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LOC129389449 MPRA-validated peak5677 silencer [ Homo sapiens (human) ]

Gene ID: 129389449, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389449
Gene description
MPRA-validated peak5677 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 LOC129389449 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 (15176245..15176445)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (15049436..15049636)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (15176476..15176676)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15104898-15105100 Neighboring gene RNA, 7SL, cytoplasmic 332, pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:15132654-15133853 Neighboring gene ribosomal protein L6 pseudogene 17 Neighboring gene uncharacterized LOC105374946 Neighboring gene MPRA-validated peak5678 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15203770-15204322 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15207084-15207636 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:15212336-15212500 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15239058-15239558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:15239559-15240059 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:15244415-15244928 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16946 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16949 Neighboring gene JARID2 antisense RNA 1 Neighboring gene JARID2 divergent transcript Neighboring gene jumonji and AT-rich interaction domain containing 2

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_155079.1 

    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
    15176245..15176445
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    15049436..15049636
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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