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LOC129388789 MPRA-validated peak786 silencer [ Homo sapiens (human) ]

Gene ID: 129388789, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388789
Gene description
MPRA-validated peak786 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 LOC129388789 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (236598775..236598975)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (235999734..235999934)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (236762075..236762275)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene EDAR associated via death domain Neighboring gene Sharpr-MPRA regulatory region 2344 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:236679601-236679779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2004 Neighboring gene enolase 1 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 1811 Neighboring gene LGALS8 antisense RNA 1 Neighboring gene MPRA-validated peak785 silencer Neighboring gene galectin 8 Neighboring gene HEAT repeat containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2825 Neighboring gene MPRA-validated peak787 silencer Neighboring gene control region 3 heart enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2005 Neighboring gene VISTA enhancer hs2135 Neighboring gene actinin alpha 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2826 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2827 Neighboring gene ribosomal protein SA pseudogene 21 Neighboring gene 5-methyltetrahydrofolate-homocysteine methyltransferase

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_154422.1 

    Range
    101..301
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    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    236598775..236598975
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    235999734..235999934
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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