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LOC129935824 ATAC-STARR-seq lymphoblastoid silent region 12425 [ Homo sapiens (human) ]

Gene ID: 129935824, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129935824
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12425
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 LOC129935824 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 (231395392..231395861)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (231879842..231880311)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (232260103..232260572)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene armadillo repeat containing 9 Neighboring gene ribosomal protein S28 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17280 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:232181499-232182000 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:232182001-232182500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232196977-232197934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232201084-232201584 Neighboring gene Sharpr-MPRA regulatory region 9410 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232233755-232234401 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232234402-232235049 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232235050-232235696 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:232235697-232236344 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:232240900-232241463 Neighboring gene microRNA 4777 Neighboring gene Sharpr-MPRA regulatory region 14998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17281 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232256876-232257459 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232258043-232258625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232258626-232259207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17282 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:232261821-232263020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232263273-232263820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232263821-232264366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232266008-232266553 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:232275119-232275724 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:232275725-232276329 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12426 Neighboring gene uncharacterized LOC124907997 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:232278424-232279184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232279185-232279944 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:232283151-232283652 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:232285114-232285614 Neighboring gene zinc finger and BTB domain containing 8 opposite strand pseudogene 2

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_168835.1 

    Range
    101..570
    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
    231395392..231395861
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    231879842..231880311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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