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LOC129390179 MPRA-validated peak969 silencer [ Homo sapiens (human) ]

Gene ID: 129390179, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390179
Gene description
MPRA-validated peak969 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 LOC129390179 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 (64476608..64476808)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (65334570..65334770)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (66236365..66236565)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902439 Neighboring gene uncharacterized LOC105378333 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3446 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:65801475-65801975 Neighboring gene Sharpr-MPRA regulatory region 2403 Neighboring gene Sharpr-MPRA regulatory region 9742 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:65880319-65880911 Neighboring gene DBF4 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 9231 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:66144462-66145292 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:66145293-66146122 Neighboring gene NANOG hESC enhancer GRCh37_chr10:66266441-66266965 Neighboring gene uncharacterized LOC105378335 Neighboring gene MPRA-validated peak971 silencer Neighboring gene MPRA-validated peak972 silencer Neighboring gene ribosomal protein L17 pseudogene 35 Neighboring gene uncharacterized LOC107984239 Neighboring gene Sharpr-MPRA regulatory region 14987 Neighboring gene cytochrome P450 family 2 subfamily C member 61, pseudogene

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_155809.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    64476608..64476808
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    65334570..65334770
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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