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LOC129389955 MPRA-validated peak6901 silencer [ Homo sapiens (human) ]

Gene ID: 129389955, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389955
Gene description
MPRA-validated peak6901 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 LOC129389955 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (10628845..10629045)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (9109915..9110115, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (10486355..10486555)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene serine protease 51 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10382638-10383436 Neighboring gene serine protease 55 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:10406483-10407477 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:10412556-10413270 Neighboring gene uncharacterized LOC105379237 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10449944-10450820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10459109-10459704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10459705-10460299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:10469845-10470570 Neighboring gene RP1 like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26993 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10489151-10489860 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:10493333-10494238 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:10494239-10495144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10503027-10503883 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10535715-10536216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10536217-10536716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10536733-10537272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10537273-10537810 Neighboring gene microRNA 4286 Neighboring gene chromosome 8 open reading frame 74 Neighboring gene RNA, 5S ribosomal pseudogene 252

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_155585.1 

    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    10628845..10629045
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p14 PATCHES

    Range
    2718035..2718235 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    9109915..9110115 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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