U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC125177524 Sharpr-MPRA regulatory region 8996 [ Homo sapiens (human) ]

Gene ID: 125177524, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC125177524
Gene description
Sharpr-MPRA regulatory region 8996
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 HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 20:ReprD, Polycomb repression w. Duke DNase/promoter and conservation enriched). [provided by RefSeq, Apr 2022]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC125177524 in Genome Data Viewer
Location:
17q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (60161608..60161902)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (61030558..61030852)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:58190476-58191424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:58191425-58192371 Neighboring gene adaptor related protein complex 1 subunit sigma 2 pseudogene Neighboring gene uncharacterized LOC100996660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12525 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12526 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:58216417-58216950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:58217485-58218018 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:58218675-58219231 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:58219938-58220447 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:58232505-58233005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:58235149-58235978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12527 Neighboring gene carbonic anhydrase 4 Neighboring gene family with sequence similarity 106 member D, pseudogene Neighboring gene ubiquitin specific peptidase 32 Neighboring gene small Cajal body-specific RNA 20

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_080579.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    60161608..60161902
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    61030558..61030852
    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