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LOC129388988 MPRA-validated peak4025 silencer [ Homo sapiens (human) ]

Gene ID: 129388988, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129388988
Gene description
MPRA-validated peak4025 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 LOC129388988 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (207202782..207202982)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (207684972..207685172)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (208067506..208067706)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene KLF transcription factor 7 Neighboring gene microRNA 2355 Neighboring gene Sharpr-MPRA regulatory region 11101 Neighboring gene NANOG hESC enhancer GRCh37_chr2:208007006-208007507 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:208013849-208014350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12271 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:208028265-208028973 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:208028974-208029682 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr2:208030391-208031099 and GRCh37_chr2:208031100-208031807 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17030 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:208031808-208032516 Neighboring gene microRNA 7845 Neighboring gene MYOSLID antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr2:208064814-208065392 Neighboring gene uncharacterized LOC124907971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17032 Neighboring gene myocardin-induced smooth muscle lncRNA, inducer of differentiation

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_154621.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    207202782..207202982
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    207684972..207685172
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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