U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC121967077 Sharpr-MPRA regulatory region 3012 [ Homo sapiens (human) ]

Gene ID: 121967077, updated on 10-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC121967077
Gene description
Sharpr-MPRA regulatory region 3012
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 DNase matched - State 8:EnhW, candidate weak enhancer and open chromatin). [provided by RefSeq, Jul 2021]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
1p
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (10961072..10961366)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (10500394..10500688)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (11021129..11021423)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 24 Neighboring gene VISTA enhancer hs241 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10969040-10969771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10969934-10970926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10972135-10972636 Neighboring gene uncharacterized LOC105376735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10994223-10995188 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10995189-10996154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10997150-10997734 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 155 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 256 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11001673-11002238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11002239-11002802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11005721-11006524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11008047-11008548 Neighboring gene chromosome 1 open reading frame 127 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:11018518-11019287 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:11020057-11020826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 157 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 257 Neighboring gene cofilin 1 pseudogene 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 258 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:11072454-11073421 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:11073783-11074029 Neighboring gene TAR DNA binding protein Neighboring gene MBL associated serine protease 2

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_076217.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    10961072..10961366
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    10500394..10500688
    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