GtRNAdb

tRNAscan-SE Analysis of Caenorhabditis brenneri (WUGSC 4.0 Jan 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 AA1076
Selenocysteine tRNAs (TCA)0
Possible suppressor tRNAs (CTA,TTA)1
tRNAs with undetermined
or unknown isotypes
19
Predicted pseudogenes0
Total tRNAs1096


Intron Summary

tRNAs with introns
51
Leu
CAA
15
Phe
GAA
1
Ile
GAT
2
Ile
TAT
7
Tyr
ATA
2
Tyr
GTA
24


Four Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
AlaAGC
34
GGC
1
CGC
7
TGC
10
52
GlyACC
 
GCC
35
CCC
25
TCC
68
128
ProAGG
11
GGG
4
CGG
8
TGG
50
73
ThrAGT
32
GGT
3
CGT
9
TGT
17
61
ValAAC
35
GAC
 
CAC
15
TAC
8
58

Six Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
SerAGA
19
GGA
 
CGA
9
TGA
13
ACT
 
GCT
14
 
 
 
 
55
ArgACG
33
GCG
 
CCG
24
TCG
17
 
 
 
 
CCT
11
TCT
13
98
LeuAAG
32
GAG
 
CAG
10
TAG
9
 
 
 
 
CAA
15
TAA
7
73

Two Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
PheAAA
 
GAA
22
 
 
 
 
22
AsnATT
 
GTT
32
 
 
 
 
32
Lys 
 
 
 
CTT
50
TTT
26
76
AspATC
 
GTC
33
 
 
 
 
33
Glu 
 
 
 
CTC
37
TTC
35
72
HisATG
 
GTG
23
 
 
 
 
23
Gln 
 
 
 
CTG
13
TTG
41
54

Two Box & Other tRNA Sets

IsotypetRNA Count by AnticodonTotal
IleAAT
36
GAT
2
 
 
TAT
27
65
Met 
 
 
 
CAT
29
 
 
29
TyrATA
2
GTA
25
 
 
 
 
27
Supres 
 
 
 
CTA
1
TTA
 
1
CysACA
3
GCA
20
 
 
 
 
23
Trp 
 
 
 
CCA
22
 
 
22
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.