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LOC130007038 ATAC-STARR-seq lymphoblastoid active region 5715 [ Homo sapiens (human) ]

Gene ID: 130007038, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130007038
Gene description
ATAC-STARR-seq lymphoblastoid active region 5715
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 LOC130007038 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 (128452122..128452301)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (128485467..128485646)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (128322017..128322196)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4053 Neighboring gene uncharacterized LOC124902787 Neighboring gene CAGE-defined T cell enhancer downstream of ETS1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5714 Neighboring gene uncharacterized LOC124902788 Neighboring gene uncharacterized LOC124902789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:128292222-128292722 Neighboring gene Sharpr-MPRA regulatory region 2302 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:128318161-128319360 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5719 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5718 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5720 Neighboring gene Sharpr-MPRA regulatory region 15716 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5723 Neighboring gene ETS proto-oncogene 1, transcription factor Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:128362337-128363536 Neighboring gene Sharpr-MPRA regulatory region 9161 Neighboring gene CRISPRi-FlowFISH-validated ETS1 regulatory element GRCh37_chr11:128391955-128393363 Neighboring gene microRNA 6090 Neighboring gene ETS1 antisense RNA 1

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_186482.1 

    Range
    101..280
    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
    128452122..128452301
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    128485467..128485646
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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