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LOC130061054 ATAC-STARR-seq lymphoblastoid silent region 8630 [ Homo sapiens (human) ]

Gene ID: 130061054, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061054
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8630
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 LOC130061054 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (47649320..47649589)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (48511104..48511373)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (45726686..45726955)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L45 pseudogene 2 Neighboring gene MPRA-validated peak2874 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45569915-45570430 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:45579384-45580583 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45598943-45599444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8629 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:45614024-45614225 Neighboring gene aminopeptidase puromycin sensitive Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:45643631-45644132 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:45644133-45644632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:45693347-45693848 Neighboring gene KPNB1 divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45725440-45726285 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8631 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12314 Neighboring gene karyopherin subunit beta 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:45771282-45771962 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45771963-45772642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:45772643-45773323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8638 Neighboring gene TBK1 binding protein 1

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_196284.1 

    Range
    101..370
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    47649320..47649589
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    48511104..48511373
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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