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Protocols

TriFLDB specifications

Information


Unique identifier OMICS_28720
Name TriFLDB
Alternative name Triticeae Full-Length CDS Database
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Oryza sativa
    • Triticum aestivum

Maintainer


This tool is not available anymore.

Publication for Triticeae Full-Length CDS Database

TriFLDB citations

 (13)
library_books

Comparative Temporal Transcriptome Profiling of Wheat near Isogenic Line Carrying Lr57 under Compatible and Incompatible Interactions

2016
Front Plant Sci
PMCID: 5179980
PMID: 28066494
DOI: 10.3389/fpls.2016.01943

[…] Consortium (IWGSC) had released wheat draft genome sequence covering 64% of wheat genome which did not include the data from repetitive elements (IWGSC, ).We BLAST searched the full length cDNA from Triticeae full-length CDS database (TriFLDB) with the IWGSC wheat genome with BLASTN at cut off e-value of 1e-5, which resulted in only partial hits. In the absence of suitable genomic reference, a re […]

library_books

SSH Analysis of Endosperm Transcripts and Characterization of Heat Stress Regulated Expressed Sequence Tags in Bread Wheat

2016
Front Plant Sci
PMCID: 4988357
PMID: 27582756
DOI: 10.3389/fpls.2016.01230

[…] ce for Triticeae (Bolser et al., ), which is very popular for retrieving the chromosomal location, position (start-end), transcript name, and gene ontologies. Further, the clones were annotated using Triticeae Full-Length CDS Database (TriFLDB) (http://trifldb.psc.riken.jp/) and TIGR (http://jcvi.org/wheat/wheat_gaad.shtml) databases.For retrieval of significant differentially expressed proteins ( […]

call_split

Differential Regulation of Genes Coding for Organelle and Cytosolic ClpATPases under Biotic and Abiotic Stresses in Wheat

2016
Front Plant Sci
PMCID: 4923199
PMID: 27446158
DOI: 10.3389/fpls.2016.00929
call_split See protocol

[…] 02g08490, Os03g31300; 4 ClpC proteins—Os04g32560, Os12g12580, Os11g16590, Os1g16770; and 2 ClpD proteins—Os02g32520, Os04g33210) (Singh et al., ) were used as query and blastp search was performed in TriFLDB (http://TriFLDB.psc.riken.jp/) (Mochida et al., ) and NCBI database to identify the wheat class I ClpATPase gene homologs. Clustal omega (http://www.ebi.ac.uk/Tools/msa/clustalo/) and MEGA 5 s […]

library_books

Single molecule real time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research

2015
BMC Genomics
PMCID: 4673716
PMID: 26645802
DOI: 10.1186/s12864-015-2257-y

[…] sults of FLNC reads were visualized using the Integrative Genome Viewer []. The proportion of FLNC reads carrying complete ORF was evaluated using 5495 wheat full-length cDNAs (downloaded from http://trifldb.psc.riken.jp/v3/index.pl) as reference and by mapping to CS draft genome sequence with the aid of GMAP. […]

library_books

Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.)

2015
BMC Plant Biol
PMCID: 4474349
PMID: 26092253
DOI: 10.1186/s12870-015-0511-8

[…] ned to wheat reference sequences including unigenes identified from wheat genome sequences released by IWGSC (accessible at http://plants.ensembl.org/Triticum_aestivum), NCBI Wheat UniGene Build #62, TriFLDB [] and our de novo assembly by Bowtie2 with the parameters ‘-5 5–3 5 --no-unal -a -phred33 --end-to-end -X 600 --reorder --score-min L,-0.6,-0.3 -L 15’ []. Reads uniquely mapped to the referen […]

library_books

Conservation of AtTZF1, AtTZF2, and AtTZF3 homolog gene regulation by salt stress in evolutionarily distant plant species

2015
Front Plant Sci
PMCID: 4468379
PMID: 26136754
DOI: 10.3389/fpls.2015.00394

[…] d other genes that belong to the RR-TZF family in wheat using an in silico search in which the Arabidopsis genes and the durum wheat TdTZF1-A and TdTZF1-B genes were used as queries against the TIGR, TriFLDB, NCBI, and IWGSC databases. As well as the bread-wheat AK330326 sequence, which is named here as TaTZF1, and a recently described bread-wheat gene, TaZnFP (TaTZF2) (), we retrieved six more CC […]

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TriFLDB institution(s)
Plant Science Center, RIKEN, Yokohama, Japan; Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan

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