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LOC129391252 MPRA-validated peak4426 silencer [ Homo sapiens (human) ]

Gene ID: 129391252, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129391252
Gene description
MPRA-validated peak4426 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 LOC129391252 in Genome Data Viewer
Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (45607304..45607504)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (43976324..43976524)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (47027218..47027418)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene collagen type XVIII alpha 1 chain Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46934825-46935332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46935840-46936346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18591 Neighboring gene Sharpr-MPRA regulatory region 1559 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:46948644-46948814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46954106-46954980 Neighboring gene solute carrier family 19 member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13402 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13403 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:46962482-46962994 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:46970045-46970201 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13405 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13406 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46975660-46976554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46980259-46980968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:46998853-46999354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47001008-47001944 Neighboring gene uncharacterized LOC107985485 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47009554-47010054 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13408 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13409 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47015623-47016124 Neighboring gene Sharpr-MPRA regulatory region 7423 Neighboring gene MPRA-validated peak4424 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47031725-47032226 Neighboring gene long intergenic non-protein coding RNA 1694 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr21:47053121-47054320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18595 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47057095-47057612 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13411 Neighboring gene poly(rC) binding protein 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:47204393-47205264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47236921-47237422 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47237423-47237922 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:47241669-47242354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47244540-47245132 Neighboring gene MPRA-validated peak4427 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47255439-47255946 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47257017-47257560 Neighboring gene PCBP3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47274544-47275220 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:47275221-47275896 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr21:47278335-47279534 Neighboring gene uncharacterized LOC124905044

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_156882.1 

    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    45607304..45607504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    43976324..43976524
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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