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LOC130006119 ATAC-STARR-seq lymphoblastoid silent region 3592 [ Homo sapiens (human) ]

Gene ID: 130006119, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006119
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3592
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 LOC130006119 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (66438607..66438746)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (66434952..66435091)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (66206078..66206217)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66181037-66181555 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66181556-66182074 Neighboring gene neuronal PAS domain protein 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66185208-66185708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66185709-66186209 Neighboring gene Sharpr-MPRA regulatory region 12876 Neighboring gene small nucleolar RNA SNORA43 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5044 Neighboring gene mitochondrial ribosomal protein L11 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:66219904-66220097 Neighboring gene chromosome 5 open reading frame 63 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66232341-66232842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66232843-66233342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3593 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3594 Neighboring gene pellino E3 ubiquitin protein ligase family member 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66243741-66244561 Neighboring gene DPP3 divergent transcript

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_185564.1 

    Range
    101..240
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    66438607..66438746
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    66434952..66435091
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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