U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129389671 MPRA-validated peak6180 silencer [ Homo sapiens (human) ]

Gene ID: 129389671, updated on 14-Oct-2023

Summary

Go to the top of the page Help
Gene symbol
LOC129389671
Gene description
MPRA-validated peak6180 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 LOC129389671 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (143866478..143866678)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (145059158..145059358)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene PHACTR2 antisense RNA 1 Neighboring gene phosphatase and actin regulator 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17630 Neighboring gene MPRA-validated peak6177 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:143958702-143959245 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:143998446-143999294 Neighboring gene MPRA-validated peak6179 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:144059920-144060420 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144065167-144065836 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:144067178-144067848 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144067849-144068518 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144068519-144069188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25205 Neighboring gene MPRA-validated peak6181 silencer Neighboring gene LTV1 ribosome biogenesis factor Neighboring gene zinc finger C2HC-type containing 1B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25207 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:144279682-144280240 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:144285771-144286284 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:144293958-144294542 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:144294543-144295127 Neighboring gene PLAG1 like zinc finger 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:144328825-144329007 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17633 Neighboring gene FKBP prolyl isomerase 7 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25208 Neighboring gene hydatidiform mole associated and imprinted

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_155301.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    143866478..143866678
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    145059158..145059358
    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