U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    LOC129389613 MPRA-validated peak6034 silencer [ Homo sapiens (human) ]

    Gene ID: 129389613, updated on 12-Sep-2024

    Summary

    Go to the top of the page Help
    Gene symbol
    LOC129389613
    Gene description
    MPRA-validated peak6034 silencer
    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 region was identified as an uncharacterized cis-regulatory element (CRE) that lacked a promoter, enhancer or CTCF-bound insulator chromatin signature. It was validated as a silencer that could repress activity of a super core promoter (SCP1) by STARR-seq massively parallel reporter assays (MPRAs) in K562 erythroleukemia cells. [provided by RefSeq, Apr 2023]
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See LOC129389613 in Genome Data Viewer
    Location:
    chromosome: 6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (111427393..111427593)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (112610376..112610576)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (111748596..111748796)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901376 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:111604271-111604834 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:111604835-111605396 Neighboring gene REV3 like, DNA directed polymerase zeta catalytic subunit Neighboring gene FCF1 pseudogene 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:111751696-111751904 Neighboring gene MPRA-validated peak6035 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24943 Neighboring gene bromodomain containing 7 pseudogene 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:111798355-111799247 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:111799845-111800569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17475 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17478 Neighboring gene TRAF3IP2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24947 Neighboring gene uncharacterized LOC107986520

    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. Candidate silencer elements for the human and mouse genomes. Doni Jayavelu N, et al. Nat Commun, 2020 Feb 26. PMID 32103011, 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_155243.1 

      Range
      101..301
      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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      111427393..111427593
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      112610376..112610576
      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