Maize TE database statistics

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Maize TE database specifications

Information


Unique identifier OMICS_09461
Name Maize TE database
Alternative name Maize transposable element database
Restrictions to use None
Maintained No

Taxon


  • Plants and Fungi
    • Zea mays

Maize TE database citations

 (5)
library_books

Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast

2018
BMC Genomics
PMCID: 5838962
PMID: 29510672
DOI: 10.1186/s12864-018-4563-7

[…] All LTR retroelement sequences were downloaded from Maize Transposable Element Database (http://maizetedb.org/~maize/) and searched for G4 motifs using the R/Bioconductor [] package pqsfinder []. Pqsfinder searches for clusters of guanines in nucleic a […]

library_books

Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome wide repressive impact on transcription

2017
BMC Plant Biol
PMCID: 5639751
PMID: 29025411
DOI: 10.1186/s12870-017-1108-1

[…] sequences related to transposable elements were identified and classified using BLAST Best Hits. All 160,488 transcript models (reference plus newly annotated transcripts []) were BLASTed against the Maize TE database containing 1526 full-length sequences of curated, non-redundant maize TEs (http://maizetedb.org/~maize/). The bit score and coverage percentage of the alignment were scored to identi […]

library_books

Genome wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize

2017
Genome Biol
PMCID: 5522596
PMID: 28732548
DOI: 10.1186/s13059-017-1273-4

[…] lable at the Gramene database (ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/gff3/zea_mays/repeat_annotation/) [] and TE families have been named according to the guidelines described at the Maize TE database (http://maizetedb.org/cgi-bin/cgiwrap/maize/TE_show_family.cgi?do_table = 1).To prepare the annotation file, nested TE insertions were resolved using RTrackLayer [] in R []. Bedtools […]

library_books

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

2015
PLoS Genet
PMCID: 4287451
PMID: 25569788
DOI: 10.1371/journal.pgen.1004915

[…] ence TE insertions were detected for Oh43 and Mo17 using relocaTE , whole genome sequence from the NCBI SRA (Oh43: SRR447831-SRR447847; Mo17: SRR447948-SRR447950), and consensus TE sequences from the maize TE database . Reads containing TEs were identified by mapping to consensus TE sequences, trimming portions of reads mapping to a TE, and mapping the remaining sequence to the reference genome. N […]

library_books

Discovery of novel transcripts and gametophytic functions via RNA seq analysis of maize gametophytic transcriptomes

2014
Genome Biol
PMCID: 4309534
PMID: 25084966
DOI: 10.1186/s13059-014-0414-2

[…] rimer trimming, quality control filtering and length sorting []. Prior to aligning reads to the maize genome, reads matching maize repetitive sequences were filtered using the list available from the maize TE database []. Reads were aligned in paired-end mode when both reads of a pair passed all preprocessing steps, otherwise reads were aligned as singles. Empirical transcripts (etranscripts) were […]

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Maize TE database funding source(s)
This material is based upon work supported by the National Science Foundation under Grant No. 1118550.

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