GtRNAdb

tRNAscan-SE Analysis of Pan troglodytes (chimp) (Mar 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 AA459
Selenocysteine tRNAs (TCA)2
Possible suppressor tRNAs (CTA,TTA)2
tRNAs with undetermined
or unknown isotypes
0
Predicted pseudogenes0
Total tRNAs463


Intron Summary

tRNAs with introns
31
Pro
AGG
1
Val
TAC
1
Arg
TCT
5
Leu
CAA
5
Ile
TAT
5
Tyr
ATA
1
Tyr
GTA
13


Four Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
AlaAGC
29
GGC
 
CGC
5
TGC
9
43
GlyACC
 
GCC
11
CCC
11
TCC
7
29
ProAGG
10
GGG
 
CGG
5
TGG
7
22
ThrAGT
9
GGT
 
CGT
4
TGT
6
19
ValAAC
10
GAC
 
CAC
12
TAC
9
31

Six Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
SerAGA
10
GGA
 
CGA
3
TGA
4
ACT
2
GCT
9
 
 
 
 
28
ArgACG
7
GCG
1
CCG
4
TCG
6
 
 
 
 
CCT
6
TCT
6
30
LeuAAG
8
GAG
 
CAG
6
TAG
3
 
 
 
 
CAA
7
TAA
8
32

Two Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
PheAAA
 
GAA
11
 
 
 
 
11
AsnATT
1
GTT
30
 
 
 
 
31
Lys 
 
 
 
CTT
16
TTT
15
31
AspATC
 
GTC
13
 
 
 
 
13
Glu 
 
 
 
CTC
7
TTC
15
22
HisATG
 
GTG
10
 
 
 
 
10
Gln 
 
 
 
CTG
10
TTG
7
17

Two Box & Other tRNA Sets

IsotypetRNA Count by AnticodonTotal
IleAAT
14
GAT
1
 
 
TAT
5
20
Met 
 
 
 
CAT
21
 
 
21
TyrATA
1
GTA
13
 
 
 
 
14
Supres 
 
 
 
CTA
1
TTA
1
2
CysACA
1
GCA
27
 
 
 
 
28
Trp 
 
 
 
CCA
7
 
 
7
SelCys 
 
 
 
 
 
TCA
2
2

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.