U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC112935946 Sharpr-MPRA regulatory region 7935 [ Homo sapiens (human) ]

Gene ID: 112935946, updated on 17-Jun-2024

Summary

Go to the top of the page Help
Gene symbol
LOC112935946
Gene description
Sharpr-MPRA regulatory region 7935
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. The major subregion includes an enhancer that was validated by the ChIP-STARR-seq massively parallel reporter assay (MPRA) in naive and primed human embryonic stem cells, where it associates with the NANOG transcription factor and is marked by the H3K27ac and H3K4me1 histone modifications. Another subregion was validated as an enhancer by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in both HepG2 liver carcinoma cells (group: HepG2 Activating non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region) and K562 erythroleukemia cells (group: K562 Activating non-DNase unmatched - State 1:Tss). This locus also includes four accessible chromatin subregions, three of which were validated as silencers and one as an enhancer based on their ability to repress or activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC112935946 in Genome Data Viewer
Location:
3p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (49411123..49412635)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (49440502..49442014)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (49449429..49449723)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ubiquitin specific peptidase 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49353925-49354426 Neighboring gene Sjoegren syndrome nuclear autoantigen 1 homolog Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49354427-49354926 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14361 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49377657-49378156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19864 Neighboring gene Sharpr-MPRA regulatory region 2568 Neighboring gene GATA motif-containing MPRA enhancer 295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19865 Neighboring gene H3K27ac hESC enhancers GRCh37_chr3:49395462-49396070 and GRCh37_chr3:49396071-49396679 Neighboring gene glutathione peroxidase 1 Neighboring gene ras homolog family member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49423846-49424400 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49424401-49424954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49426165-49426934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19868 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49455091-49455809 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49458781-49459533 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49459534-49460287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19869 Neighboring gene T cell leukemia translocation altered Neighboring gene aminomethyltransferase Neighboring gene nicolin 1, tubulin polyglutamylase complex subunit Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19871 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49496363-49497118 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49498631-49499386 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49502186-49502686 Neighboring gene RNA, 5S ribosomal pseudogene 130

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. PMID 35858748, Free PMC Article
  3. Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells. Barakat TS, et al. Cell Stem Cell, 2018 Aug 2. PMID 30033119, 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

  • ATAC-STARR-seq lymphoblastoid active region 19867
  • ATAC-STARR-seq lymphoblastoid silent region 14363
  • ATAC-STARR-seq lymphoblastoid silent region 14364
  • ATAC-STARR-seq lymphoblastoid silent region 14365
  • NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49448556-49449530

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_061460.3 

    Range
    101..1613
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    49411123..49412635
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    49440502..49442014
    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