U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC113939974 Sharpr-MPRA regulatory region 11104 [ Homo sapiens (human) ]

Gene ID: 113939974, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC113939974
Gene description
Sharpr-MPRA regulatory region 11104
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 both HepG2 liver carcinoma cells (group: HepG2 Repressive DNase matched - State 9:DNaseU, primarily UW DNase, weaker open chromatin sites) and K562 erythroleukemia cells (group: K562 Repressive DNase unmatched - State 20:ReprD, Polycomb repression with Duke DNase/promoter and conservation enriched). [provided by RefSeq, Jan 2019]
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 (5404078..5404372)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (5390730..5391024)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (5404089..5404383)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene protein tyrosine phosphatase receptor type S Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9922 Neighboring gene uncharacterized LOC105372253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5294563-5295180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5295181-5295797 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5298210-5298710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5301231-5301731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5319701-5320202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5320203-5320702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13801 Neighboring gene uncharacterized LOC105372252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5338211-5338884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9923 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5364893-5365392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5395257-5395803 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51701 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:5477057-5477274 Neighboring gene uncharacterized LOC124904622 Neighboring gene zinc and ring finger 4

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_063755.1 

    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
    5404078..5404372
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    5390730..5391024
    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