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LOC129390104 MPRA-validated peak7312 silencer [ Homo sapiens (human) ]

Gene ID: 129390104, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390104
Gene description
MPRA-validated peak7312 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 LOC129390104 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (105276774..105276974)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (117451374..117451574)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (108039055..108039255)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376197 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:107875055-107875555 Neighboring gene RN7SK pseudogene 191 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:107899749-107900728 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:107900729-107901708 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:107901709-107902688 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:107902689-107903668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20149 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28737 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:107935529-107936117 Neighboring gene uncharacterized LOC112268038 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:108006574-108007478 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:108007479-108008382 Neighboring gene solute carrier family 44 member 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:108061257-108062456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28738 Neighboring gene MPRA-validated peak7314 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20153 Neighboring gene fibronectin type III and SPRY domain containing 1 like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28740 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28741 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28742 Neighboring gene RALGAPA1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28744 Neighboring gene FKTN antisense RNA 1 Neighboring gene fukutin

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_155734.1 

    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    105276774..105276974
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    117451374..117451574
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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