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LOC130006134 ATAC-STARR-seq lymphoblastoid silent region 3600 [ Homo sapiens (human) ]

Gene ID: 130006134, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006134
Gene description
ATAC-STARR-seq lymphoblastoid silent region 3600
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 LOC130006134 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 (66677810..66678089)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (66674058..66674337)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (66445281..66445560)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66384051-66384984 Neighboring gene RBM14-RBM4 readthrough Neighboring gene hESC enhancers GRCh37_chr11:66405625-66406338 and GRCh37_chr11:66406339-66407050 Neighboring gene RNA binding motif protein 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66410755-66411278 Neighboring gene MPRA-validated peak1306 silencer Neighboring gene RNA binding motif protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3599 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66453249-66453749 Neighboring gene RNA binding motif protein 4B Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:66462288-66462788 Neighboring gene spectrin beta, non-erythrocytic 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66487347-66488304 Neighboring gene RNA, 7SL, cytoplasmic 12, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66511467-66511967 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5056 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5057 Neighboring gene TOP6B like initiator of meiotic double strand breaks Neighboring gene fragile site, folic acid type, rare, fra(11)(q13.3) Neighboring gene complement C1q binding protein pseudogene 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_185579.1 

    Range
    101..380
    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
    66677810..66678089
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    66674058..66674337
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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