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LOC130004245 ATAC-STARR-seq lymphoblastoid silent region 2573 [ Homo sapiens (human) ]

Gene ID: 130004245, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004245
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2573
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 LOC130004245 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (86756132..86757101)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (87640202..87641171)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (88515889..88516858)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3695 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:88433149-88433337 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_17910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88441665-88442166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88442167-88442666 Neighboring gene VISTA enhancer hs2143 Neighboring gene opsin 4 Neighboring gene LIM domain binding 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88459642-88460142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:88460143-88460643 Neighboring gene hESC enhancers GRCh37_chr10:88470545-88471164 and GRCh37_chr10:88471165-88471784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3696 Neighboring gene bone morphogenetic protein receptor type 1A Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:88552774-88553500 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:88597221-88597813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88615649-88616230 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88624164-88624816 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88624817-88625468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88627361-88627948 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:88631460-88632021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3697 Neighboring gene RNA polymerase II associated protein 2 pseudogene 1 Neighboring gene RNA, U1 small nuclear 19, 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 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_183691.1 

    Range
    101..1070
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    86756132..86757101
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    87640202..87641171
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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