GtRNAdb

tRNAscan-SE Analysis of Mus musculus (mm9 July 2007)

>> Main Overview
>> tRNAs by Isotype
>> tRNAs by Locus
>> Secondary Structures
>> tRNA Alignments
>> FASTA Seqs
>> Run Options/Stats
>> Analysis Notes
>> Genome DB
>> 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 AA430
Selenocysteine tRNAs (TCA)2
Possible suppressor tRNAs (CTA,TTA)1
tRNAs with undetermined
or unknown isotypes
0
Predicted pseudogenes0
Total tRNAs433


Intron Summary

tRNAs with introns
24
Ser
AGA
1
Arg
TCT
4
Leu
CAA
4
Ile
TAT
4
Met
CAT
1
Tyr
GTA
10


Four Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
AlaAGC
19
GGC
 
CGC
10
TGC
11
40
GlyACC
1
GCC
14
CCC
7
TCC
7
29
ProAGG
7
GGG
 
CGG
3
TGG
8
18
ThrAGT
9
GGT
 
CGT
5
TGT
4
18
ValAAC
8
GAC
1
CAC
11
TAC
3
23

Six Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
SerAGA
9
GGA
1
CGA
3
TGA
3
ACT
 
GCT
8
 
 
 
 
24
ArgACG
6
GCG
 
CCG
3
TCG
5
 
 
 
 
CCT
5
TCT
5
24
LeuAAG
8
GAG
 
CAG
10
TAG
3
 
 
 
 
CAA
4
TAA
4
29

Two Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
PheAAA
 
GAA
7
 
 
 
 
7
AsnATT
 
GTT
14
 
 
 
 
14
Lys 
 
 
 
CTT
19
TTT
11
30
AspATC
 
GTC
16
 
 
 
 
16
Glu 
 
 
 
CTC
13
TTC
8
21
HisATG
1
GTG
10
 
 
 
 
11
Gln 
 
 
 
CTG
10
TTG
6
16

Two Box & Other tRNA Sets

IsotypetRNA Count by AnticodonTotal
IleAAT
11
GAT
1
 
 
TAT
5
17
Met 
 
 
 
CAT
18
 
 
18
TyrATA
 
GTA
10
 
 
 
 
10
Supres 
 
 
 
CTA
 
TTA
1
1
CysACA
 
GCA
57
 
 
 
 
57
Trp 
 
 
 
CCA
8
 
 
8
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.