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    LOC130003014 ATAC-STARR-seq lymphoblastoid silent region 20524 [ Homo sapiens (human) ]

    Gene ID: 130003014, updated on 14-Oct-2023

    Summary

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    Gene symbol
    LOC130003014
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 20524
    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 LOC130003014 in Genome Data Viewer
    Location:
    chromosome: 9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136488861..136488910)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148717966..148718015)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139330456-139330964 Neighboring gene hESC enhancers GRCh37_chr9:139332501-139333134 to GRCh37_chr9:139333770-139334403 Neighboring gene inositol polyphosphate-5-phosphatase E Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:139342099-139343298 Neighboring gene SEC16 homolog A, endoplasmic reticulum export factor Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:139376640-139377385 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139378131-139378875 Neighboring gene chromosome 9 putative open reading frame 163 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:139392592-139393791 Neighboring gene notch receptor 1 Neighboring gene uncharacterized LOC124902310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139420763-139421634 Neighboring gene microRNA 4673 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29311 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139433302-139433969 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139434130-139434814 Neighboring gene Sharpr-MPRA regulatory region 6589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139436183-139436865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20527 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20528 Neighboring gene microRNA 4674

    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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

    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_182460.1 

      Range
      101..150
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      136488861..136488910
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      148717966..148718015
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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