U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC121838565 Sharpr-MPRA regulatory region 12411 [ Homo sapiens (human) ]

Gene ID: 121838565, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC121838565
Gene description
Sharpr-MPRA regulatory region 12411
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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 enhancer 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 Activating non-DNase unmatched - State 23:Low, low signal proximal to active elements). This region also displayed repressive activity by Sharpr-MPRA in K562 erythroleukemia cells (group: K562 Repressive DNase matched - State 5:Enh, candidate strong enhancer, open chromatin). [provided by RefSeq, Jul 2021]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC121838565 in Genome Data Viewer
Location:
12q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (116561464..116561758)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (116542666..116542960)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (116999269..116999563)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:116956174-116956674 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:116956675-116957175 Neighboring gene long intergenic non-protein coding RNA 2457 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:116965601-116966800 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:116971051-116971252 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:116972615-116973149 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7093 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:116977845-116978345 Neighboring gene long intergenic non-protein coding RNA 173 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:116996681-116997190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7096 Neighboring gene microtubule associated protein 1 light chain 3 beta 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:117010377-117010877 Neighboring gene Sharpr-MPRA regulatory region 4921 Neighboring gene uncharacterized LOC124903028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:117096334-117096837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:117100573-117101197 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:117103598-117104149 Neighboring gene long intergenic non-protein coding RNA 3088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7097 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7099 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:117154997-117155526 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:117155527-117156056 Neighboring gene SREBF pathway regulator in golgi 1 Neighboring gene NANOG hESC enhancer GRCh37_chr12:117164433-117164934 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:117174416-117175374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4904 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4905

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_075928.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    116561464..116561758
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    116542666..116542960
    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