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LOC129390198 MPRA-validated peak1006 silencer [ Homo sapiens (human) ]

Gene ID: 129390198, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390198
Gene description
MPRA-validated peak1006 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 LOC129390198 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (69488959..69489159)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (70357006..70357206)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (71248715..71248915)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2432 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2433 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71176444-71177178 Neighboring gene Sharpr-MPRA regulatory region 2430 Neighboring gene tachykinin receptor 2 Neighboring gene ATP synthase membrane subunit c locus 1 pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71207805-71208306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71209624-71210242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71210243-71210860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71211741-71212241 Neighboring gene tetraspanin 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3493 Neighboring gene Sharpr-MPRA regulatory region 14270 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2435 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:71284727-71284879 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71287440-71288387 Neighboring gene transmembrane protein 256 pseudogene 1 Neighboring gene uncharacterized LOC105378345

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_155828.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    69488959..69489159
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    70357006..70357206
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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