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LOC129388458 MPRA-validated peak84 silencer [ Homo sapiens (human) ]

Gene ID: 129388458, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388458
Gene description
MPRA-validated peak84 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 LOC129388458 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (15912000..15912200)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (15353270..15353470)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (16238495..16238695)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16161483-16162468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 248 Neighboring gene Sharpr-MPRA regulatory region 11658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 314 Neighboring gene SPEN antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 315 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 249 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:16173332-16173844 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:16173845-16174356 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 317 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:16175780-16176374 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16191755-16192255 Neighboring gene spen family transcriptional repressor Neighboring gene NFE2L2 motif-containing MPRA enhancer 216 Neighboring gene MPRA-validated peak83 silencer Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16261375-16261876 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:16268619-16269818 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 252 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 253 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:16276391-16277178 Neighboring gene uncharacterized LOC124903855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 254 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:16278891-16280090 Neighboring gene zinc finger and BTB domain containing 17 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:16287659-16288532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 255 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 257 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 319 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:16302461-16302960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:16320391-16321231 Neighboring gene TBC1 domain family member 3 pseudogene 6

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_154092.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    15912000..15912200
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    15353270..15353470
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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