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LOC129933565 ATAC-STARR-seq lymphoblastoid silent region 11398 [ Homo sapiens (human) ]

Gene ID: 129933565, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129933565
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11398
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 LOC129933565 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (42048540..42048609)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (42054037..42054106)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (42275680..42275749)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905996 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:42164451-42165045 Neighboring gene Sharpr-MPRA regulatory region 382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:42166828-42167422 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42175498-42176148 Neighboring gene long intergenic non-protein coding RNA 2898 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11391 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11392 Neighboring gene VISTA enhancer hs2553 Neighboring gene uncharacterized LOC105374517 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_58491 Neighboring gene Sharpr-MPRA regulatory region 7749 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:42220647-42221044 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:42222752-42223418 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11393 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:42259331-42259881 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42273538-42274041 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42274042-42274546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11397 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:42276763-42277264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:42279935-42280650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42280651-42281365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:42285233-42285733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15636 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:42296167-42296331 Neighboring gene uncharacterized LOC105374531 Neighboring gene protein kinase domain containing, cytoplasmic Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11399 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15640 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42328443-42329270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15642 Neighboring gene MPRA-validated peak3676 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15643 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42359847-42360820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42360821-42361792 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42367980-42368777 Neighboring gene EML4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15644 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:42396227-42396879 Neighboring gene EMAP like 4

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 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_166591.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    42048540..42048609
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    42054037..42054106
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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