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LOC129389494 MPRA-validated peak5764 silencer [ Homo sapiens (human) ]

Gene ID: 129389494, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389494
Gene description
MPRA-validated peak5764 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 LOC129389494 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 (35152858..35153058)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (34975066..34975266)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (35120635..35120835)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ankyrin repeat and sterile alpha motif domain containing 1A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24394 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 11 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35012271-35012922 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35015552-35016400 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35016401-35017247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35025703-35026222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35027261-35027778 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35036049-35036712 Neighboring gene NANOG hESC enhancer GRCh37_chr6:35037908-35038409 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:35049025-35049696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35054004-35054504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35055243-35056070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:35056071-35056896 Neighboring gene MPRA-validated peak5763 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24395 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:35115441-35116234 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:35116235-35117028 Neighboring gene t-complex 11 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:35152333-35152714 Neighboring gene Sharpr-MPRA regulatory region 4993 Neighboring gene uncharacterized LOC112267955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17084 Neighboring gene SCUBE3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 1078 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17085 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:35211069-35212268 Neighboring gene signal peptide, CUB domain and EGF like domain containing 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24396

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_155124.1 

    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    35152858..35153058
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    34975066..34975266
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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