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LOC129390204 MPRA-validated peak1019 silencer [ Homo sapiens (human) ]

Gene ID: 129390204, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129390204
Gene description
MPRA-validated peak1019 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 LOC129390204 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 (74907317..74907517)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (75780848..75781048)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (76667075..76667275)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3598 Neighboring gene VISTA enhancer hs1500 Neighboring gene family with sequence similarity 32 member C, pseudogene Neighboring gene MPRA-validated peak1017 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:76555535-76556121 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:76584665-76585436 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:76585437-76586208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2504 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:76615828-76616038 Neighboring gene lysine acetyltransferase 6B Neighboring gene ReSE screen-validated silencer GRCh37_chr10:76630209-76630443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3602 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:76776654-76776821 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:76789883-76790382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3604 Neighboring gene small nucleolar RNA, C/D box 172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:76817979-76818530 Neighboring gene dual specificity phosphatase 29 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:76829139-76829638

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_155834.1 

    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
    74907317..74907517
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_009646202.1 Reference GRCh38.p14 PATCHES

    Range
    111993..112193
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    75780848..75781048
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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