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LOC129388548 MPRA-validated peak283 silencer [ Homo sapiens (human) ]

Gene ID: 129388548, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388548
Gene description
MPRA-validated peak283 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 LOC129388548 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (70458893..70459093)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (70337377..70337577)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (70924576..70924776)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ANKRD13C divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr1:70826052-70826245 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:70833556-70834402 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:70837138-70838020 Neighboring gene long intergenic non-protein coding RNA 3102 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:70838021-70838902 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1194 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1195 Neighboring gene cystathionine gamma-lyase Neighboring gene uncharacterized LOC105378793 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:70925492-70926298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1196 Neighboring gene NANOG hESC enhancer GRCh37_chr1:70994367-70994868 Neighboring gene CHORDC1 pseudogene 5 Neighboring gene uncharacterized LOC105378794

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 Variation Viewer (GRCh37.p13)

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_154182.1 

    Range
    101..301
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    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    70458893..70459093
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    70337377..70337577
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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