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LOC129992608 ATAC-STARR-seq lymphoblastoid silent region 15433 [ Homo sapiens (human) ]

Gene ID: 129992608, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129992608
Gene description
ATAC-STARR-seq lymphoblastoid silent region 15433
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 sequence represents an accessible chromatin region that was validated as a silencer based on its ability to repress an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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See LOC129992608 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (54064673..54064912)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (57551917..57552156)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (54930840..54931079)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene nucleic acid binding protein 2 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr4:54796254-54796418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:54828360-54828888 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:54828889-54829416 Neighboring gene ribosomal protein L21 pseudogene 44 Neighboring gene VISTA enhancer hs687 Neighboring gene cysteine rich hydrophobic domain 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:54930180-54930680 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:54932677-54933876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:54959191-54959810 Neighboring gene mortality factor 4 like 2 pseudogene 1 Neighboring gene VISTA enhancer hs678 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:54966174-54966964 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:54966965-54967756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:54967757-54968546 Neighboring gene GS homeobox 2

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. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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_172054.1 

    Range
    101..340
    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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    54064673..54064912
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    57551917..57552156
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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