U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC122149297 Sharpr-MPRA regulatory region 3225 [ Homo sapiens (human) ]

Gene ID: 122149297, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC122149297
Gene description
Sharpr-MPRA regulatory region 3225
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 DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). [provided by RefSeq, Jul 2021]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC122149297 in Genome Data Viewer
Location:
1q
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (172510589..172510883)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (171867294..171867588)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (172479729..172480023)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene dynamin 3 Neighboring gene uncharacterized LOC102724528 Neighboring gene NANOG hESC enhancer GRCh37_chr1:172397968-172398490 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:172413041-172413564 Neighboring gene chromosome 1 open reading frame 105 Neighboring gene Sharpr-MPRA regulatory region 10840 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:172466106-172466606 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:172466607-172467107 Neighboring gene Sharpr-MPRA regulatory region 5023 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2092 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2093 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2094 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:172539927-172540926 Neighboring gene SUN domain containing ossification factor Neighboring gene RNA, U6 small nuclear 693, 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

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)

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_076498.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    172510589..172510883
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    171867294..171867588
    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