U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    LOC130007832 ATAC-STARR-seq lymphoblastoid silent region 4429 [ Homo sapiens (human) ]

    Gene ID: 130007832, updated on 12-Sep-2024

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC130007832
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 4429
    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 LOC130007832 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 (49336952..49337361)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (49299142..49299551)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (49730735..49731144)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49688028-49688945 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49688946-49689862 Neighboring gene Sharpr-MPRA regulatory region 11953 Neighboring gene TROAP and PRPH antisense RNA 1 Neighboring gene peripherin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6312 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6313 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:49724253-49724754 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:49729567-49730366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:49736353-49736864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4430 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4432 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4433 Neighboring gene trophinin associated protein Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:49741370-49742313 Neighboring gene complement C1q like 4 Neighboring gene DnaJ heat shock protein family (Hsp40) member C22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6314 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4435 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4436 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6315 Neighboring gene spermatogenesis associated serine rich 2 Neighboring gene FGFR1 oncogene partner 2 pseudogene

    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_186666.1 

      Range
      101..510
      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
      49336952..49337361
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      49299142..49299551
      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