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LOC130000107 ATAC-STARR-seq lymphoblastoid silent region 19054 [ Homo sapiens (human) ]

Gene ID: 130000107, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130000107
Gene description
ATAC-STARR-seq lymphoblastoid silent region 19054
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 LOC130000107 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (28385451..28385520)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (28663618..28663687)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (28242968..28243037)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L5 pseudogene 22 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28175778-28176290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28176291-28176802 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27162 Neighboring gene prepronociceptin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28200887-28201454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28203430-28203930 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:28205819-28206378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:28206379-28206938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28216758-28217258 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28217259-28217759 Neighboring gene zinc finger protein 395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27167 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:28222946-28223446 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27168 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:28241577-28241751 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19055 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19056 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19058 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27171 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:28268555-28269173 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:28269174-28269793 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:28277089-28277305 Neighboring gene RNA, U6 small nuclear 178, pseudogene Neighboring gene F-box protein 16 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27174

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_179553.1 

    Range
    101..170
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    28385451..28385520
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    28663618..28663687
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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