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LOC129389409 MPRA-validated peak5565 silencer [ Homo sapiens (human) ]

Gene ID: 129389409, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389409
Gene description
MPRA-validated peak5565 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 LOC129389409 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 (164073589..164073789)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (164608777..164608977)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (163500595..163500795)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene zinc finger protein 709 pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr5:163319797-163320352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23583 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:163342579-163343125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16592 Neighboring gene LSM1 homolog, mRNA degradation associated pseudogene 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:163546314-163547513 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:163559545-163559889 Neighboring gene NANOG hESC enhancer GRCh37_chr5:163611210-163611711 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:163616370-163616914 Neighboring gene MPRA-validated peak5567 silencer Neighboring gene MPRA-validated peak5568 silencer Neighboring gene long intergenic non-protein coding RNA 3000 Neighboring gene uncharacterized LOC102546299 Neighboring gene long intergenic non-protein coding RNA 2143

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_155039.1 

    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
    164073589..164073789
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    164608777..164608977
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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