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LOC129388610 MPRA-validated peak418 silencer [ Homo sapiens (human) ]

Gene ID: 129388610, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388610
Gene description
MPRA-validated peak418 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 LOC129388610 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 (154377520..154377720)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (153514664..153514863)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (154349996..154350196)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1352 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1353 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1354 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1355 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:154303097-154304296 Neighboring gene aquaporin 10 Neighboring gene ATPase phospholipid transporting 8B2 Neighboring gene RNA, U7 small nuclear 57 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154320806-154321790 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:154321791-154322774 Neighboring gene MPRA-validated peak417 silencer Neighboring gene mitochondrial ribosomal protein S33 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1778 Neighboring gene ribosomal protein SA pseudogene 17 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1356 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1357 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:154378343-154378949 Neighboring gene IL6R antisense RNA 1 Neighboring gene interleukin 6 receptor

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_154243.1 

    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    154377520..154377720
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    153514664..153514863
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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