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    LOC130008128 ATAC-STARR-seq lymphoblastoid silent region 4579 [ Homo sapiens (human) ]

    Gene ID: 130008128, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130008128
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 4579
    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 LOC130008128 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 (57239127..57239396)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57207365..57207634)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (57632910..57633179)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57609975-57610474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57610622-57611230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57611231-57611837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57617093-57617999 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6528 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57624967-57625547 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57625548-57626129 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57626711-57627291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6532 Neighboring gene Sharpr-MPRA regulatory region 225 Neighboring gene neurexophilin 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57631624-57632226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:57633295-57634200 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr12:57636011-57636914 Neighboring gene NDUFA4 mitochondrial complex associated like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6534 Neighboring gene serine hydroxymethyltransferase 2 Neighboring gene Sharpr-MPRA regulatory region 5413 Neighboring gene SH3 and cysteine rich domain 3 Neighboring gene R3H domain containing 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:57673563-57674762 Neighboring gene Sharpr-MPRA regulatory region 11351 Neighboring gene Sharpr-MPRA regulatory region 7317 Neighboring gene RNA, U6 small nuclear 879, 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 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_188657.1 

      Range
      101..370
      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
      57239127..57239396
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      57207365..57207634
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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