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LOC130065135 ATAC-STARR-seq lymphoblastoid silent region 11055 [ Homo sapiens (human) ]

Gene ID: 130065135, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065135
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11055
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 LOC130065135 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (55648288..55648407)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (58744217..58744336)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (56159654..56159773)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107983998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15101 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:56146823-56146990 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11051 Neighboring gene zinc finger protein 581 Neighboring gene Sharpr-MPRA regulatory region 1979 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15102 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11053 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:56155949-56156914 Neighboring gene zinc finger protein 580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15105 Neighboring gene coiled-coil domain containing 106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15106 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11058 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15107 Neighboring gene U2 small nuclear RNA auxiliary factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11061 Neighboring gene Sharpr-MPRA regulatory region 14549 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56192159-56192659 Neighboring gene epsin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:56213120-56214004 Neighboring gene vomeronasal 1 receptor 106 pseudogene

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_199552.1 

    Range
    101..220
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    55648288..55648407
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    58744217..58744336
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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