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LOC129388865 MPRA-validated peak3709 silencer [ Homo sapiens (human) ]

Gene ID: 129388865, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388865
Gene description
MPRA-validated peak3709 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 LOC129388865 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (58005820..58006020)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (58010519..58010719)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (58232955..58233155)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124907769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11505 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15791 Neighboring gene uncharacterized LOC124907770 Neighboring gene VRK serine/threonine kinase 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:58206217-58206824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15792 Neighboring gene formin-2-like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:58273209-58273764 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:58273765-58274320 Neighboring gene Sharpr-MPRA regulatory region 1372 Neighboring gene VRK2 intron CAGE-defined low expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:58343433-58343934 Neighboring gene NANOG hESC enhancer GRCh37_chr2:58345900-58346401 Neighboring gene MPRA-validated peak3710 silencer Neighboring gene FA complementation group L Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:58434313-58435228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11507

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_154498.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    58005820..58006020
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    58010519..58010719
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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