U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC125371493 Sharpr-MPRA regulatory region 9725 [ Homo sapiens (human) ]

Gene ID: 125371493, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC125371493
Gene description
Sharpr-MPRA regulatory region 9725
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 K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, May 2022]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
19p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (18771579..18771873)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (18907175..18907469)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10412 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10413 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10414 Neighboring gene Sharpr-MPRA regulatory region 5939 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18748277-18748791 Neighboring gene RNA, 7SL, cytoplasmic 155, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18758904-18759714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18759715-18760525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18762196-18762783 Neighboring gene kelch like family member 26 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18768110-18768641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18768642-18769172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18771679-18772215 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18783189-18783923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18806569-18807467 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18810877-18811723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14331 Neighboring gene CREB regulated transcription coactivator 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18820620-18821614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18859933-18860916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18878537-18879414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18879415-18880291 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18900694-18901273 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18901274-18901854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18901855-18902433 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18905989-18906518 Neighboring gene Sharpr-MPRA regulatory region 2922 Neighboring gene cartilage oligomeric matrix protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10419 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10421 Neighboring gene NANOG hESC enhancer GRCh37_chr19:18944963-18945515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14333 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18960435-18960659 Neighboring gene UPF1 RNA helicase and ATPase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10422

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

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_080794.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    18771579..18771873
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    18907175..18907469
    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