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LOC129391293 MPRA-validated peak7356 silencer [ Homo sapiens (human) ]

Gene ID: 129391293, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129391293
Gene description
MPRA-validated peak7356 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 LOC129391293 in Genome Data Viewer
Location:
chromosome: X
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (9440248..9440448)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (9022845..9023045)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905242 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9260651-9261238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29398 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrX:9320474-9321673 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:9374111-9375310 Neighboring gene uncharacterized LOC107985634 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:9382495-9382700 Neighboring gene chromodomain Y like protein pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chrX:9420158-9420316 Neighboring gene Sharpr-MPRA regulatory region 2097 Neighboring gene Sharpr-MPRA regulatory region 7028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9431698-9432526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9471641-9472141 Neighboring gene transducin beta like 1 X-linked Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9490972-9491496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29402 Neighboring gene Sharpr-MPRA regulatory region 11092 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9500568-9501137 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9528031-9528532 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9528533-9529032 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9536306-9537137 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9537138-9537968 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:9554716-9555236 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chrX:9555237-9555756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9561459-9561960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9561961-9562460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9603687-9604186 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chrX:9629664-9630863 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:9650484-9650984 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:9675799-9676456 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:9676457-9677113 Neighboring gene uncharacterized LOC105373126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29403 Neighboring gene G protein-coupled receptor 143

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

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_156923.1 

    Range
    101..301
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    9440248..9440448
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    9022845..9023045
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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