GtRNAdb

tRNAscan-SE Analysis of Macaca mulatta (Rhesus) (Jan 2006)

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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 AA378
Selenocysteine tRNAs (TCA)1
Possible suppressor tRNAs (CTA,TTA)0
tRNAs with undetermined
or unknown isotypes
0
Predicted pseudogenes0
Total tRNAs379


Intron Summary

tRNAs with introns
23
Arg
TCT
4
Leu
CAA
3
Ile
TAT
5
Tyr
GTA
11


Four Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
AlaAGC
15
GGC
1
CGC
5
TGC
8
29
GlyACC
 
GCC
11
CCC
7
TCC
5
23
ProAGG
8
GGG
 
CGG
4
TGG
5
17
ThrAGT
8
GGT
 
CGT
4
TGT
6
18
ValAAC
6
GAC
 
CAC
12
TAC
7
25

Six Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
SerAGA
9
GGA
 
CGA
4
TGA
5
ACT
 
GCT
8
 
 
 
 
26
ArgACG
7
GCG
 
CCG
4
TCG
5
 
 
 
 
CCT
5
TCT
5
26
LeuAAG
9
GAG
 
CAG
5
TAG
4
 
 
 
 
CAA
3
TAA
4
25

Two Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
PheAAA
 
GAA
9
 
 
 
 
9
AsnATT
1
GTT
18
 
 
 
 
19
Lys 
 
 
 
CTT
12
TTT
13
25
AspATC
 
GTC
14
 
 
 
 
14
Glu 
 
 
 
CTC
6
TTC
11
17
HisATG
 
GTG
10
 
 
 
 
10
Gln 
 
 
 
CTG
10
TTG
5
15

Two Box & Other tRNA Sets

IsotypetRNA Count by AnticodonTotal
IleAAT
10
GAT
4
 
 
TAT
5
19
Met 
 
 
 
CAT
17
 
 
17
TyrATA
 
GTA
11
 
 
 
 
11
Supres 
 
 
 
CTA
 
TTA
 
0
CysACA
 
GCA
26
 
 
 
 
26
Trp 
 
 
 
CCA
7
 
 
7
SelCys 
 
 
 
 
 
TCA
1
1

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.