GtRNAdb

tRNAscan-SE Analysis of Pongo pygmaeus abelii (orangutan) (July 2007)

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>> Genome Seq
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 AA468
Selenocysteine tRNAs (TCA)2
Possible suppressor tRNAs (CTA,TTA)0
tRNAs with undetermined
or unknown isotypes
1
Predicted pseudogenes0
Total tRNAs471


Intron Summary

tRNAs with introns
34
Pro
AGG
1
Arg
TCT
7
Leu
CAA
5
Ile
TAT
6
Tyr
ATA
1
Tyr
GTA
14


Four Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
AlaAGC
22
GGC
 
CGC
4
TGC
9
35
GlyACC
 
GCC
13
CCC
9
TCC
8
30
ProAGG
11
GGG
 
CGG
4
TGG
7
22
ThrAGT
12
GGT
 
CGT
6
TGT
5
23
ValAAC
8
GAC
 
CAC
15
TAC
7
30

Six Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
SerAGA
9
GGA
 
CGA
6
TGA
4
ACT
 
GCT
8
 
 
 
 
27
ArgACG
7
GCG
 
CCG
6
TCG
6
 
 
 
 
CCT
8
TCT
8
35
LeuAAG
10
GAG
 
CAG
10
TAG
3
 
 
 
 
CAA
5
TAA
6
34

Two Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
PheAAA
 
GAA
11
 
 
 
 
11
AsnATT
2
GTT
33
 
 
 
 
35
Lys 
 
 
 
CTT
20
TTT
14
34
AspATC
 
GTC
11
 
 
 
 
11
Glu 
 
 
 
CTC
7
TTC
19
26
HisATG
 
GTG
10
 
 
 
 
10
Gln 
 
 
 
CTG
9
TTG
6
15

Two Box & Other tRNA Sets

IsotypetRNA Count by AnticodonTotal
IleAAT
13
GAT
3
 
 
TAT
6
22
Met 
 
 
 
CAT
18
 
 
18
TyrATA
1
GTA
15
 
 
 
 
16
Supres 
 
 
 
CTA
 
TTA
 
0
CysACA
 
GCA
27
 
 
 
 
27
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.