U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC113146422 Sharpr-MPRA regulatory region 5218 [ Homo sapiens (human) ]

Gene ID: 113146422, updated on 17-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC113146422
Gene description
Sharpr-MPRA regulatory region 5218
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 enhancer 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 Activating DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites). It also displayed weak repressive activity by Sharpr-MPRA in HepG2 liver carcinoma cells (group: HepG2 Repressive non-DNase unmatched - State 22:ReprW, weaker Polycomb repression). [provided by RefSeq, Sep 2018]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC113146422 in Genome Data Viewer
Location:
6q
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (144202712..144203006)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (145395335..145395629)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (144523849..144524143)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144507610-144508110 Neighboring gene syntaxin 11 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:144537315-144537779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25213 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:144550475-144550694 Neighboring gene tRNA-Leu (anticodon TAA) 1-1 Neighboring gene TPT1 pseudogene 4 Neighboring gene MPRA-validated peak6183 silencer Neighboring gene MPRA-validated peak6184 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:144586575-144587308 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:144587309-144588042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25214 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17640 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17641 Neighboring gene uncharacterized LOC124901418 Neighboring gene utrophin

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_061647.1 

    Range
    101..395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    144202712..144203006
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    145395335..145395629
    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