GtRNAdb

tRNAscan-SE Analysis of Strongylocentrotus purpuratus (Sea urchin) (Version 2.1)

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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 AA1065
Selenocysteine tRNAs (TCA)0
Possible suppressor tRNAs (CTA,TTA)1
tRNAs with undetermined
or unknown isotypes
2
Predicted pseudogenes0
Total tRNAs1068


Intron Summary

tRNAs with introns
39
Ser
ACT
1
Ile
TAT
13
Tyr
GTA
24


Four Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
AlaAGC
32
GGC
 
CGC
7
TGC
17
56
GlyACC
 
GCC
42
CCC
4
TCC
33
79
ProAGG
19
GGG
 
CGG
9
TGG
21
49
ThrAGT
27
GGT
 
CGT
9
TGT
21
57
ValAAC
20
GAC
 
CAC
16
TAC
11
47

Six Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
SerAGA
25
GGA
 
CGA
6
TGA
15
ACT
1
GCT
17
 
 
 
 
64
ArgACG
29
GCG
 
CCG
1
TCG
19
 
 
 
 
CCT
19
TCT
18
86
LeuAAG
18
GAG
 
CAG
5
TAG
8
 
 
 
 
CAA
2
TAA
14
47

Two Box tRNA Sets

IsotypetRNA Count by AnticodonTotal
PheAAA
2
GAA
 
 
 
 
 
2
AsnATT
 
GTT
39
 
 
 
 
39
Lys 
 
 
 
CTT
42
TTT
57
99
AspATC
 
GTC
82
 
 
 
 
82
Glu 
 
 
 
CTC
29
TTC
26
55
HisATG
 
GTG
26
 
 
 
 
26
Gln 
 
 
 
CTG
21
TTG
17
38

Two Box & Other tRNA Sets

IsotypetRNA Count by AnticodonTotal
IleAAT
69
GAT
2
 
 
TAT
22
93
Met 
 
 
 
CAT
73
 
 
73
TyrATA
 
GTA
24
 
 
 
 
24
Supres 
 
 
 
CTA
 
TTA
1
1
CysACA
 
GCA
31
 
 
 
 
31
Trp 
 
 
 
CCA
18
 
 
18
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.