U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC123493314 Sharpr-MPRA regulatory region 13834 [ Homo sapiens (human) ]

Gene ID: 123493314, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC123493314
Gene description
Sharpr-MPRA regulatory region 13834
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 repressive element by Sharpr-MPRA (Systematic high-resolution activation and repression profiling with reporter tiling using massively parallel reporter assays) in K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 1:Tss, active promoter, TSS/CpG island region). This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to 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
Location:
5q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (57174482..57174776)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (58002787..58003081)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (56470309..56470603)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16029 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22576 Neighboring gene Sharpr-MPRA regulatory region 9364 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_86327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:56389593-56390094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:56391121-56391620 Neighboring gene MPRA-validated peak5252 silencer Neighboring gene RLIG1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22577 Neighboring gene Sharpr-MPRA regulatory region 13785 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22581 Neighboring gene GC-rich promoter binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:56498073-56498573 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:56507443-56507608 Neighboring gene uncharacterized LOC107986381 Neighboring gene TSR1, 20S rRNA accumulation, homolog (S. cerevisiae) pseudogene

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

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 22579

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_077738.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    57174482..57174776
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    58002787..58003081
    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