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LOC129390240 MPRA-validated peak1130 silencer [ Homo sapiens (human) ]

Gene ID: 129390240, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390240
Gene description
MPRA-validated peak1130 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 LOC129390240 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 (130924213..130924413)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (131853900..131854100)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (132722476..132722676)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:132152999-132153675 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132176128-132176628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132176629-132177129 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132197359-132197860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132197861-132198360 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:132294461-132294961 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132310601-132311101 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:132358601-132359102 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:132373035-132373208 Neighboring gene uncharacterized LOC105378562 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:132517184-132518383 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:132642120-132643319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132699511-132700403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132722795-132723295 Neighboring gene Sharpr-MPRA regulatory region 8952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132796630-132797497 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132797498-132798364 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132800566-132801066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132801067-132801567 Neighboring gene microRNA 378c Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:132821112-132821721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132822677-132823607 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132834068-132834857 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:132834858-132835646 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:132845839-132846362 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:132846885-132847407 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr10:132847408-132847929 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:132848100-132849299 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:132854747-132855248 Neighboring gene uncharacterized LOC107984186

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_155870.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    130924213..130924413
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    131853900..131854100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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