U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC123620094 Sharpr-MPRA regulatory region 1078 [ Homo sapiens (human) ]

Gene ID: 123620094, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC123620094
Gene description
Sharpr-MPRA regulatory region 1078
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 non-DNase unmatched - State 23:Low, low signal proximal to active elements). [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 LOC123620094 in Genome Data Viewer
Location:
6p
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (35238812..35239106)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (35061892..35062186)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (35206589..35206883)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene t-complex 11 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:35115441-35116234 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:35116235-35117028 Neighboring gene MPRA-validated peak5764 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr6:35152333-35152714 Neighboring gene Sharpr-MPRA regulatory region 4993 Neighboring gene uncharacterized LOC112267955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17084 Neighboring gene SCUBE3 antisense RNA 1 Neighboring gene signal peptide, CUB domain and EGF like domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17085 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:35211069-35212268 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17087 Neighboring gene zinc finger protein 76 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:35253595-35254794 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:35263932-35264096 Neighboring gene Sharpr-MPRA regulatory region 9100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35280323-35280822 Neighboring gene DEF6 guanine nucleotide exchange factor

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_078078.1 

    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
    35238812..35239106
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    35061892..35062186
    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