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LOC129388682 MPRA-validated peak553 silencer [ Homo sapiens (human) ]

Gene ID: 129388682, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388682
Gene description
MPRA-validated peak553 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 LOC129388682 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 (189999886..190000086)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (189346146..189346346)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (189969016..189969216)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1701 Neighboring gene MPRA-validated peak549 silencer Neighboring gene MPRA-validated peak550 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr1:189868671-189869595 Neighboring gene DExH-box helicase 29 pseudogene Neighboring gene MPRA-validated peak555 silencer Neighboring gene BMP/retinoic acid inducible neural specific 3 Neighboring gene MPRA-validated peak561 silencer Neighboring gene uncharacterized LOC105371659 Neighboring gene MPRA-validated peak563 silencer Neighboring gene MPRA-validated peak564 silencer Neighboring gene MPRA-validated peak566 silencer Neighboring gene uncharacterized LOC105371658

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

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_154315.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    189999886..190000086
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    189346146..189346346
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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