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LOC129388440 MPRA-validated peak54 silencer [ Homo sapiens (human) ]

Gene ID: 129388440, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388440
Gene description
MPRA-validated peak54 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 LOC129388440 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (9482836..9483036)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (9019170..9019370)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (9542895..9543095)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:9487788-9488422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 128 Neighboring gene long intergenic non-protein coding RNA 2606 Neighboring gene RNA, 5S ribosomal pseudogene 40 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9533371-9533922 Neighboring gene Sharpr-MPRA regulatory region 9854 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 129 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:9601405-9601904 Neighboring gene solute carrier family 25 member 33 Neighboring gene MPRA-validated peak56 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 223 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 224 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 225 Neighboring gene ribosomal protein L9 pseudogene 11 Neighboring gene hESC enhancers GRCh37_chr1:9653469-9654066 and GRCh37_chr1:9654067-9654663 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:9657808-9659007 Neighboring gene transmembrane protein 201 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:9671778-9672013 Neighboring gene uncharacterized LOC124903837

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_154074.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    9482836..9483036
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    9019170..9019370
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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