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LOC129389696 MPRA-validated peak6247 silencer [ Homo sapiens (human) ]

Gene ID: 129389696, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129389696
Gene description
MPRA-validated peak6247 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 LOC129389696 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 (156809281..156809481)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (158011566..158011766)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (157130415..157130615)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC115308161 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17712 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157099729-157100264 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17715 Neighboring gene microRNA 4466 Neighboring gene AT-rich interaction domain 1B Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:157141145-157141772 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17716 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157150990-157151957 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:157173517-157174214 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:157174215-157174910 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17717 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157234632-157235132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25321 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157263165-157263666 Neighboring gene Sharpr-MPRA regulatory region 494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157266367-157267095 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157267096-157267823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25324 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25323 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157283836-157284476 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25325 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17718 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17719 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157369601-157370102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157370103-157370603 Neighboring gene MPRA-validated peak6251 silencer Neighboring gene MPRA-validated peak6252 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25326 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25328 Neighboring gene NANOG hESC enhancer GRCh37_chr6:157402195-157402696 Neighboring gene MPRA-validated peak6253 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157466013-157466862 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:157466863-157467711 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157471440-157471940 Neighboring gene Sharpr-MPRA regulatory region 1838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157507076-157507576 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157507577-157508077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157528125-157528624 Neighboring gene uncharacterized LOC124901445 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157548108-157548608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157548609-157549109 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157552291-157552791 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:157638855-157639639 Neighboring gene uncharacterized LOC105378075

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_155326.1 

    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
    156809281..156809481
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    158011566..158011766
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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