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LOC129390772 MPRA-validated peak2513 silencer [ Homo sapiens (human) ]

Gene ID: 129390772, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129390772
Gene description
MPRA-validated peak2513 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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Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (17149959..17150159)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (17156933..17157133)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:17200215-17200782 Neighboring gene TCERG1 pseudogene 2 Neighboring gene uncharacterized LOC102723692 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10502 Neighboring gene xylosyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:17360175-17361046 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:17390476-17390750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7235 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:17399758-17400258 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:17414499-17414998 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:17424561-17425084 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:17439467-17439968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7236 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:17498817-17500016 Neighboring gene uncharacterized LOC124903654 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:17516896-17517632 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:17523609-17523772 Neighboring gene uncharacterized LOC107987234 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10511 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10512

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

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_156402.1 

    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    17149959..17150159
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_019805500.1 Reference GRCh38.p14 PATCHES

    Range
    151220..151420
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    17156933..17157133
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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