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LOC129389963 MPRA-validated peak6937 silencer [ Homo sapiens (human) ]

Gene ID: 129389963, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389963
Gene description
MPRA-validated peak6937 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 LOC129389963 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 (22424073..22424273)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (22697901..22698101)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (22281586..22281786)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22133109-22133754 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_102848 Neighboring gene Sharpr-MPRA regulatory region 10265 Neighboring gene piwi like RNA-mediated gene silencing 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_102863 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_102872 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_102873 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22223390-22223890 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18984 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27078 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:22226031-22226209 Neighboring gene solute carrier family 39 member 14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:22241071-22241684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:22250571-22251133 Neighboring gene ribosomal protein L21 pseudogene 77 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27079 Neighboring gene RNA, U6 small nuclear 336, pseudogene Neighboring gene protein phosphatase 3 catalytic subunit gamma Neighboring gene uncharacterized LOC124901905 Neighboring gene BTF3 pseudogene 3

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 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_155593.1 

    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
    22424073..22424273
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    22697901..22698101
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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