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LOC129389438 MPRA-validated peak5648 silencer [ Homo sapiens (human) ]

Gene ID: 129389438, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389438
Gene description
MPRA-validated peak5648 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 LOC129389438 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (8031103..8031303)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (7899858..7900058)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (8031336..8031536)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene bone morphogenetic protein 6 Neighboring gene BLOC1S5-TXNDC5 readthrough (NMD candidate) Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:7882299-7883498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16891 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23952 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:7919793-7920992 Neighboring gene thioredoxin domain containing 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23954 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16894 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:7986177-7986678 Neighboring gene EEF1E1-BLOC1S5 readthrough (NMD candidate) Neighboring gene ReSE screen-validated silencer GRCh37_chr6:8012284-8012492 Neighboring gene phosphatidylinositol-4-phosphate 5-kinase type 1 pseudogene 1 Neighboring gene biogenesis of lysosomal organelles complex 1 subunit 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:8063830-8064456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23957 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:8102180-8102365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16895 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16896 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:8109366-8109558 Neighboring gene small Cajal body-specific RNA 27 Neighboring gene eukaryotic translation elongation factor 1 epsilon 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23958 Neighboring gene uncharacterized LOC105374910 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:8180101-8180646 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:8230067-8230588

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_155068.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    8031103..8031303
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    7899858..7900058
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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