U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129391274 MPRA-validated peak4474 silencer [ Homo sapiens (human) ]

Gene ID: 129391274, updated on 14-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC129391274
Gene description
MPRA-validated peak4474 silencer
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 region was identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. It was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. [provided by RefSeq, Apr 2023]
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See LOC129391274 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (24876009..24876209)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (25337547..25337747)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene cysteine rich protein 1 pseudogene 4 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr22:25126732-25127306 Neighboring gene piwi like RNA-mediated gene silencing 3 Neighboring gene DNA topoisomerase I pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13556 Neighboring gene small G protein signaling modulator 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:25287609-25288110 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:25293734-25294234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:25294235-25294735 Neighboring gene small nucleolar RNA SNORD56 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:25307870-25308029 Neighboring gene Sharpr-MPRA regulatory region 9438 Neighboring gene LHFPL tetraspan subfamily member 7

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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, 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

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_156904.1 

    Range
    101..301
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    24876009..24876209
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    25337547..25337747
    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