GtRNAdb

tRNAscan-SE Analysis of Rattus norvegicus (rn4 Nov 2004)

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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 AA437
Selenocysteine tRNAs (TCA)1
Possible suppressor tRNAs (CTA,TTA)0
tRNAs with undetermined
or unknown isotypes
6
Predicted pseudogenes0
Total tRNAs444


Intron Summary

tRNAs with introns
23
Thr
AGT
1
Arg
TCT
6
Leu
CAA
3
Phe
AAA
1
Asp
ATC
1
Ile
TAT
3
Tyr
GTA
8


Four Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
AlaAGC
34
GGC
2
CGC
4
TGC
15
55
GlyACC
 
GCC
15
CCC
5
TCC
9
29
ProAGG
30
GGG
 
CGG
3
TGG
6
39
ThrAGT
9
GGT
 
CGT
3
TGT
5
17
ValAAC
8
GAC
 
CAC
7
TAC
5
20

Six Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
SerAGA
8
GGA
 
CGA
3
TGA
4
ACT
1
GCT
9
 
 
 
 
25
ArgACG
6
GCG
 
CCG
3
TCG
5
 
 
 
 
CCT
9
TCT
8
31
LeuAAG
6
GAG
 
CAG
14
TAG
4
 
 
 
 
CAA
3
TAA
2
29

Two Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
PheAAA
1
GAA
7
 
 
 
 
8
AsnATT
 
GTT
14
 
 
 
 
14
Lys 
 
 
 
CTT
17
TTT
9
26
AspATC
1
GTC
15
 
 
 
 
16
Glu 
 
 
 
CTC
10
TTC
10
20
HisATG
 
GTG
12
 
 
 
 
12
Gln 
 
 
 
CTG
9
TTG
5
14

Two Box & Other tRNA Sets

IsotypetRNA Count by AnticodonTotal
IleAAT
12
GAT
 
 
 
TAT
3
15
Met 
 
 
 
CAT
13
 
 
13
TyrATA
 
GTA
8
 
 
 
 
8
Supres 
 
 
 
CTA
 
TTA
 
0
CysACA
 
GCA
38
 
 
 
 
38
Trp 
 
 
 
CCA
8
 
 
8
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.