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LOC129390833 MPRA-validated peak2716 silencer [ Homo sapiens (human) ]

Gene ID: 129390833, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390833
Gene description
MPRA-validated peak2716 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 LOC129390833 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (8444588..8444788)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (8350751..8350951)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (8347906..8348106)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:8285969-8286686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:8286687-8287404 Neighboring gene ribosomal protein L26 Neighboring gene Sharpr-MPRA regulatory region 12124 Neighboring gene ring finger protein 222 Neighboring gene Sharpr-MPRA regulatory regions 4336 and 10869 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8184 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8183 Neighboring gene nudE neurodevelopment protein 1 like 1 Neighboring gene MPRA-validated peak2717 silencer Neighboring gene Sharpr-MPRA regulatory region 9669 Neighboring gene uncharacterized LOC107987245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:8390687-8391187 Neighboring gene Sharpr-MPRA regulatory region 1803 Neighboring gene myosin heavy chain 10 Neighboring gene uncharacterized LOC102724262 Neighboring gene RNA, U7 small nuclear 43 pseudogene

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 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_156463.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    8444588..8444788
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    8350751..8350951
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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