GtRNAdb

tRNAscan-SE Analysis of Equus caballus (horse) (Jan 2007)

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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 AA499
Selenocysteine tRNAs (TCA)4
Possible suppressor tRNAs (CTA,TTA)0
tRNAs with undetermined
or unknown isotypes
0
Predicted pseudogenes0
Total tRNAs503


Intron Summary

tRNAs with introns
32
Arg
TCT
6
Leu
CAA
6
Glu
CTC
1
Ile
TAT
4
Tyr
ATA
1
Tyr
GTA
14


Four Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
AlaAGC
27
GGC
 
CGC
8
TGC
10
45
GlyACC
 
GCC
10
CCC
8
TCC
5
23
ProAGG
10
GGG
 
CGG
3
TGG
7
20
ThrAGT
9
GGT
 
CGT
3
TGT
7
19
ValAAC
12
GAC
3
CAC
16
TAC
6
37

Six Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
SerAGA
12
GGA
 
CGA
4
TGA
4
ACT
 
GCT
12
 
 
 
 
32
ArgACG
10
GCG
1
CCG
4
TCG
5
 
 
 
 
CCT
7
TCT
6
33
LeuAAG
8
GAG
 
CAG
3
TAG
5
 
 
 
 
CAA
6
TAA
4
26

Two Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
PheAAA
 
GAA
13
 
 
 
 
13
AsnATT
1
GTT
21
 
 
 
 
22
Lys 
 
 
 
CTT
18
TTT
15
33
AspATC
1
GTC
10
 
 
 
 
11
Glu 
 
 
 
CTC
50
TTC
11
61
HisATG
1
GTG
12
 
 
 
 
13
Gln 
 
 
 
CTG
10
TTG
6
16

Two Box & Other tRNA Sets

IsotypetRNA Count by AnticodonTotal
IleAAT
20
GAT
 
 
 
TAT
4
24
Met 
 
 
 
CAT
23
 
 
23
TyrATA
1
GTA
14
 
 
 
 
15
Supres 
 
 
 
CTA
 
TTA
 
0
CysACA
 
GCA
26
 
 
 
 
26
Trp 
 
 
 
CCA
7
 
 
7
SelCys 
 
 
 
 
 
TCA
4
4

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.