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LOC129388869 MPRA-validated peak3717 silencer [ Homo sapiens (human) ]

Gene ID: 129388869, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388869
Gene description
MPRA-validated peak3717 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 LOC129388869 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (61508640..61508840)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (61514788..61514988)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (61735775..61735975)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ubiquitin specific peptidase 34 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:61652307-61652984 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:61652985-61653662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:61653663-61654340 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:61657175-61657369 Neighboring gene small nucleolar RNA, H/ACA box 70B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11526 Neighboring gene MPRA-validated peak3715 silencer Neighboring gene Sharpr-MPRA regulatory region 6736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:61692432-61692952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:61692953-61693472 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:61694001-61694500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11528 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11529 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11527 Neighboring gene MPRA-validated peak3716 silencer Neighboring gene USP34 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:61743599-61744099 Neighboring gene exportin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15831 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15832 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15833 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:61766044-61766833 Neighboring gene proteasome 26S subunit, non-ATPase 12 pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:61809253-61809844 Neighboring gene ribosomal protein S29 pseudogene 10

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_154502.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    61508640..61508840
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    61514788..61514988
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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