U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

LOC129389010 MPRA-validated peak4085 silencer [ Homo sapiens (human) ]

Gene ID: 129389010, updated on 12-Sep-2024

Summary

Go to the top of the page Help
Gene symbol
LOC129389010
Gene description
MPRA-validated peak4085 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 LOC129389010 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (232075466..232075666)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (232562069..232562269)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (232940176..232940376)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232769840-232770458 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:232770459-232771076 Neighboring gene microRNA 1471 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12451 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12452 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12453 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232791796-232792450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12454 Neighboring gene natriuretic peptide C Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:232854631-232855252 Neighboring gene DIS3 like 3'-5' exoribonuclease 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:232986245-232986439 Neighboring gene Sharpr-MPRA regulatory region 7061 Neighboring gene microRNA 562 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233096173-233096674 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12456 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12457 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:233141549-233142064 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:233156819-233157542 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:233157543-233158264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17321 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233194285-233195258 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233197669-233198468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233198469-233199268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233201669-233202468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233207551-233208060 Neighboring gene NRBF2 pseudogene 6

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_154642.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    232075466..232075666
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    232562069..232562269
    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