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    LOC129390535 MPRA-validated peak1899 silencer [ Homo sapiens (human) ]

    Gene ID: 129390535, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC129390535
    Gene description
    MPRA-validated peak1899 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]
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    Genomic context

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    See LOC129390535 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 (95519060..95519260)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (95500107..95500307)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (95912836..95913036)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6810 Neighboring gene ribosomal protein L29 pseudogene 26 Neighboring gene methionyl aminopeptidase 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:95916458-95916958 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:95936387-95936886 Neighboring gene ubiquitin specific peptidase 44 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6811 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:96004940-96005508 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:96005509-96006077 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:96008766-96009393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:96016523-96017477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4739 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:96026735-96027934 Neighboring gene Sharpr-MPRA regulatory region 15569 Neighboring gene phosphoglycerate mutase 1 pseudogene 5 Neighboring gene netrin 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:96087614-96088118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:96088119-96088623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6813 Neighboring gene uncharacterized LOC105369919 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:96125327-96125544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6815

    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. 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

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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_156165.1 

      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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      95519060..95519260
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      95500107..95500307
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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