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LOC129389417 MPRA-validated peak5588 silencer [ Homo sapiens (human) ]

Gene ID: 129389417, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389417
Gene description
MPRA-validated peak5588 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 LOC129389417 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (176508075..176508275)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177052651..177052851)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (175935076..175935276)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ARF like GTPase 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16650 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16652 Neighboring gene clathrin light chain B Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:175861163-175861909 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23685 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23686 Neighboring gene uncharacterized LOC124901142 Neighboring gene Fas associated factor family member 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:175918968-175920167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23687 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175961121-175961790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16655 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23688 Neighboring gene uncharacterized LOC124901143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23689 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175968985-175969591 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16656 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16657 Neighboring gene ring finger protein 44 Neighboring gene RNA, 7SL, cytoplasmic 684, pseudogene Neighboring gene cadherin related family member 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_155047.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    176508075..176508275
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    177052651..177052851
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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