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Life Science Database Archive
tRNADB-CE

tRNA sequence data, annotation data and curation data

Data detail

info Data name tRNA sequence data, annotation data and curation data
info DOI 
info Description of data contents 

Data of tRNA search results and curation data. Three prediction programs (tRNAScan-SE, Aragorn and tRNA finder) were used together to search tRNA genes. If the prediction results did not match, curation was carried out by experts.
The following three types of determinations are used for determining the results.
- reliable tRNA gene　("circle" mark at the original website.)
- ambiguous case　("triangle" mark at the original website.)
- not tRNA gene　("x" mark at the original website.)

The data are classified into nine types as follows according to sources.
- Prokaryotic complete genome: 95,512 entries.
- Prokaryotic draft genome (WGS): 196,032 entries.
- Plant: 1,608 entries.
- Fungus: 2,773 entries.
- Virus: 151 entries.
- Phage: 962 entries.
- Chloroplast: 4,376 entries.
- Environmental sample (ENV) from GenBank: 101,837 entries.
- Environmental sample (ENV) from Sequence Read Archive: 54,872 entries.

The number of data is 458,123 in total. The data are given in a CSV format text file.

info Data file 
File name:
trnadb_ce.zip
File URL:
https://dbarchive.biosciencedbc.jp/data/trnadb_ce/LATEST/trnadb_ce.zip
File size:
22.7 MB
info Simple search URL 
info Data acquisition method 

-

info Data analysis method 

Three prediction programs (tRNAScan-SE, Aragorn and tRNA finder) were used together to search tRNA genes. If the prediction results did not match, curation was carried out by experts.

info Number of data entries 

458,123 entries

Data itemDescription
Data type Types of acquired data. Classified into nine types including "Prokaryotic complete genome", "Prokaryotic draft genome (WGS)", "Plant", "Fungus", "Virus", "Phage", "Chloroplast", "Environmental sample (ENV) from GenBank" and "Environmental sample (ENV) from Sequence Read Archive".
Sequence ID Sequence ID
Genome ID Genome ID (Genome ID of DDBJ GIB is used.)
Phylum/Class Taxon name
Species Species name
Start position tRNA gene start position on the genome
End position tRNA gene end position on the genome
Direction Direction of tRNA gene on the genome
Amino Acid Amino acid type
Anticodon Anticodon
1st Intron start position Start position of first intron
1st Intron end position End position of first intron
Seq tRNA sequence
Upstream seq. tRNA gene upstream sequence (10 bps)
tRNA1-7 1st to 7th nucleotides in the clover-leaf secondary structures (*1) of tRNA gene
tRNA8-9 8th to 9th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA10-13 10th to 13th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA14-21 14th to 21st nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA22-25 22nd to 25th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA26 26th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA27-31 27th to 31st nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA32-38 32nd to 38th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA39-43 39th to 43rd nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA44-48 44th to 48th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA49-53 49th to 53rd nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA54-60 54th to 60th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA61-65 61st to 65th nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA66-72 66th to 72nd nucleotides in the clover-leaf secondary structures of tRNA gene
tRNA73-76 73rd to 76th nucleotides in the clover-leaf secondary structures of tRNA gene
Downstream seq. tRNA gene downstream sequence (10 bps)
1st Intron seq. First intron sequence
2nd Intron start position Start position of second intron
2nd Intron end position End position of second intron
2st Intron seq. Second intron sequence
Decision from Dr. Muto Determination 1 (Dr. Muto)
Decision from Dr. Inokuchi Determination 2 (Dr. Inokuchi)
Decision from Dr. Yamada Determination 3 (Dr. Yamada)
Comment of Dr. Muto Comment 1 (Dr. Muto)
Comment of Dr. Inokuchi Comment 2 (Dr. Inokuchi)
Comment of Dr. Yamada Comment 3 (Dr. Yamada)
Final decision Final Determination
Comments Comment
Original database Genome sequence source information

*1Registered for each common position on the clover-leaf secondary structure of tRNA gene. (For common position, see http://trna.ie.niigata-u.ac.jp/trnadb/tRNA_structure.jpg.)