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LOC129390278 MPRA-validated peak1251 silencer [ Homo sapiens (human) ]

Gene ID: 129390278, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390278
Gene description
MPRA-validated peak1251 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 LOC129390278 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (34329388..34329588)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (34466122..34466322)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (34350935..34351135)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902660 Neighboring gene cell cycle associated protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4592 Neighboring gene N-acetyltransferase 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4593 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34171467-34171996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4595 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34177103-34177604 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34181310-34181810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34181811-34182311 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34195130-34196052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34196053-34196973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34204513-34205014 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34205015-34205514 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:34208067-34208830 Neighboring gene ankyrin repeat and BTB domain containing 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:34213997-34214182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:34214651-34215536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34215704-34216532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:34226078-34226684 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:34255548-34256072 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:34260669-34261168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34261893-34262392 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:34263557-34264756 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:34264949-34265620 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4600 Neighboring gene Sharpr-MPRA regulatory region 14004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34306064-34306564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34306565-34307065 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4601 Neighboring gene MMADHC pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3251 Neighboring gene CRISPRi-validated cis-regulatory element chr11.1764 Neighboring gene MPRA-validated peak1252 silencer Neighboring gene CIR1 pseudogene 3

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_155908.1 

    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    34329388..34329588
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    34466122..34466322
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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