GtRNAdb

tRNAscan-SE Analysis of Danio rerio (Zebrafish) (Zv9 Jul 2010)

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tRNA Gene Summary

tRNA-derived SINEs are found in a number of eukaryotes especially mammalian genomes. After manual inspection and analysis, we apply the following filter to this genome for eliminating these tRNA-derived elements from true tRNAs. If the tRNA candidates have hits in both tRNAscan and Eufind first-pass scanners, we use a combination of at least 20 bits COVE score, 10 bits HMM score, and 5 bits 2' structure score to define a true tRNA. If the tRNA candidates only have hits in one of the first-pass scanners, the threshold of a true tRNA will be 55 bits COVE score.



tRNAs Decoding Standard 20 AA12794
Selenocysteine tRNAs (TCA)14
Possible suppressor tRNAs (CTA,TTA)16
tRNAs with undetermined
or unknown isotypes
20
Predicted pseudogenes0
Total tRNAs12844


Intron Summary

tRNAs with introns
748
Ala
TGC
1
Gly
CCC
2
Gly
TCC
2
Pro
AGG
7
Val
AAC
1
Arg
TCT
259
Leu
AAG
4
Leu
TAG
8
Leu
CAA
173
Leu
TAA
5
Phe
AAA
1
Lys
TTT
4
Asp
GTC
1
Ile
AAT
1
Ile
TAT
59
Met
CAT
1
Tyr
ATA
4
Tyr
GTA
215


Four Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
AlaAGC
90
GGC
4
CGC
112
TGC
367
573
GlyACC
8
GCC
826
CCC
279
TCC
40
1153
ProAGG
346
GGG
2
CGG
209
TGG
226
783
ThrAGT
384
GGT
10
CGT
70
TGT
303
767
ValAAC
247
GAC
5
CAC
235
TAC
243
730

Six Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
SerAGA
359
GGA
2
CGA
92
TGA
213
ACT
14
GCT
436
 
 
 
 
1116
ArgACG
191
GCG
25
CCG
59
TCG
104
 
 
 
 
CCT
101
TCT
264
744
LeuAAG
306
GAG
4
CAG
314
TAG
270
 
 
 
 
CAA
182
TAA
61
1137

Two Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
PheAAA
10
GAA
220
 
 
 
 
230
AsnATT
25
GTT
1138
 
 
 
 
1163
Lys 
 
 
 
CTT
1018
TTT
565
1583
AspATC
1
GTC
166
 
 
 
 
167
Glu 
 
 
 
CTC
238
TTC
233
471
HisATG
11
GTG
405
 
 
 
 
416
Gln 
 
 
 
CTG
297
TTG
110
407

Two Box & Other tRNA Sets

IsotypetRNA Count by AnticodonTotal
IleAAT
285
GAT
9
 
 
TAT
73
367
Met 
 
 
 
CAT
612
 
 
612
TyrATA
5
GTA
225
 
 
 
 
230
Supres 
 
 
 
CTA
9
TTA
7
16
CysACA
9
GCA
98
 
 
 
 
107
Trp 
 
 
 
CCA
38
 
 
38
SelCys 
 
 
 
 
 
TCA
14
14

The Genomic tRNA Database is curated by Todd Lowe and Patricia Chan. Please email lowe@soe.ucsc.edu with any questions and comments. To submit corrections, please use our Bug and Request Tracking System.