U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129389122 MPRA-validated peak4798 silencer [ Homo sapiens (human) ]

Gene ID: 129389122, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129389122
Gene description
MPRA-validated peak4798 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 LOC129389122 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (122874188..122874388)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (125593382..125593582)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (122593035..122593235)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:122399197-122399969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20384 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:122419937-122420437 Neighboring gene poly(ADP-ribose) polymerase family member 14 Neighboring gene small nucleolar RNA U13 Neighboring gene HSPB1 associated protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14645 Neighboring gene solute carrier family 49 member 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20387 Neighboring gene long intergenic non-protein coding RNA 2035 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:122632187-122632687 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:122645367-122645867 Neighboring gene semaphorin 5B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:122693322-122694086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:122694087-122694852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20389 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:122701773-122702273 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:122739281-122739946 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:122739947-122740611 Neighboring gene NANOG hESC enhancer GRCh37_chr3:122747214-122747721

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

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_154753.1 

    Range
    101..301
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    122874188..122874388
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    125593382..125593582
    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