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LOC129389237 MPRA-validated peak5117 silencer [ Homo sapiens (human) ]

Gene ID: 129389237, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389237
Gene description
MPRA-validated peak5117 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 LOC129389237 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (133515801..133516001)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (136838060..136838260)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (134436956..134437156)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15691 Neighboring gene protocadherin 10 Neighboring gene uncharacterized LOC124900863 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:134184427-134185124 Neighboring gene Sharpr-MPRA regulatory region 13606 Neighboring gene MPRA-validated peak5118 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:134882009-134882508 Neighboring gene Sharpr-MPRA regulatory region 7344 Neighboring gene NANOG hESC enhancer GRCh37_chr4:134933235-134933765 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:134935198-134935698 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:134935699-134936199 Neighboring gene poly(A) binding protein cytoplasmic 4 like Neighboring gene ReSE screen-validated silencer GRCh37_chr4:134981541-134981750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:134991841-134992529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:135129339-135129839 Neighboring gene pescadillo ribosomal biogenesis factor 1 pseudogene 1

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_154868.1 

    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    133515801..133516001
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    136838060..136838260
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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