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LOC129390138 MPRA-validated peak878 silencer [ Homo sapiens (human) ]

Gene ID: 129390138, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390138
Gene description
MPRA-validated peak878 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 LOC129390138 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (15784036..15784236)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (15802040..15802240)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (15826035..15826235)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376433 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:15290229-15290730 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:15297713-15298356 Neighboring gene family with sequence similarity 171 member A1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:15310079-15310579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3094 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:15366997-15368196 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2171 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2173 Neighboring gene Sharpr-MPRA regulatory region 1502 Neighboring gene MPRA-validated peak874 silencer Neighboring gene Sharpr-MPRA regulatory region 6046 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:15514928-15515649 Neighboring gene MPRA-validated peak875 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2174 Neighboring gene integrin subunit alpha 8 Neighboring gene Sharpr-MPRA regulatory region 12763 Neighboring gene Sharpr-MPRA regulatory region 7083 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:15731307-15731808 Neighboring gene MPRA-validated peak877 silencer Neighboring gene uncharacterized LOC124902383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3095 Neighboring gene MINDY lysine 48 deubiquitinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3096 Neighboring gene Sharpr-MPRA regulatory region 8556 Neighboring gene small nucleolar RNA U13 Neighboring gene ferritin light chain pseudogene 19

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_155768.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    15784036..15784236
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    15802040..15802240
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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