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LOC129389830 MPRA-validated peak6654 silencer [ Homo sapiens (human) ]

Gene ID: 129389830, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389830
Gene description
MPRA-validated peak6654 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 LOC129389830 in Genome Data Viewer
Location:
chromosome: 7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (98334144..98334344)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (99564890..99565090)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (97963456..97963656)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901705 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:97909829-97910813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:97915383-97916095 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:97916808-97917520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26307 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:97925226-97925340 Neighboring gene brain protein I3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:97925951-97926452 Neighboring gene BAR/IMD domain containing adaptor protein 2 like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:97935156-97935656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:97935657-97936157 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:97942170-97942317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:97946925-97947425 Neighboring gene Sharpr-MPRA regulatory region 688 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:97989013-97989890 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:97989891-97990770 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:97991721-97992482 Neighboring gene uncharacterized LOC124901862 Neighboring gene RPS3A pseudogene 26

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_155460.1 

    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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    98334144..98334344
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    99564890..99565090
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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