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LOC129390431 MPRA-validated peak1664 silencer [ Homo sapiens (human) ]

Gene ID: 129390431, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390431
Gene description
MPRA-validated peak1664 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 LOC129390431 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 (32271462..32271662)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (32147682..32147882)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (32424396..32424596)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6181 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:32260751-32261388 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:32271849-32272465 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:32273271-32273980 Neighboring gene BICD1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:32284941-32285442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6182 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6184 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6185 Neighboring gene NANOG hESC enhancer GRCh37_chr12:32308728-32309229 Neighboring gene BICD cargo adaptor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:32326137-32326651 Neighboring gene WW domain binding protein 2 pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:32401528-32402727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6187 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6189 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:32451501-32451672 Neighboring gene MPRA-validated peak1665 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_28311 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:32552038-32552978 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:32552979-32553918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:32553919-32554859 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:32554860-32555799 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:32558711-32559696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:32563517-32564117 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:32572153-32573139 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:32590359-32590858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:32597499-32598044 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:32606043-32606832 Neighboring gene FYVE, RhoGEF and PH domain containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4338 Neighboring gene RNA, U6 small nuclear 494, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:32676322-32676822 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:32715914-32716598 Neighboring gene NANOG hESC enhancer GRCh37_chr12:32719564-32720065 Neighboring gene uncharacterized LOC124902914

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_156061.1 

    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
    32271462..32271662
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    32147682..32147882
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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