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LOC129388815 MPRA-validated peak3579 silencer [ Homo sapiens (human) ]

Gene ID: 129388815, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388815
Gene description
MPRA-validated peak3579 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 LOC129388815 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 (253175..253375)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (253430..253630)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (253175..253375)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 110 member C Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:67739-68240 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:150593-151572 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:151573-152550 Neighboring gene uncharacterized LOC105373324 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:162049-163248 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:197602-198801 Neighboring gene MPRA-validated peak3578 silencer Neighboring gene SH3 and SYLF domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15215 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:284666-285865 Neighboring gene uncharacterized LOC101927262 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11100 Neighboring gene acid phosphatase 1 Neighboring gene ALK and LTK ligand 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_154448.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    253175..253375
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    253430..253630
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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