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    LOC130008940 ATAC-STARR-seq lymphoblastoid silent region 4950 [ Homo sapiens (human) ]

    Gene ID: 130008940, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130008940
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 4950
    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 LOC130008940 in Genome Data Viewer
    Location:
    chromosome: 12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (120468987..120469156)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (120458169..120458338)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (120906790..120906959)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:120883528-120884727 Neighboring gene TP53 regulated inhibitor of apoptosis 1 Neighboring gene ribosomal protein L31 pseudogene 52 Neighboring gene glutamyl-tRNA amidotransferase subunit C Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4951 Neighboring gene serine and arginine rich splicing factor 9 Neighboring gene dynein light chain LC8-type 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4952 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:120933574-120934240 Neighboring gene negative regulator of antiviral response Neighboring gene coenzyme Q5, methyltransferase Neighboring gene ribosomal protein L29 pseudogene 24

    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_187509.1 

      Range
      101..270
      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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      120468987..120469156
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      120458169..120458338
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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