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LOC129388879 MPRA-validated peak3752 silencer [ Homo sapiens (human) ]

Gene ID: 129388879, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129388879
Gene description
MPRA-validated peak3752 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]
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Genomic context

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See LOC129388879 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (80190851..80191051)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (80191045..80191245)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene catenin alpha 2 Neighboring gene microRNA 8080 Neighboring gene NANOG hESC enhancer GRCh37_chr2:80204933-80205434 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:80235029-80235530 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:80235531-80236030 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:80363322-80363951 Neighboring gene uncharacterized LOC107985903 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:80458363-80459016 Neighboring gene RBM7 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:80530694-80531319 Neighboring gene leucine rich repeat transmembrane neuronal 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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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

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

NCBI Reference Sequences (RefSeq)

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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_154512.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    80190851..80191051
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    80191045..80191245
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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