GtRNAdb

tRNAscan-SE Analysis of Glycine max (soybean) (Dec 2008 Glyma 1.0)

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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 AA860
Selenocysteine tRNAs (TCA)0
Possible suppressor tRNAs (CTA,TTA)0
tRNAs with undetermined
or unknown isotypes
1
Predicted pseudogenes0
Total tRNAs861


Intron Summary

tRNAs with introns
39
Ser
TGA
1
Met
CAT
18
Tyr
GTA
20


Four Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
AlaAGC
24
GGC
 
CGC
8
TGC
17
49
GlyACC
 
GCC
29
CCC
9
TCC
18
56
ProAGG
21
GGG
 
CGG
5
TGG
32
58
ThrAGT
10
GGT
2
CGT
4
TGT
11
27
ValAAC
22
GAC
2
CAC
13
TAC
9
46

Six Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
SerAGA
15
GGA
1
CGA
6
TGA
11
ACT
 
GCT
32
 
 
 
 
65
ArgACG
27
GCG
 
CCG
5
TCG
9
 
 
 
 
CCT
13
TCT
19
73
LeuAAG
16
GAG
 
CAG
7
TAG
25
 
 
 
 
CAA
27
TAA
9
84

Two Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
PheAAA
 
GAA
23
 
 
 
 
23
AsnATT
2
GTT
35
 
 
 
 
37
Lys 
 
 
 
CTT
22
TTT
21
43
AspATC
 
GTC
34
 
 
 
 
34
Glu 
 
 
 
CTC
24
TTC
17
41
HisATG
 
GTG
25
 
 
 
 
25
Gln 
 
 
 
CTG
13
TTG
17
30

Two Box & Other tRNA Sets

IsotypetRNA Count by AnticodonTotal
IleAAT
31
GAT
 
 
 
TAT
8
39
Met 
 
 
 
CAT
63
 
 
63
TyrATA
 
GTA
22
 
 
 
 
22
Supres 
 
 
 
CTA
 
TTA
 
0
CysACA
 
GCA
16
 
 
 
 
16
Trp 
 
 
 
CCA
29
 
 
29
SelCys 
 
 
 
 
 
TCA
 
0

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.