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LOC129390818 MPRA-validated peak2673 silencer [ Homo sapiens (human) ]

Gene ID: 129390818, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129390818
Gene description
MPRA-validated peak2673 silencer
Gene type
biological region
Feature type(s)
regulatory: enhancer, 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. A subregion 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. This locus also includes an accessible chromatin subregion that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) MPRA in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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Genomic context

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Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (1198286..1198490)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (1087382..1087586)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ABR activator of RhoGEF and GTPase Neighboring gene mitochondrial ribosomal protein L14 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1083316-1084082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11446 Neighboring gene ABR antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1119641-1120638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1123483-1123982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11447 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1131887-1132591 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11448 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:1167109-1167284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1170929-1171732 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1171733-1172535 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1174140-1174890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1202102-1202696 Neighboring gene basic helix-loop-helix family member a9 Neighboring gene trafficking regulator of GLUT4 (SLC2A4) 1

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
  2. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, 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

General gene information

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Other Names

  • ATAC-STARR-seq lymphoblastoid active region 11445

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_156448.2 

    Range
    101..305
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    1198286..1198490
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    1087382..1087586
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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