U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC121725085 Sharpr-MPRA regulatory region 13650 [ Homo sapiens (human) ]

Gene ID: 121725085, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC121725085
Gene description
Sharpr-MPRA regulatory region 13650
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 Sharpr-MPRA (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 22:ReprW, weaker Polycomb repression). A subregion was also identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. That subregion was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq MPRAs in K562 erythroleukemia cells. [provided by RefSeq, Apr 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
2p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (28550402..28550696)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (28594080..28594374)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (28773269..28773563)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:28674597-28675110 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:28675111-28675624 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15516 Neighboring gene phospholipase B1 Neighboring gene Sharpr-MPRA regulatory region 15095 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:28768409-28768908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11309 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11310 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15517 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:28813372-28814338 Neighboring gene Sharpr-MPRA regulatory region 1316 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:28829144-28829775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:28829776-28830406 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:28830407-28831038 Neighboring gene Sharpr-MPRA regulatory region 9151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:28833844-28834508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15519 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15522 Neighboring gene uncharacterized LOC124907746 Neighboring gene uncharacterized LOC105374384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15523 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:28905611-28905817

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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, Free PMC Article
  2. 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)

General gene information

Go to the top of the page Help

Other Names

  • MPRA-validated peak3640 silencer

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_075554.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    28550402..28550696
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    28594080..28594374
    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