U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC123575644 Sharpr-MPRA regulatory region 10202 [ Homo sapiens (human) ]

Gene ID: 123575644, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC123575644
Gene description
Sharpr-MPRA regulatory region 10202
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 5:Enh, candidate strong enhancer, open chromatin) and K562 erythroleukemia cells (group: K562 Repressive non-DNase unmatched - State 19:H4K20, transcription, primarily H4K20me1, more intronic). [provided by RefSeq, Dec 2021]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC123575644 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (2226755..2227049)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (2090386..2090680)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (2226989..2227283)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23866 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23867 Neighboring gene GDP-mannose 4,6-dehydratase Neighboring gene NANOG hESC enhancer GRCh37_chr6:1729872-1730373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23868 Neighboring gene uncharacterized LOC124901239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23870 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1873801-1874302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:1874303-1874803 Neighboring gene NANOG hESC enhancer GRCh37_chr6:1919859-1920404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16825 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:1952649-1953848 Neighboring gene MPRA-validated peak5622 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr6:2117206-2117756 Neighboring gene Sharpr-MPRA regulatory region 5333 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23871 Neighboring gene NANOG hESC enhancer GRCh37_chr6:2222412-2223029 Neighboring gene uncharacterized LOC107986512 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:2245481-2245981 Neighboring gene GMDS divergent transcript Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 28

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_077903.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    2226755..2227049
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    2090386..2090680
    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