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LOC129390578 MPRA-validated peak2016 silencer [ Homo sapiens (human) ]

Gene ID: 129390578, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390578
Gene description
MPRA-validated peak2016 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 LOC129390578 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 (122142489..122142689)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (122138268..122138468)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (122627036..122627236)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5004 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122460343-122461158 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7196 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7197 Neighboring gene BAF chromatin remodeling complex subunit BCL7A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122492684-122493298 Neighboring gene Sharpr-MPRA regulatory region 9922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7198 Neighboring gene Sharpr-MPRA regulatory region 8907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7199 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122509410-122510254 Neighboring gene long intergenic non-protein coding RNA 2985 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7202 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7203 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122580754-122581254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122581255-122581755 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:122582507-122583160 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122583161-122583814 Neighboring gene MLX interacting protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7205 Neighboring gene Sharpr-MPRA regulatory region 11163 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122611084-122611596 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:122611597-122612107 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:122614034-122615233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122622713-122623575 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:122651061-122651663 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5010 Neighboring gene leucine rich repeat containing 43 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7209 Neighboring gene interleukin 31 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5011 Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4 Neighboring gene diablo IAP-binding mitochondrial protein

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_156208.1 

    Range
    101..301
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    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
    122142489..122142689
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332697.1 Reference GRCh38.p14 PATCHES

    Range
    83446..83646
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    122138268..122138468
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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