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LOC129391275 MPRA-validated peak4478 silencer [ Homo sapiens (human) ]

Gene ID: 129391275, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129391275
Gene description
MPRA-validated peak4478 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 LOC129391275 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (29716827..29717027)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (30180190..30180390)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (30112816..30113016)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene nipsnap homolog 1 Neighboring gene Sharpr-MPRA regulatory region 2653 Neighboring gene Sharpr-MPRA regulatory region 10387 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:29976263-29976875 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13593 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13595 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr22:30002345-30002866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30009952-30010452 Neighboring gene ribulose-5-phosphate-3-epimerase pseudogene 4 Neighboring gene NF2, moesin-ezrin-radixin like (MERLIN) tumor suppressor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30026831-30027330 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30084213-30084714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30084715-30085214 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:30085434-30085934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30087218-30087838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30087839-30088460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30088461-30089081 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30101159-30101822 Neighboring gene CABP7 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30117301-30118091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30133259-30134112 Neighboring gene calcium binding protein 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30143413-30144160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30144161-30144906 Neighboring gene zinc finger matrin-type 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30162231-30162880 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:30162881-30163530 Neighboring gene ubiquinol-cytochrome c reductase, complex III subunit X

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_156905.1 

    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    29716827..29717027
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    30180190..30180390
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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