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LOC129390321 MPRA-validated peak1376 silencer [ Homo sapiens (human) ]

Gene ID: 129390321, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390321
Gene description
MPRA-validated peak1376 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 LOC129390321 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 (86594813..86595013)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (86305855..86306055)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369421 Neighboring gene Sharpr-MPRA regulatory region 8024 Neighboring gene coiled-coil domain containing 81 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:86153050-86154249 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:86158730-86158943 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:86171015-86171543 Neighboring gene PTP4A1 pseudogene 6 Neighboring gene Sharpr-MPRA regulatory region 11231 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:86208417-86209018 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:86209019-86209620 Neighboring gene MPRA-validated peak1375 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3827 Neighboring gene malic enzyme 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:86234525-86235724 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:86270243-86270744 Neighboring gene Sharpr-MPRA regulatory region 6909 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21738 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:86451485-86452099 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:86452100-86452713 Neighboring gene uncharacterized LOC102724775 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_21766 Neighboring gene NANOG hESC enhancer GRCh37_chr11:86522581-86523167 Neighboring gene Sharpr-MPRA regulatory region 1521 Neighboring gene serine protease 23 Neighboring gene MOB4 pseudogene 2

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_155951.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    86594813..86595013
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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