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LOC129390866 MPRA-validated peak2828 silencer [ Homo sapiens (human) ]

Gene ID: 129390866, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390866
Gene description
MPRA-validated peak2828 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 LOC129390866 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (37043118..37043318)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (38030090..38030290)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (35400416..35400616)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:35294081-35294922 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:35295765-35296606 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:35298089-35298612 Neighboring gene VISTA enhancer hs363 Neighboring gene LIM homeobox 1 Neighboring gene apoptosis antagonizing transcription factor Neighboring gene uncharacterized LOC105371753 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:35405396-35405896 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:35421791-35422346 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:35422902-35423456 Neighboring gene microRNA 2909 Neighboring gene NANOG hESC enhancer GRCh37_chr17:35446662-35447163 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:35453499-35454698 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:35460987-35461591 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:35464014-35464618 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:35464619-35465223 Neighboring gene acetyl-CoA carboxylase alpha Neighboring gene ribosomal protein S2 pseudogene 49

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_156496.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    37043118..37043318
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187614.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    1279481..1279681
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    38030090..38030290
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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