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LOC129390910 MPRA-validated peak2934 silencer [ Homo sapiens (human) ]

Gene ID: 129390910, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390910
Gene description
MPRA-validated peak2934 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 LOC129390910 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (62511135..62511335)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (63381091..63381291)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (60588496..60588696)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:60500991-60501521 Neighboring gene methyltransferase 2A, tRNA N3-cytidine Neighboring gene uncharacterized LOC112268200 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60541227-60541728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60541729-60542228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8805 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8808 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:60562255-60562754 Neighboring gene tousled like kinase 2 Neighboring gene ribosomal protein S10 pseudogene 26 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:60622822-60623322 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:60636816-60637174 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:60642433-60643632 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:60645420-60645891 Neighboring gene MPRA-validated peak2935 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12540 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:60696223-60696734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60702756-60703256 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:60703257-60703757 Neighboring gene uncharacterized LOC107985020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8809 Neighboring gene mannose receptor C-type 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_156540.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    62511135..62511335
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    63381091..63381291
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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