U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC122889067 Sharpr-MPRA regulatory region 3248 [ Homo sapiens (human) ]

Gene ID: 122889067, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC122889067
Gene description
Sharpr-MPRA regulatory region 3248
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, Oct 2021]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC122889067 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 (36938458..36938752)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (36939819..36940113)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (36979949..36980243)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr3:36863988-36864163 Neighboring gene long intergenic non-protein coding RNA 2033 Neighboring gene tetratricopeptide repeat and ankyrin repeat containing 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:36899292-36899475 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:36907187-36907362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19661 Neighboring gene CBX3 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19663 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19664 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:36952104-36952272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19665 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:36964989-36965490 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:36965491-36965990 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19666 Neighboring gene CRISPRi-validated cis-regulatory element chr3.1267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19668 Neighboring gene RNA, U6atac small nuclear 4, pseudogene Neighboring gene protease associated domain containing 1 pseudogene 1

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_077199.1 

    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    36938458..36938752
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    36939819..36940113
    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