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LOC129390465 MPRA-validated peak1743 silencer [ Homo sapiens (human) ]

Gene ID: 129390465, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390465
Gene description
MPRA-validated peak1743 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 LOC129390465 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (56660471..56660671)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (56628467..56628667)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (57054255..57054455)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATP synthase F1 subunit beta Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57038866-57039576 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57039577-57040285 Neighboring gene small nucleolar RNA, C/D box 59B Neighboring gene small nucleolar RNA, C/D box 59A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4563 Neighboring gene prostaglandin E synthase 3 Neighboring gene RNA, 7SL, cytoplasmic 809, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57074705-57075584 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4564 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6513 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6514 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57081953-57082478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6515 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:57083531-57084056 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:57094539-57094693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6516 Neighboring gene nascent polypeptide associated complex subunit alpha Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6517 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6519

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_156095.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    56660471..56660671
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    56628467..56628667
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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