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LOC130066650 ATAC-STARR-seq lymphoblastoid silent region 13299 [ Homo sapiens (human) ]

Gene ID: 130066650, updated on 27-Aug-2024

Summary

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Gene symbol
LOC130066650
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13299
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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Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (37266930..37267239)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (35649135..35649445)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene tetratricopeptide repeat domain 3 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr21:38567734-38568933 Neighboring gene TTC3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38579468-38580304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18445 Neighboring gene RNA, 7SL, cytoplasmic 678, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18446 Neighboring gene Down syndrome critical region 9 Neighboring gene VPS26 endosomal protein sorting factor C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38629775-38630367 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:38630368-38630960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18449 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:38655347-38656273 Neighboring gene uncharacterized LOC124905018 Neighboring gene uncharacterized LOC124905019

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

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_201066.1 

    Range
    101..410
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    37266930..37267239
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    35649135..35649445
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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