U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    LOC130061979 ATAC-STARR-seq lymphoblastoid silent region 9161 [ Homo sapiens (human) ]

    Gene ID: 130061979, updated on 12-Sep-2024

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC130061979
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 9161
    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]
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See LOC130061979 in Genome Data Viewer
    Location:
    chromosome: 17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (81891603..81892142)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (82758765..82759304)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (79849479..79850018)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79825239-79825867 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79825868-79826497 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79826498-79827126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9160 Neighboring gene Rho GDP dissociation inhibitor alpha Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12983 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:79846281-79847480 Neighboring gene Aly/REF export factor Neighboring gene ReSE screen-validated silencer GRCh37_chr17:79850899-79851114 Neighboring gene anaphase promoting complex subunit 11 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9162 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9163 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9164 Neighboring gene phosphate cytidylyltransferase 2, ethanolamine Neighboring gene neuropeptide B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9166 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9167 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79875237-79876133 Neighboring gene sirtuin 7

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See Variation Viewer (GRCh37.p13)

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_197067.1 

      Range
      101..640
      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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      81891603..81892142
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      82758765..82759304
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases