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LOC129390098 MPRA-validated peak7301 silencer [ Homo sapiens (human) ]

Gene ID: 129390098, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129390098
Gene description
MPRA-validated peak7301 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 LOC129390098 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (96602693..96602893)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (108774468..108774668)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28652 Neighboring gene zinc finger protein 367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20080 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:99180933-99181466 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:99181467-99182000 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:99182517-99183716 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:99185787-99186288 Neighboring gene NSA2 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20083 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20085 Neighboring gene hyaluronan binding protein 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:99256389-99257179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:99257792-99258292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:99273815-99274314 Neighboring gene cell division cycle 14B Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:99284685-99285884 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20087 Neighboring gene MPRA-validated peak7299 silencer Neighboring gene uncharacterized LOC105376163 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:99381276-99381776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20088 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20089 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:99428933-99429433 Neighboring gene peroxiredoxin like 2C Neighboring gene Sharpr-MPRA regulatory region 12242 Neighboring gene makorin ring finger protein 10, pseudogene

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_155728.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    96602693..96602893
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    108774468..108774668
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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