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LOC130006653 ATAC-STARR-seq lymphoblastoid active region 5447 [ Homo sapiens (human) ]

Gene ID: 130006653, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006653
Gene description
ATAC-STARR-seq lymphoblastoid active region 5447
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an enhancer based on its ability to activate 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 LOC130006653 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (102453019..102453128)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (102455146..102455255)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (102323750..102323859)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5441 Neighboring gene baculoviral IAP repeat containing 2 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:102245101-102245686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:102245687-102246271 Neighboring gene transmembrane protein 123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5442 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:102299689-102299866 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3861 Neighboring gene TMEM123 divergent transcript Neighboring gene uncharacterized LOC124902740 Neighboring gene uncharacterized LOC102723838 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3862 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_18559 Neighboring gene matrix metallopeptidase 7

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_186098.1 

    Range
    101..210
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    102453019..102453128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    102455146..102455255
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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