U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129391096 MPRA-validated peak3448 silencer [ Homo sapiens (human) ]

Gene ID: 129391096, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129391096
Gene description
MPRA-validated peak3448 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 LOC129391096 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (35349032..35349232)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (37893765..37893965)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (35839935..35840135)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14466 Neighboring gene myelin associated glycoprotein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:35795633-35796520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:35802349-35802850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:35802851-35803350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14467 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14470 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:35824208-35824417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14471 Neighboring gene CD22 molecule Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:35831571-35832072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14477 Neighboring gene microRNA 5196 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:35843089-35843955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10525 Neighboring gene free fatty acid receptor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:35850683-35851210 Neighboring gene free fatty acid receptor 3 Neighboring gene G protein-coupled receptor 42

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_156726.1 

    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    35349032..35349232
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    37893765..37893965
    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