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LOC129390370 MPRA-validated peak1494 silencer [ Homo sapiens (human) ]

Gene ID: 129390370, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390370
Gene description
MPRA-validated peak1494 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 LOC129390370 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (120061126..120061326)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (120084474..120084674)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (119931835..119932035)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2744 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119884626-119885231 Neighboring gene NANOG hESC enhancer GRCh37_chr11:119893768-119894269 Neighboring gene uncharacterized LOC105369527 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_19353 Neighboring gene NANOG hESC enhancer GRCh37_chr11:119926297-119926798 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119932166-119933158 Neighboring gene uncharacterized LOC105378956 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:119952219-119953418 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:119967440-119968306 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5635 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:119994383-119994890 Neighboring gene tripartite motif containing 29 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:119995312-119996511 Neighboring gene uncharacterized LOC105369529

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_156000.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    120061126..120061326
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    120084474..120084674
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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