated peak5963 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24837 Neighboring gene microRNA 4643 Neighboring gene NANOG hESC enhancer GRCh37_chr6:92363967-92364476 Neighboring gene cancer susceptibility 6

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

See Variation Viewer (GRCh37.p13)

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_078153.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    91473751..91474045
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    92685469..92685763
    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