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LOC129391155 MPRA-validated peak4143 silencer [ Homo sapiens (human) ]

Gene ID: 129391155, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129391155
Gene description
MPRA-validated peak4143 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 LOC129391155 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (9218729..9218929)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (9261641..9261841)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (9199376..9199576)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene phospholipase C beta 1 Neighboring gene Sharpr-MPRA regulatory region 2883 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:8917332-8917836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:8917837-8918339 Neighboring gene RNA, U105B small nucleolar Neighboring gene uncharacterized LOC105372522 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:9031646-9032845 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:9055836-9056336 Neighboring gene Sharpr-MPRA regulatory region 7247 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:9160877-9161492 Neighboring gene phospholipase C beta 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17537 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:9496172-9496756 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:9499300-9500006 Neighboring gene uncharacterized LOC105372523 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:9553223-9553723 Neighboring gene LAMP5 antisense RNA 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:9557290-9557799 Neighboring gene lysosomal associated membrane protein family member 5 Neighboring gene p21 (RAC1) activated kinase 5

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_156785.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    9218729..9218929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    9261641..9261841
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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