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LOC129388787 MPRA-validated peak784 silencer [ Homo sapiens (human) ]

Gene ID: 129388787, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388787
Gene description
MPRA-validated peak784 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 LOC129388787 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 (236381795..236381995)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (235784129..235784334)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (236545095..236545295)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene FKBP prolyl isomerase 3 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:236453609-236453847 Neighboring gene uncharacterized LOC124904852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2821 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:236528741-236529521 Neighboring gene EDAR associated via death domain Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2822 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:236553124-236553300 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2823 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236588023-236588524 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2003 Neighboring gene NANOG hESC enhancer GRCh37_chr1:236634853-236635427 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236636352-236636876 Neighboring gene Sharpr-MPRA regulatory region 2344 Neighboring gene enolase 1 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:236679601-236679779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2004 Neighboring gene LGALS8 antisense RNA 1 Neighboring gene galectin 8

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_154420.1 

    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
    236381795..236381995
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    235784129..235784334
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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