Pseudogenes for contig
| Features | Start | End | Frame Joins | Pseudo Tag | Seq | GenePRIMP Notes |
|---|---|---|---|---|---|---|
| RNA_38 - or2100 | 2093789 | 2094024 | complement (join (2093789..2093863, 2093863..2093952, 2093954..2094001, 2094001..2094024)) | pseudogene, missed gene |
G
T
G
G
C
T
A
C
A
T
T
C
A
A
T
G
C
T
A
T
G C A T T A C A T G A G G A A T T A T A A A A A G G T A C T G G A T C A G A T G G T G A G G G T C T G T G A A T A T G G G A A G A A A G T T G T C G C T G A A A G A C A C A A A G A G A G A G G A A G C C A T C A T G A A G C A A A T A T A A G C A T T G A A G A T A T T G C A A A G T A T T T A G A A G T T G A A T A T G G T T T A A T A G G A G A A A T A A A A A A G T C A G A A A G G A C A G A T A T T T T T A T A T C C A A A A A G T G A
V
A
T
F
N
A
M
H
Y
M
R
N
Y
K
K
V
L
D
Q
M
V R V C E Y G K K V V A E R H K E R G S H H E A N I S I E D I A K Y L E V E Y G L I G E I K K S E R T D I F I S K K * |
Comments=Pseudogene, >1 frameshift are present |
| RNA_5 - ffs | 35442 | 35588 | pseudogene, missed gene |
T
T
G
C
G
C
A
G
G
A
C
T
C
A
A
G
T
A
T
C
A A C G C C A C T T A C T T A T G C C A G A C C T T A C A A T G G T C A G G C C T C A G C C T G G G A A T T C G A C C C T G C T A T A G C G G G T T G C A G G T T A C A G G G C A C C G C T A C C T C C C C A T C T A G T A C G G C C A A G A A T T A C C T T
L
R
R
T
Q
V
S
T
P
L
T
Y
A
R
P
Y
N
G
Q
A
S A W E F D P A I A G C R L Q G T A T S P S S T A K N Y L |
Comments=Pseudogene, start/stop is absent | |
| or0008 - or0009 | 8759 | 8869 | pseudogene, missed gene |
A
T
A
C
A
A
A
T
T
G
C
T
G
A
C
T
T
C
G
T
A T C C G A A G T T T T A G G A G T A G A T G A T G A A G A A G G A A A T G T A G T A T T G C T T T A A C C A G A A A G A A G A G T A A A A A T A G G A A A T A A A A T T T A C T A G
I
Q
I
A
D
F
V
S
E
V
L
G
V
D
D
E
E
G
N
V
V L L * P E R R V K I G N K I Y * |
Comments=Pseudogene, TAA stop codon in frame | |
| or0024 - or0025, or0025, or0025 - or0026 | 28722 | 30234 | complement (join (28722..28814, 28813..30234)) | pseudogene |
A
T
G
A
T
A
G
T
A
A
T
A
C
A
G
G
C
T
A
A
A C T T A T T T T C C T A A C T T A A C A A G A C A A A C A A A T A G T G C T G G A T T T A A T G A G A A G A T G G T C A T C A T G T A T A A G A T T T G C G T A C A A A A G G C T T C T A C A A G G C T A T G A T A G A A A C A C A T T A A A A A G A G A C C T T C A G G G A A T T T T C A A T T T A A A C T C A A G A T A C G T A G A T G A C G C A A T A A T G A A A G C A A G A A G C G T A T T A G A A T C C T C C A A A G A A T T A G G G A A T A A T C C A A A G A A A G T A A T T T T T G G A G A G A A A G A T T T A T T T A A A A A A C T T C A A A A A C G C C A T A T A A C T G G G A A A G A G T A T C A A A A G C T A A A A A C A A A A T G G C A A G A G A A A A G A A A A G G A A A T C T C T A T T C A A G A G G A G A T A A A A G C A A G A A A G G A A A T C T C A A C A C A A G A A T A G A A G T A A A A G A A A A T G G C A T T T T T T T A A G G A T A A A T G T G G G A A A A A G A A A A T A C A T A T A T G C C A A A A T A G A A G C A G G C T A T A A A A A G A A T A A G A G C A G A G A A G A A C T C C T A C A G G A A A T C G C C G A A T C A A A C A T A C C T T A C T C T G T A G A A T T A A A A C T C A A A A A T G G C A G C A T A T A C G C C T A T T T T T C T A T T G A A G A A G A A T A T C C A G A A A C A A A A A T A A C A A A A G A A A A A G G G G T C A T A G G A A T A G A T G T A A A T G C A T A T C C A G A C A A C A T A T C A T G G G C A G A G A C A G A T G A A A A A G G A A A T C T A A T A A G T T A T G A T A A G A T A C C A A T G C C A G A G C T A T C A A G T G G A A A T A A A G A C A A A A G A G A A T A C T T T A G A T G G C A G T A T G C C C A T G A G A T A G T A A A A A T A G C A A A A G A A A A A C G A A A A G C G A T T G T G A T T G A A G A A T T G G A C A T A A A A G A A A A A G G A A A A A G A G G A G A C T T T T C A G G A A G A A A A T C A A G G A G A A T A A G A C A T A A C T T T A G C T A C A A A T C A C T T C T T T C A A A A A T A A A A A C A C T A G C A A A A A G A G A A G G G A T A G A A G T A A T A G A A G T C A A T C C T T C T T A C A C C T C A A T A A T A G G G A T G T T A A A A T A T G C A C C A C A G T A T A T G A C A A C A A A A G A C A T A G C A G C A G C C T A T G T A A T A G C A A G A A G A G G A T T A G G C A A A G A A G A A A A G A T A C C G A A T A A C T A T G T A A A C T T C C T C A A C A C A T T G A C T G A A A A G G A A T T A G A A G A G T T A A A A G A A C A T G T A A A A T A T A C A G T C A A A A A T A A G C A T T T A A A G A A A A A G C A T T T A A T G G A A A T A A A C A A A G C A A T A A A A T T T A T A C A A A G C C T T G G G A G T G A G T C A G A A A G G G T G C T A A G A C C T C T G T A C G A A A C A A G T T T T A G T A C C T A T G A T T T C T G G C A A G T T C T C A A G G T A G C G G T G G T G A C A C C A C T C T C C C C T G A G A A A G T A C C A A G A G A C T T C T C T G T C C T G A A G G A A T T A T T A A T T C A G G G C A A G A G T G G G G A G A C T C G T A A G G G C G C A A G T T C C T G C T T C T T G G G G C A G G G G C T A T G G C T T T T C C A A A A A C C G C C T G C T G G G G C T G G G A A A G C C T G A
M
I
V
I
Q
A
K
L
I
F
L
T
*
Q
D
K
Q
I
V
L
D L M R R W S S C I R F A Y K R L L Q G Y D R N T L K R D L Q G I F N L N S R Y V D D A I M K A R S V L E S S K E L G N N P K K V I F G E K D L F K K L Q K R H I T G K E Y Q K L K T K W Q E K R K G N L Y S R G D K S K K G N L N T R I E V K E N G I F L R I N V G K R K Y I Y A K I E A G Y K K N K S R E E L L Q E I A E S N I P Y S V E L K L K N G S I Y A Y F S I E E E Y P E T K I T K E K G V I G I D V N A Y P D N I S W A E T D E K G N L I S Y D K I P M P E L S S G N K D K R E Y F R W Q Y A H E I V K I A K E K R K A I V I E E L D I K E K G K R G D F S G R K S R R I R H N F S Y K S L L S K I K T L A K R E G I E V I E V N P S Y T S I I G M L K Y A P Q Y M T T K D I A A A Y V I A R R G L G K E E K I P N N Y V N F L N T L T E K E L E E L K E H V K Y T V K N K H L K K K H L M E I N K A I K F I Q S L G S E S E R V L R P L Y E T S F S T Y D F W Q V L K V A V V T P L S P E K V P R D F S V L K E L L I Q G K S G E T R K G A S S C F L G Q G L W L F Q K P P A G A G K A * |
Maingene=or0025; Extension SUCCEEDED with start of type START; Comments=Pseudogene, both frameshift and stop-codon are present |
| or0025, or0025 - or0026 | 28798 | 30303 | pseudogene |
A
T
G
A
A
T
C
G
A
A
G
A
A
A
A
A
G
G
A
A
G A T T G A C A A T A C T T G T T A G A A C A T C A A A A A G A C A A A G G G G C A A A A A A A C A T G A T A G T A A T A C A G G C T A A A C T T A T T T T C C T A A C T T A A C A A G A C A A A C A A A T A G T G C T G G A T T T A A T G A G A A G A T G G T C A T C A T G T A T A A G A T T T G C G T A C A A A A G G C T T C T A C A A G G C T A T G A T A G A A A C A C A T T A A A A A G A G A C C T T C A G G G A A T T T T C A A T T T A A A C T C A A G A T A C G T A G A T G A C G C A A T A A T G A A A G C A A G A A G C G T A T T A G A A T C C T C C A A A G A A T T A G G G A A T A A T C C A A A G A A A G T A A T T T T T G G A G A G A A A G A T T T A T T T A A A A A A C T T C A A A A A C G C C A T A T A A C T G G G A A A G A G T A T C A A A A G C T A A A A A C A A A A T G G C A A G A G A A A A G A A A A G G A A A T C T C T A T T C A A G A G G A G A T A A A A G C A A G A A A G G A A A T C T C A A C A C A A G A A T A G A A G T A A A A G A A A A T G G C A T T T T T T T A A G G A T A A A T G T G G G A A A A A G A A A A T A C A T A T A T G C C A A A A T A G A A G C A G G C T A T A A A A A G A A T A A G A G C A G A G A A G A A C T C C T A C A G G A A A T C G C C G A A T C A A A C A T A C C T T A C T C T G T A G A A T T A A A A C T C A A A A A T G G C A G C A T A T A C G C C T A T T T T T C T A T T G A A G A A G A A T A T C C A G A A A C A A A A A T A A C A A A A G A A A A A G G G G T C A T A G G A A T A G A T G T A A A T G C A T A T C C A G A C A A C A T A T C A T G G G C A G A G A C A G A T G A A A A A G G A A A T C T A A T A A G T T A T G A T A A G A T A C C A A T G C C A G A G C T A T C A A G T G G A A A T A A A G A C A A A A G A G A A T A C T T T A G A T G G C A G T A T G C C C A T G A G A T A G T A A A A A T A G C A A A A G A A A A A C G A A A A G C G A T T G T G A T T G A A G A A T T G G A C A T A A A A G A A A A A G G A A A A A G A G G A G A C T T T T C A G G A A G A A A A T C A A G G A G A A T A A G A C A T A A C T T T A G C T A C A A A T C A C T T C T T T C A A A A A T A A A A A C A C T A G C A A A A A G A G A A G G G A T A G A A G T A A T A G A A G T C A A T C C T T C T T A C A C C T C A A T A A T A G G G A T G T T A A A A T A T G C A C C A C A G T A T A T G A C A A C A A A A G A C A T A G C A G C A G C C T A T G T A A T A G C A A G A A G A G G A T T A G G C A A A G A A G A A A A G A T A C C G A A T A A C T A T G T A A A C T T C C T C A A C A C A T T G A C T G A A A A G G A A T T A G A A G A G T T A A A A G A A C A T G T A A A A T A T A C A G T C A A A A A T A A G C A T T T A A A G A A A A A G C A T T T A A T G G A A A T A A A C A A A G C A A T A A A A T T T A T A C A A A G C C T T G G G A G T G A G T C A G A A A G G G T G C T A A G A C C T C T G T A C G A A A C A A G T T T T A G T A C C T A T G A T T T C T G G C A A G T T C T C A A G G T A G C G G T G G T G A C A C C A C T C T C C C C T G A G A A A G T A C C A A G A G A C T T C T C T G T C C T G A A G G A A T T A T T A A T T C A G G G C A A G T G G G G A G A C T C G T A A
M
N
R
R
K
R
K
I
D
N
T
C
*
N
I
K
K
T
K
G
Q K N M I V I Q A K L I F L T * Q D K Q I V L D L M R R W S S C I R F A Y K R L L Q G Y D R N T L K R D L Q G I F N L N S R Y V D D A I M K A R S V L E S S K E L G N N P K K V I F G E K D L F K K L Q K R H I T G K E Y Q K L K T K W Q E K R K G N L Y S R G D K S K K G N L N T R I E V K E N G I F L R I N V G K R K Y I Y A K I E A G Y K K N K S R E E L L Q E I A E S N I P Y S V E L K L K N G S I Y A Y F S I E E E Y P E T K I T K E K G V I G I D V N A Y P D N I S W A E T D E K G N L I S Y D K I P M P E L S S G N K D K R E Y F R W Q Y A H E I V K I A K E K R K A I V I E E L D I K E K G K R G D F S G R K S R R I R H N F S Y K S L L S K I K T L A K R E G I E V I E V N P S Y T S I I G M L K Y A P Q Y M T T K D I A A A Y V I A R R G L G K E E K I P N N Y V N F L N T L T E K E L E E L K E H V K Y T V K N K H L K K K H L M E I N K A I K F I Q S L G S E S E R V L R P L Y E T S F S T Y D F W Q V L K V A V V T P L S P E K V P R D F S V L K E L L I Q G K W G D S * |
Maingene=or0025; Extension SUCCEEDED with start of type START; Comments=Pseudogene, TAA stop codon seen in alignment | |
| or0030 | 34477 | 34668 | pseudogene |
A
T
G
A
C
G
C
C
G
G
A
A
C
A
G
A
T
A
A
G
A G C T A T T T T A A T G G G A A T G C T T A T T A G T G G A G G A A T G T T A A T T C A A G G T A A T A T C C C A A A C A T C A T T T C A G C G G G C A A A T T A A A A A T A A A A A G T A C T G A A A G G G C A C G A A T T G C T G T T C C T C T A G G T G C A A T A C T T T T G A T A G T G T A T T A T A T T G T A T T G T T T G T G A T T T A A
M
T
P
E
Q
I
R
A
I
L
M
G
M
L
I
S
G
G
M
L
I Q G N I P N I I S A G K L K I K S T E R A R I A V P L G A I L L I V Y Y I V L F V I * |
Maingene=or0030; Extension FAILED; Comments=Pseudogene, failed extension, extended gene length<=100aa and < 70% the length of the second shortest homolog | |
| or0047, or0048 | 50952 | 51254 | pseudogene |
G
T
G
G
A
T
A
T
C
A
A
C
C
C
T
T
C
T
G
T
T C A A C T T G A T A T T A A C C G C T G G A A T A G G G T A A T T T C T T A C A A G C C T C T A A A T A A T G A C G G G A A A G A A G T T T T G A A G G A T A T A A A T T T A A A A A A C A A A G A T A T A G A A G A A G C T A T T G A T A A A G T A G T A G A A C A A T C T A T A A A G A A A A A A T A T A T T A A T G A C A G T T A T A A A A T T T A T T C T A A T A C C A A C A A A A A A A T C C G T A T T A C T A T T T A T A G T A A A A A A G A A A T T A A G T T A A A C T T G G T A A A A G C A G A A C A G A A A A T C A G T C A G A A A C T G C A C T T T G C C T A A
V
D
I
N
P
S
V
Q
L
D
I
N
R
W
N
R
V
I
S
Y
K P L N N D G K E V L K D I N L K N K D I E E A I D K V V E Q S I K K K Y I N D S Y K I Y S N T N K K I R I T I Y S K K E I K L N L V K A E Q K I S Q K L H F A * |
Maingene=or0047; Extension FAILED; Comments=Pseudogene, failed extension, extended gene length>100aa and < 50% the length of the second shortest homolog | |
| or0049 - or0050 | 53022 | 53105 | pseudogene, missed gene |
T
T
G
T
T
A
A
T
A
G
T
A
T
T
T
G
T
G
A
T
T G C C A T A A G C G G G G T A T T T G T T C T A G T G A A T A A T A T G C C G G G T G A C C C C G C T T A T G G T G A T T A G
L
L
I
V
F
V
I
A
I
S
G
V
F
V
L
V
N
N
M
P
G D P A Y G D * |
Comments=Pseudogene, good start found, extended gene length<=100aa and < 70% the length of the second shortest homolog. Found common hit with non-adjoining gene: or0058 | |
| or0049 - or0050, or0050 | 53102 | 53686 | pseudogene |
T
T
A
G
A
A
G
A
C
C
C
A
A
G
G
A
T
A
G
T
C A A A A T T G A C G G C A T T T A T T A T A T G A T G T A C A C A G G T T T T G G A G A C A G A T T T C A A G A T G A C T A T A G G A T C T G T T T G G C T A C C T C C A A A A A C C T T A T A G A T T G G G A G A G A A A A G G A G T A G T T T T A G A T G A A C C T A A T A A A G A C G C C T C T T T A T T T C C T G A A A A A A T T A A T G G T A A A T A T G T G A T G T T G C A C A G G A G A T A T C C C G A C A T T T G G A T A G C A T T T T C T G A T G A T T T A A A A A A T T G G T A C G A C C A T A A A C C A A T A C T A A A A C C T A T T C C A A A T A C A T G G G A G A G T G C G A G A G T A G G A A T T G G A G G G C C T C C T A T T A A G A C A A A G G A C G G T T G G T T T T T G A T A T A C C A T G C A G C T G A T G A C A A T A A T G T G T A T A G A T T G G G A G C A G T C C T T T T A G A T T T A G A A G A T C C A T C A A A G G T T A T T G C A A G G C A A A A A G A A C C T A T C T T A G A G C C A G A A C T G G G T T G G G A A A A A G A A G G A T A C A T C C C T A A T G T T G T A T T T A G T T G T G G T A A T G C A G T A A A A G A T G A T A C T A T T T A C G T T T A T T A T G G G G T G C G G A T A C T G T C A T A G
L
E
D
P
R
I
V
K
I
D
G
I
Y
Y
M
M
Y
T
G
F
G D R F Q D D Y R I C L A T S K N L I D W E R K G V V L D E P N K D A S L F P E K I N G K Y V M L H R R Y P D I W I A F S D D L K N W Y D H K P I L K P I P N T W E S A R V G I G G P P I K T K D G W F L I Y H A A D D N N V Y R L G A V L L D L E D P S K V I A R Q K E P I L E P E L G W E K E G Y I P N V V F S C G N A V K D D T I Y V Y Y G V R I L S * |
Maingene=or0050; Extension SUCCEEDED with start of type ALNSTART; Comments=Pseudogene, extend to start of alignment | |
| or0050 - or0051 | 53796 | 54137 | pseudogene, missed gene |
T
A
T
A
G
A
T
G
G
T
T
T
T
T
A
G
G
A
T
A
T G G A T T A A A C G A A G A A A T A C C T C A C T T A T C T A C C T T T G G T A A A A A C T A T G A A A G G A G A T T C A A A A A T A C A G A T A T T T T T G A A A A A A T A T T T A C A A A A A T A C T A G A A G A A G C A A T A A A G C A C A A T T T C A T A A A T G C A G A A G A A G T A T T C A T A G A C G C A A C C C A T G T A A A A G C A A G T G C C T A T A A G A A A A A A T A C A C C A A A G A A G T A A T A G A A A A A G A G A G C A T A A C A T A T C A A G C G A A A T T A G A A G A A G A G A T A G C A A A A G A T A G A G A A G C C C A T G G G A A A A A G C C A T T A A A G C A A A T C A A G A C A A T T T A T A T C C A A A T A T A A
Y
R
W
F
L
G
Y
G
L
N
E
E
I
P
H
L
S
T
F
G
K N Y E R R F K N T D I F E K I F T K I L E E A I K H N F I N A E E V F I D A T H V K A S A Y K K K Y T K E V I E K E S I T Y Q A K L E E E I A K D R E A H G K K P L K Q I K T I Y I Q I * |
Comments=Pseudogene, start/stop is absent | |
| or0055, or0056 | 56466 | 57511 | join (56466..57038, 57038..57511) | putative pseudogene |
t
t
g
a
c
g
g
c
a
a
t
t
a
a
a
a
g
g
a
a
a a a a g t g a c c a t g a a a g a t a t c g c t g a a a g g t t g a a c t t a t c a a t t a a t g c t g t g t c c c t g g c t t t a a a t g a c a a g g t g g g g g t g a g c g a a g a g a c a a g g a a a a t a g t t t t a a a a a c a g c t g a t g a a a t g g g g t a t t t t g a t g a a a a t c c c t c t t t t a t t g c t a a a a a t c a c t t c a g g a a t a t t t g t c t a t t g a t t g a a g a g a g a a a t t t c c g c g a t a c t c a t t t t t a t a c a a a a g t a a t t t t a g g t a t a g a g a a t g a a g c a a a g a a a a a t a a t t a c g a t a t t t t a g t a a a c t t c a t g a a t c a a g a t g a t t t t c a g g t a c c t t c c a g t g t t g a a a c g a g a a a a g t t t c a g g a a t t t t a g t g g t t g g t a c t a t t a a a g a t g a a c a t c t g g a a a a a t t a t t g a a g t a t g a t a t a c c a a c t g t c c t t g t a g a c c a t g c t t c a t t t a c t a t a a g t a c a g a t g c t g t a t t a a c t c a a a a t a t g c c t g g a a c a t a t a t g g c a a c a c a a t a t c t t a t t c g a a a a g g a c a t a c t c a a a t a g g t t t t t t t g g t g a a a t a g a t t t t t c t t t a a g t t t t a a a g a a a g a t g g t t a g g c t t t a a c g a g g c g a t g a g a a a t g c a g g a c t t a a t g t a g a t c c c a t a t t t a a t g t a a a t c c t g g a t a t t g t g t a a t a g g a c a g g t a g a a c a a t a t g t t t t a a g c a a a a a c t a c a a a g a g g t a g c a a a t a t t a t c t c a a a g t t a g a t a a a c t t c c t a c t g c a t g g g t a t g c t c c a a c g a t a g t g c t g c t a t t a c c t t g t a c a a t g c a t t g a g c a t t t t g g g t a t t a a a g t a c c t g a c g a t a t c t c t g t a g t t g g c t t t g a t g a t a t t g a t a t a t g t a a c a t t g t g a c a c c g c a t t t g a c t a c t a t c c g c a t a a a t a a a g a a c t t a t g g g a g a a a a a g c t g t a a a a a g a c t t t t g t g g a g g a t g g a a a a t c c a a a a g a g c c c t g t g a c c a t a t a c g g a t g g a g g t t a a g c t a a t a g a a a g a g a g t c c g t t a a a g a g a t t t a t t a a
L
T
A
I
K
R
K
K
V
T
M
K
D
I
A
E
R
L
N
L
S I N A V S L A L N D K V G V S E E T R K I V L K T A D E M G Y F D E N P S F I A K N H F R N I C L L I E E R N F R D T H F Y T K V I L G I E N E A K K N N Y D I L V N F M N Q D D F Q V P S S V E T R K V S G I L V V G T I K D E H L E K L L K Y D I P T V L V D H A S F T I S T D A V L T Q N M P G T Y M A T Q Y L I R K G H T Q I G F F G E I D F S L S F K E R W L G F N E A M R N A G L N V D P I F N V N P G Y C V I G Q V E Q Y V L S K N Y K E V A N I I S K L D K L P T A W V C S N D S A A I T L Y N A L S I L G I K V P D D I S V V G F D D I D I C N I V T P H L T T I R I N K E L M G E K A V K R L L W R M E N P K E P C D H I R M E V K L I E R E S V K E I Y * |
Comments=For manual analysis, pseudo or ribosomal slippage, gene with one frameshift, more than 80% of the length of the second shortest homolog |
| or0075 - or0076 | 81995 | 82402 | join (81995..82135, 82135..82149, 82148..82402) | pseudogene, missed gene |
t
t
g
a
g
c
a
g
g
a
a
a
a
a
g
a
g
g
t
g
t a g a t a c c t a a c a t c c g g a g t a a t g c t a a a c g g a g t a a a a g t t a a g a g t g a a g a a g g c a c t c c a t a a g g a g g g c c a t t a a g t c c g c t t t t a g c a a a t a t a a t a c t t g a c g a t t t a g a t a a a a g a c t a g a a a a a a g g g g a c a c a a a t t c t g t a g a t a c g c a g a c g a c t g t a a t a t a t t t g t t a a a a g c a a a a g g g c a g c a g a c a g g g t t a a a g a g a g c a t a a c t g a a t t t a t t g a a g a a a t t c t t a a a c t t a a g g t a a a t a a a g a g a g a a g t g t a g t t g a t a g g c c a t g g a a g a g g a a g t t t t t g g g a t t t t c a t t t t a t a t g g a c a a g g g a a a a t c c a a c a t a a g g a t a g c c g g a a a a a g t a t a a g a a a a t t t a a g a a g a a a t c t t t t t a g
L
S
R
K
K
R
C
R
Y
L
T
S
G
V
M
L
N
G
V
K
V K S E E G T P * G G P L S P L L A N I I L D D L D K R L E K R G H K F C R Y A D D C N I F V K S K R A A D R V K E S I T E F I E E I L K L K V N K E R S V V D R P W K R K F L G F S F Y M D K G K S N I R I A G K S I R K F K K K S F * |
Comments=Pseudogene, >1 frameshift are present. Found common hit with non-adjoining gene: or0194 |
| or0084 - or0085 | 93132 | 93365 | pseudogene, missed gene |
A
T
G
A
C
A
A
A
C
T
T
T
C
G
C
A
A
A
G
T
A G A T A T T T T A C A T A A G T T G C G A C T T G T G A C A A A G C G C T A A C A A A G C T T A G C A A G A C T G A G G A T G G A G G C G G G G C C G A A G C C A A G G A G G G C G G A G G C G G G C A C C T A A G A C A G G A C G T C G A A T G T G C C C G G T A C C C C G C C G T A A T C C G A A A G T C G C G C T T T A G C T T T G T C G C T T T G G A A C T T C G G A G C A A C G A T G C A A A A T A T C T A C T T T A A A T A A
M
T
N
F
R
K
V
D
I
L
H
K
L
R
L
V
T
K
R
*
Q S L A R L R M E A G P K P R R A E A G T * D R T S N V P G T P P * S E S R A L A L S L W N F G A T M Q N I Y F K * |
Comments=Pseudogene, >1 in frame stop codons | |
| or0097, or0098 | 103493 | 104314 | putative pseudogene |
A
T
T
A
A
T
A
A
T
T
A
T
A
A
A
A
C
T
A
G
T T G C A G G A G T G T T A A T G C A T T C A A T G G T G G T A A T T T C T G C A G C T A T A G A T T C T T C A A T A G A T T T A A T A G C C A G T T T A A T T G C T T T T T T T C T A T A A G A G T A T C A G T A A A A C C A G C A G A C G A A G A C C A T C C T T A C G G A C A C G A T A A A T A T G A G A A C A T T T C T G G T T T T A T A G A G G C T A T T T T A A T A T T C T T T G C T G C T G T A C T T A T C A T A T A T G A A G C T G T T G G A A G A A T A A T T G C T G G C A C G T A T G T A G A G A A A T T A G A A A T G G G A A T T G C A G T C A T G T T G T T T G T A T C T T T T G T A A A A G G A A T T G T T T C A T A C G T T T T G T T T A A A G T A T C T A A A A A A G A A A A T T C T A T T G C T T T A A A G G C A G A T G C A A C G A A T T T A T T G A C G G A T G T A T T T A C T T C A T T G G G A G T T A C T A C A G G G C T T G T A A T T A T A A A A G T C A C T A A A T T A G A C A T T T T A G A C C C C A T T A T A T C C A T T T T T G T T G C G T T G A T T A T T A T A A A A A C T T C A T T T G A T T T G A C A A A G G A A G T A T T A A A A G A T T T G A C A G A T A G C A G T C T A C C T G A C G A A G A G G T C A A A G A A A T A G A A A A C A T A A T A A A A T C C A A T C C T G A A G T T A C C A G T T T T C A T A A A C T A A G G A C G A G A A A G T C C G G T A C T A A G A G A G A A A T A G A T G T T C A C G T G A G A G T A G A T A G A A A T T A T A A C A T A G T A A A A G C C C A T G A A T T G T C C C A T A A A G T T T C A A A A C A A A T A A C G G A T A A A T T T C C T G A T T C C C A T G T G A T A A T C C A T A T A G A A C C G G A A G G A A A A A A A G A A G A G G A T A A A T A A
I
N
N
Y
K
T
S
C
R
S
V
N
A
F
N
G
G
N
F
C
S Y R F F N R F N S Q F N C F F S I R V S V K P A D E D H P Y G H D K Y E N I S G F I E A I L I F F A A V L I I Y E A V G R I I A G T Y V E K L E M G I A V M L F V S F V K G I V S Y V L F K V S K K E N S I A L K A D A T N L L T D V F T S L G V T T G L V I I K V T K L D I L D P I I S I F V A L I I I K T S F D L T K E V L K D L T D S S L P D E E V K E I E N I I K S N P E V T S F H K L R T R K S G T K R E I D V H V R V D R N Y N I V K A H E L S H K V S K Q I T D K F P D S H V I I H I E P E G K K E E D K * |
Comments=For manual analysis, pseudo or non-canonical start codon, extended gene length > 80% the length of the second shortest homolog | |
| or0124, or0124 - or0125 | 126279 | 126629 | putative pseudogene |
A
T
G
A
G
T
A
A
A
A
T
T
T
T
A
G
T
T
T
T
A G A C G A T A A T A A G G G A A T C T G T A G T T T A A T A G A A G A A A T T T T C A C G A T G G A T G G C C A T G A A G T G A G A A C T T A C A G T G A T A T T A G C C A T T T T G A C A A A G A G A T A G A A A A A T T T A G A C C T G A T G T A G G A T T G T T T G A T T T A C A C A T G G C A A A A G A T A T G C T A A A A A T C A T C A A A A A A G T T A A G A A T A T T C A T C C A A A C A T G A A A G G T A T T A T A A T G T C A G C A G A T G A G C C A C A A G A G C C T T T T A C G G A G T T T C C T T T T A T C T C T A A A C C T T T T G A C A T A A T A A C A C T A A A A A A T T T A G T T T A T G A T A G T C T A A A G C A A G A A A T G T T T G T A T A A
M
S
K
I
L
V
L
D
D
N
K
G
I
C
S
L
I
E
E
I
F T M D G H E V R T Y S D I S H F D K E I E K F R P D V G L F D L H M A K D M L K I I K K V K N I H P N M K G I I M S A D E P Q E P F T E F P F I S K P F D I I T L K N L V Y D S L K Q E M F V * |
Maingene=or0124; Extension FAILED; Comments=For manual analysis, pseudo, failed extension, extended gene length>100aa and between 70% length of second shortest homolog and 90% the length of the second longest homolog | |
| or0149 - or0150 | 149044 | 149306 | complement (join (149044..149160, 149160..149306)) | pseudogene, missed gene |
T
T
G
C
A
T
A
A
G
G
A
G
C
G
A
C
T
T
G
T
G A C A A A G C G G T A A C A A A A C T T A G C G A G A C T G A G G G T G G A G G C A G G G C C G A A G C C A A G G A G G G C G G A G G C G G G C A C C T G A G A C A G G A C G T C G A T T G T G C C C G G T A C C C T G C C G G A A C C C G A A A G T C G A A G T T T A G T T T T G T C G C T T T G G A A C A T C G G A G C G A C G A T G C A A A A T A T C T C C T T T G A A T A T T T T T T A A C T T T G T C A A C A A A C T G T A A A A A G G G C A A G C G C C C T T T T A C A C T T T C T T A G
L
H
K
E
R
L
V
T
K
R
*
Q
N
L
A
R
L
R
V
E
A G P K P R R A E A G T * D R T S I V P G T L P E P E S R S L V L S L W N I G A T M Q N I S F E Y F L T L S T N C K K G K R P F T L S * |
Comments=Pseudogene, >1 in frame stop codons |
| or0157, or0158 | 154706 | 157638 | join (154706..157453, 157453..157638) | putative pseudogene |
a
t
g
a
t
t
g
a
a
a
g
g
a
t
t
t
t
t
g
a
a a t t a t a c a a a a a g a g g a t a a a a a g a a t c c t t t a a c a g a t g a c c a a a t a g c g g c a a t t c t c a a t a t t a a a a g a g a a g a t g t g a c a c a a t t t a g a c t g a a a a a t a a t a t t c c t g a c t c a a g a g a a a g a a g a a a a c c t t a c c t t t t a g a a g a t g c a a a a a a a a t a a t t t c a a a g g a c c c a a a t a t t t c a g a t a g a a a t t t g a c a a a a c a a t t a a a t a a t t t a g g a t a t a a t a t t t c t c g t t t t g t a g c t a c a c a a a t a a a a a a g g a a a t t t t a a a a g a t a a a a t t g c a g a t a a t t t a g t g c a a c g a a g t a c t a t t a a a a a c g a t a c t g t a a a t t t t g a a a c t c c t a a a a c a g c t a a a a g c t t a c t c t c a t t t a a a g a g a t t a t t g g a a g c g a a g g a a g t c t t a a a g t g c a g a t a a g c c t t g c a a a a g c t g c a g t a c t t t a t c c t c c c c a t g g a t t g c a t a c t t t a a t a g t a g g a c c a t c t g g a t c t g g a a a a a g c c a g c t g g c t g a a g c a a t g t a c a a c t a t g c a a t a g a g t c t g g a a g a t t t a a t g a a a a t g c g c c t t t t g t a g t t t t t a a c t g t g c t g a t t a t g c g g a t a a t c c a c a a c t a c t c a t g g c g c a a c t t t t t g g t t a t g t a a a a g g c g c t t t c a c a g g g g c t g a t a c t g c a a a a g c g g g a t t g g t a g a a a a a g c t g a t g g t g g a a t t t t g t t t t t g g a c g a a g t c c a c a g a c t c c c c a g t g a a g g a c a a g a g a t a c t c t t t t a t t t g t t g g a c a a a g g a a a a t t c a g a c g a t t a g g g g a a a c a g a a a g t a c t a g a g a g g c a c a a a t t a t g c t t a t t g c t g c t a c t a c t g a a a a t c c t g a a t c t t c g c t a t t a c t t a c t t t t a g g a g a a g a a t t c c t a t g g t g a t a g a a c t t c c t t c t c t t t c a g a a a g a c c t c c c c a a g a a a g a t a t g a a a t t a t a c a t c a t t t t t t c t c a a a a g a g t c t t t t a g a a t t a a t a a a t c g a t t a t t g t a a a a a a a g a g g c a g t a a g a g c t c t t a t g c t t t a t g a c t g t c c g g g g a a t a t a g g g c a g c t a a g g a g c g a t a t t c a a g t t g c t t g t g c g a g g a g c t t t t t a a a t t c a t t a g g g a g t a a a a g c t c t t c a t t g a c a a t a g a c c t t t c a g a t t t a c c t a a c c a c g t a a a a a t g g g g a t a a t c a g a g t a a a t a a a a g a g a t c c c g a a a t a g a a a g a t a t t c a a a t g a a g a c a t t a t g g t g t a t c c t g a c a a g g a a a t t a a g t t a t a t c c a a a a g a a g a t a g a t a t a t g c t g c c t g a t g a a a t a t a t c a a t t t a t a g a a g a a a g g t t t a t t g a c t t a a a a a g a c a a g g a c t t a c a a a a g a g g a g a t a g a t a a a a t t c t c g g g a a a g a g a t a g a g g c g g a g c t g a a g a a a t t t g c t g t a a a t g t a a a a t c t a a c a t a a c a a t t t c a a a a a a a g a a t t g a c a a a c a t a g t a g g a g a a a a a a t t g t a a a t g c t g t t g a a a a a g c a t a c g a g a t t g c t a a a a a a a g t t t t a a a a a c t t a g a g g a t a a t c t c t t t t a t t c c c t t g c t a t a c a c t t a a g t g c t g c t t a t g a a a g a a t a t t a a g t g g c a a a c c a a t a a t t a a t c c t c a a c t t g a a a a c a t a g t g a a a g a a t a t c c t g t t g a g t a t t c t a t t g c t a a a a t t a t g g c a a a a c a a a t t a a c a a a g a a t t a g a a a t a c a g c t g c c t g a t g a a g a a g t g g g c t t t a t t g c t a t g t a t c t a a g g a c a t t c t c a g g g g a c a a a g a a a t a a c t a a a g g c a g a g t g g g c g t a g t t g t g c t t a c g c a c g g c c a t g t t g c a a g t g g c a t g g c a g a g g t g g c a a a t a a a c t c t t a g g g g t a a a t c a t g c a g t c g g t a t a g a t a t g g c t c t t g a t g a a a g c c c a g a a t c t g t t c t t g a g a g g a c a a t t g a a g t a g t g a a a a g a a t a g a c g a a g g c a a a g g c t g c a t t a t t t t g g t t g a c a t g g g t t c a t t a a t t a c c t t t g g t g a a a t t a t a a c c a a a a g g a c a g g g a t a c c t a c a a g a g t g g t a g g a a g a g t a g a t a c g g t t a t g g t g t t g g a a g c t g t c a g a a g a g c t a t t a t a c c g g a t a c t a a t t t a g a t g a a a t a g c a g a t g c g t t a g a c g t a g a t a a a a c a t a t a t a g g a a g a g t t g a a g g t a t a a a g a g t a a a g a t a a g c t t c c a a a a g c a a t t g t a a c t g t a t g t a t t a c a g g a g a g g g a a c a g c g t t a a a a a t a a a g a a a t a t a t t g a a g a t g t c t t a c c a c a a c t a a a a g a t g a t t a c a a a a t a a t a c c t g t t g g a a t g c t c a g g c a g g a a g a t a t t g a a a a a g a a a t t t c a a a a a t a a g a g a a g a a a a t g a a g t g g t a g c t t t t g t t g g t a c a a t a a a t c c c g g c a t a a a a a g t a t a c c t t t t a t a t c t g t t g a a g a t a t t t t a c a t g g c a c a g g g a t t g a a a a g c t t a a a a a a a t c c t c a a t t t a a a g g t t g a a a a t c c a t t g a a a g a a a t c a t t g a t g a a a a c c t t a t c t t a t g t g a t g t g g a t a t t t c t a t g a a a a g t g a t g t c a t a g a t a a a t t a g t a g a a t t g c t t c a a g a t a a a g g t t a t g t a g a t g a t a a g t t t t t g c t a a g t g t a t a c a a a a g a g a a t c a a t g g g a g c c a c c t g g a t g a a a g g c g g t a t a g c t a t a c c a c a t g g a t a c a c g a a a a a c g t t a c g a a a t c t g c c a t a g c a a t t g c a a a a t t a a a a a a a c c t a t t t t t t g g g a a g g a g a g c t t a a a g c g g a t t t a g t t t t t a t g a t a g c g t t a a a a g a a g a t t c g a a g g a t t a t a t g c t t g a t t t a t a t a a a g t a a t g a c a g a c g a a a a g a t t g t a a a t g c t t t g a a g g g a g c t a a a a g t c c g g t t c a a a t a a a a g a a a t a a t a t t a a a a a a t a c a c t a c c g g c c a a t t a a
M
I
E
R
I
F
E
I
I
Q
K
E
D
K
K
N
P
L
T
D
D Q I A A I L N I K R E D V T Q F R L K N N I P D S R E R R K P Y L L E D A K K I I S K D P N I S D R N L T K Q L N N L G Y N I S R F V A T Q I K K E I L K D K I A D N L V Q R S T I K N D T V N F E T P K T A K S L L S F K E I I G S E G S L K V Q I S L A K A A V L Y P P H G L H T L I V G P S G S G K S Q L A E A M Y N Y A I E S G R F N E N A P F V V F N C A D Y A D N P Q L L M A Q L F G Y V K G A F T G A D T A K A G L V E K A D G G I L F L D E V H R L P S E G Q E I L F Y L L D K G K F R R L G E T E S T R E A Q I M L I A A T T E N P E S S L L L T F R R R I P M V I E L P S L S E R P P Q E R Y E I I H H F F S K E S F R I N K S I I V K K E A V R A L M L Y D C P G N I G Q L R S D I Q V A C A R S F L N S L G S K S S S L T I D L S D L P N H V K M G I I R V N K R D P E I E R Y S N E D I M V Y P D K E I K L Y P K E D R Y M L P D E I Y Q F I E E R F I D L K R Q G L T K E E I D K I L G K E I E A E L K K F A V N V K S N I T I S K K E L T N I V G E K I V N A V E K A Y E I A K K S F K N L E D N L F Y S L A I H L S A A Y E R I L S G K P I I N P Q L E N I V K E Y P V E Y S I A K I M A K Q I N K E L E I Q L P D E E V G F I A M Y L R T F S G D K E I T K G R V G V V V L T H G H V A S G M A E V A N K L L G V N H A V G I D M A L D E S P E S V L E R T I E V V K R I D E G K G C I I L V D M G S L I T F G E I I T K R T G I P T R V V G R V D T V M V L E A V R R A I I P D T N L D E I A D A L D V D K T Y I G R V E G I K S K D K L P K A I V T V C I T G E G T A L K I K K Y I E D V L P Q L K D D Y K I I P V G M L R Q E D I E K E I S K I R E E N E V V A F V G T I N P G I K S I P F I S V E D I L H G T G I E K L K K I L N L K V E N P L K E I I D E N L I L C D V D I S M K S D V I D K L V E L L Q D K G Y V D D K F L L S V Y K R E S M G A T W M K G G I A I P H G Y T K N V T K S A I A I A K L K K P I F W E G E L K A D L V F M I A L K E D S K D Y M L D L Y K V M T D E K I V N A L K G A K S P V Q I K E I I L K N T L P A N * |
Maingene=or0158; Extension SUCCEEDED with start of type START; Comments=For manual analysis, pseudo or ribosomal slippage, gene with one frameshift, more than 80% of the length of the second shortest homolog |
| or0180 - or0181 | 180082 | 180267 | pseudogene, missed gene |
A
G
G
G
G
G
G
T
A
A
G
T
G
G
C
G
A
C
A
G
G G T A A G G G A C C T T A A A G C G C G C T G G A G G C A G G A T T G T C T T G A C T T A A A A C C T G A T T A G G T T T C T A T A C T C A T A G G A A T C A A C G A T T G T T G G A G A A G A T A T G A C A G C A A C G A T C C C A C A T C A G T A G A A G C T T T T G A G G C T G A T T A C A G G T A T A T A T T G G A T C A A C T A
R
G
V
S
G
D
R
V
R
D
L
K
A
R
W
R
Q
D
C
L
D L K P D * V S I L I G I N D C W R R Y D S N D P T S V E A F E A D Y R Y I L D Q L |
Comments=Pseudogene, start/stop is absent | |
| or0186, or0186 - or0187 | 186309 | 186719 | putative pseudogene |
A
T
G
C
A
G
C
A
G
G
C
C
T
G
C
G
A
G
A
T
A G C T C T T T C T T T A A C T T T T C A A A A C A T T G A G C A T C T C A A A A G G C A G A T T A A A A G C T T T G A T A A G G T G A T T T C T A G A G A G C T T A G G G C T A T T C C T C A A A C T C T C A C T A C G T T T A A G G G T T T A G G T G A G G T G T C G G T T G C A G G G A T A A T C G C T G A A A T A G G C G A T A T C A A G C G T T T C A A G A A C A A A G C C T C T T T T G C T C A G T A T G C T G G C C T C A C C T G G A C C C G G T A T C A G T C G G G C A A T T T T G G C G C C G A A G A G C G T C G T T T G A C A A A G A G C G G G A A C A A A T A C C T C C G C T A T T A C T T G G T C A T G G C T G C A A A C T C G T T G C G G G T G C A C A A C G A G G A A T A C A A G G C C T A T T A T C A G A C C A A G T A T C A G G A G G T G C A A A A G C A C C A G C G G T G A
M
Q
Q
A
C
E
I
A
L
S
L
T
F
Q
N
I
E
H
L
K
R Q I K S F D K V I S R E L R A I P Q T L T T F K G L G E V S V A G I I A E I G D I K R F K N K A S F A Q Y A G L T W T R Y Q S G N F G A E E R R L T K S G N K Y L R Y Y L V M A A N S L R V H N E E Y K A Y Y Q T K Y Q E V Q K H Q R * |
Maingene=or0186; Extension FAILED; Comments=For manual analysis, pseudo, failed extension, extended gene length>100aa and between 70% length of second shortest homolog and 90% the length of the second longest homolog | |
| or0190, or0190 - or0191 | 189279 | 189754 | complement (join (189279..189647, 189650..189754)) | pseudogene |
A
T
G
G
A
A
A
A
T
T
T
G
G
A
C
C
T
T
T
T
C G A G A A C C T T T A C C G C A G G T A T T T T T C A A A A G C T T A C A G G T C G G C G T A C C T G G T C G C C C A G G A C T G C G T T C A G G A A G C T T T T T T G G A C C T A C G A A A T A T T A A A A A A A A C C T T G T G G A C C T T T C C C G A T T C C A G G C G C T G G T C T G A G C T A T C G C T A C C A A A A A A G C C G T T A A C C T T A T C C G A A A T A A G G C A A A G T A T G T G C T C A T A G A T G A G A G C T T T A T G G A T A A G A T A G T T T C T C T G A A T A C C A A T C T G G A A G T T T C G C T C G A T A C A A T T A C G G A T G C T G A A A A T A G G A T A G A T C T G G A T T A C G C T T T A A A G C A G C T C A A T C C A A C T T A C A G G C A G A T C G T A G T A T T G A A G T A C T A T A A C G A C C T T T C A G A A A A T G A A A T A T C A A A G T A T C T C A G T G T A C C A T T A G G A A C C G T C A A A A A C A G G C T C T A C C G C G C A A G G A T G T T T T T A C G G T A A
M
E
N
L
D
L
F
E
N
L
Y
R
R
Y
F
S
K
A
Y
R
S A Y L V A Q D C V Q E A F L D L R N I K K N L V D L S R F Q A L V * A I A T K K A V N L I R N K A K Y V L I D E S F M D K I V S L N T N L E V S L D T I T D A E N R I D L D Y A L K Q L N P T Y R Q I V V L K Y Y N D L S E N E I S K Y L S V P L G T V K N R L Y R A R M F L R * |
Maingene=or0190; Extension SUCCEEDED with start of type START; Comments=Pseudogene, both frameshift and stop-codon are present |
| or0193 - or0194 | 194538 | 194862 | complement (join (194548..194562, 194562..194615, 194615..194707)) | pseudogene, missed gene |
T
C
A
G
C
C
T
C
T
T
A
T
C
T
G
G
T
T
C
T
T G T T C A T C A G A C C G A G A T T T T G C C T T A A G C T T C C T T C A G A T T C C A C C T C A C G A T G G A C A C C C T T G C T C T T G G C C T A G T G G T T C C C A C T A C C A A G C C C A C A G C G G A C T T T C A C C G C C T A G C T A T C G C C C C A T G C C G G G C G C A C
S
A
S
Y
L
V
L
V
H
Q
T
E
I
L
P
*
A
S
F
R
F H L T M D T L A L G L V V P T T K P T A D F H R L A I A P C R A H |
Comments=Pseudogene, >1 frameshift are present |
| or0205 - or0206 | 207351 | 207627 | complement (join (207351..207440, 207440..207493, 207493..207627)) | pseudogene, missed gene |
G
T
G
T
T
G
G
A
C
T
T
C
G
T
T
T
T
G
T
T
A C G C A A A C T C A T C C A T C C C A A T T C A G C C T C T T A T C T G G T T C T T G T T C A T C A G A C C G A G A T T T T G C C T T A A G C T T C C T T C A G A T T C C A C C T C A C G A T G G A C A C C C T T G C T C T T G G C C T A G T G G T T C C C A C T A C C A A G C C C A C A G C G G A C T T T C A C C G C C T A G C T A T C G C C C C A T G C C G G G C G C A C G T A A A A A A G C C C G C C C A A A A C A C G G C A G G C T T T T T A G A T T C G C A T T C G T T T T T C T A T T T T C C T T A T C T G T A T T G A
V
L
D
F
V
L
L
R
K
L
I
H
P
N
S
A
S
Y
L
V
L V H Q T E I L P * A S F R F H L T M D T L A L G L V V P T T K P T A D F H R L A I A P C R A H V K K P A Q N T A G F L D S H S F F Y F P Y L Y * |
Comments=Pseudogene, >1 frameshift are present |
| or0206 - or0207 | 209555 | 209733 | join (209555..209617, 209617..209733) | pseudogene, missed gene |
a
a
a
g
a
t
a
t
a
t
a
t
t
c
a
t
t
t
c
c
t t t g a a c a a t g a g g a t t t a g a a a t t g g g a c t t t a a a t t a g g t a a g a c c a a a t a a a t t a t t t a c a g c t g a t a g t a a g a t t g t a a t t t a c a a a g t c g g t a c t a t a a a t c a a g a a a a g c t t a a a g a a g t a a t t g a t a a a t t g g t t c a a a t t a t a a a a g a a t a a
K
D
I
Y
S
F
P
L
N
N
E
D
L
E
I
G
T
L
N
*
V R P N K L F T A D S K I V I Y K V G T I N Q E K L K E V I D K L V Q I I K E * |
Comments=Pseudogene, start/stop is absent |
| or0261 - or0262 | 270037 | 270210 | pseudogene, missed gene |
T
T
G
A
A
A
T
C
A
A
A
A
A
C
A
A
C
A
A
T
G A A A C G T T T G A T A T T A G G T A A A T C C A T T G A T T C T T G G T T T A C C G T A G A T A T A G G A A A A C C T G A A G T T T T C A T A T T A A A C T C A C T C C T T T C G C A C A T G A A C C A A A A A G G T A T A T A T C C T C T G C A A A T T C C A C A C T C A A G C A A G T T T A T G A T A T A A
L
K
S
K
T
T
M
K
R
L
I
L
G
K
S
I
D
S
W
F
T V D I G K P E V F I L N S L L S H M N Q K G I Y P L Q I P H S S K F M I * |
Comments=Pseudogene, good start found, extended gene length<=100aa and < 70% the length of the second shortest homolog | |
| or0329 - or0330 | 347834 | 347982 | complement (join (347834..347893, 347892..347921, 347923..347982)) | pseudogene, missed gene |
A
T
T
G
C
C
T
G
A
G
G
A
T
A
C
T
A
T
A
C
G C A T A C T C C T A T A T T G C T G C T T G A T A A A G C C G C T T C C G T T T T A G A T T C A G T C T C A G A A A A A C A G C T A C A A A A A A G T G C T A A A G G T G T T A A T A A A G G G C T T A C T A C T A T T G T A G T A G C C C A T A G A C T T T A G
I
A
*
G
Y
Y
T
H
T
P
I
L
L
L
D
K
A
A
S
V
L D S V S E K Q L Q K S A K G V N K G L T T I V V A H R L * |
Comments=Pseudogene, abnormal start as well as frameshift |
| or0334, or0334 - or0335 | 351472 | 352043 | complement (join (351472..352020, 352020..352043)) | putative pseudogene |
A
T
G
C
C
A
T
T
G
C
C
C
G
A
A
A
A
A
A
A
T A A A A A A T A T A C T T A T G C C G A C T A T T T A A C C T G G T C T G A A G A A G A A A G A T G G G A A A T T A T T A A T G G T G T T C C C T A T C T A C A A G C A G C T C C A A C A T G G C A A C A T C A A G C A G T A T T G T T A G A A C T A G C A A G G C A A T T T G C A A A C T A T C T G C A G G A T A A A T C T T G C A G A G T A T T T A C T G C T C C T T T C G A T T T G C G A A T A C C A G A A G C A A A T G A A A A A G A T G A A G A A A C T A T C A A T G T A G T A C A G C C T G A T A T A A T C A T T A T A T G T G A T A A T T C A A G A C T T A A A A A G A C A G G T T A T T A T G G A G T T C C A G A A T T G A T T A T A G A A G T A G T T T C T C C T T C A A C T G G T C A A A A A G A T A A A A T A G A A A A G T T T A A T T T A T A C G A A A A A G C A G G G G T A A A A G A A T A T T G G A T T G T A G A A C C T G A T G A A A A G G T G G T T A T G G T A T T C A C A C T T G A A G A A G G A C G T T A T G G A A G A C C C C A A A T G T A T T C T G A A G A G G A T A A A G T A A A A G T T A G T A T A T T T G A T G A C C T T G T A A T T G A T T T A A A G C C T G T A T T T G A G A G A A T T T A A
M
P
L
P
E
K
N
K
K
Y
T
Y
A
D
Y
L
T
W
S
E
E E R W E I I N G V P Y L Q A A P T W Q H Q A V L L E L A R Q F A N Y L Q D K S C R V F T A P F D L R I P E A N E K D E E T I N V V Q P D I I I I C D N S R L K K T G Y Y G V P E L I I E V V S P S T G Q K D K I E K F N L Y E K A G V K E Y W I V E P D E K V V M V F T L E E G R Y G R P Q M Y S E E D K V K V S I F D D L V I D L K P V F E R I * |
Maingene=or0334; Extension SUCCEEDED with start of type START; Comments=For manual analysis, pseudo or ribosomal slippage, gene with one frameshift, more than 80% of the length of the second shortest homolog |
| or0367 - or0368 | 381554 | 381735 | complement (join (381554..381661, 381661..381735)) | pseudogene, missed gene |
G
T
G
T
C
T
T
C
C
C
C
T
G
T
A
G
G
A
G
C
G T G G G C G G G C T C T G C C G A C A C T T T T A T A A C A C T T T C A G C A A A T G T T G C T G T A A T A A C C C C T A G T A G T A G A A T A G G C G T T G C C C A T C C C G T G T C A A T G G A A G A T G A C A G C G C T C T C T T T G G A T A T T T T A C A G C A A T T A T T C T C T T C A G G A C A A A A A G A A A A T A A
V
S
S
P
V
G
A
W
A
G
S
A
D
T
F
I
T
L
S
A
N V A V I T P S S R I G V A H P V S M E D D S A L F G Y F T A I I L F R T K R K * |
Comments=Pseudogene, gene with one frameshift, less than 80% of the length of the second shortest homolog |
| or0369, or0369 - or0370 | 383097 | 383430 | complement (join (383097..383300, 383302..383430)) | putative pseudogene |
A
T
G
T
T
A
T
C
T
G
G
T
A
G
T
G
C
C
A
C
G G A A T A T C A A A A C A A A A A C A G C G A T A T T G A T T T T G C A G T T T T A T A C A A T A A A A A T G T C T C A T T G G A G G A A G A A C T T A C A T T A G A A G T T A A A A T A A G T G A A A T A T T C A A A A G A G A T G A C A T T G A T G T G A T A A A T T T A A A T A A A G C T C C T T T A A A C C T T C A A C A C A A T G T C A T T T A T A C G G G A G A A T T A T T A T A T T G C A G T G A T T A T T T G A A A C T G G C G G A T T T T A A A G A A A A A G T T T T T A A A T A C C A T G G A G A C T A T G G A A T T A C T C T C A A A T T C T T T T A T G A T T A T T A T T T G G A G G G A C T G A T T A A A A A A T G A
M
L
S
G
S
A
T
E
Y
Q
N
K
N
S
D
I
D
F
A
V
L Y N K N V S L E E E L T L E V K I S E I F K R D D I D V I N L N K A P L N L Q H N V I Y T G E L L Y C S D Y L K L A D F K E K V F K Y H G D Y G I T L K F F Y D Y Y L E G L I K K * |
Maingene=or0369; Extension SUCCEEDED with start of type START; Comments=For manual analysis, pseudo or ribosomal slippage, gene with one frameshift, more than 80% of the length of the second shortest homolog |
| or0369 - or0370 | 383572 | 383698 | join (383572..383670, 383672..383698) | pseudogene, missed gene |
a
t
g
g
a
c
t
t
t
t
t
a
t
g
t
c
c
g
c
a
g g a g g a a t t a c t t t c t t c t t a t a a a c g a t g c a g t a a a a t g g g t a t t g a c c a t t c a a t a a c t g c g c c a t t a a t a a t g c t a a a t c a a g c a g a t t t a g a a a t g a t g t a a
M
D
F
L
C
P
Q
E
E
L
L
S
S
Y
K
R
C
S
K
M
G I D H S I T A P L I M L N Q A D L E M M * |
Comments=Pseudogene, gene with one frameshift, less than 80% of the length of the second shortest homolog. Found common hit with non-adjoining gene: or0373 |
| or0395, or0395 - or0397 | 403320 | 403994 | putative pseudogene |
A
T
G
A
A
A
A
G
C
A
A
A
G
C
T
A
A
G
T
A
T T T A C T A A T A A C T T T T A A T G T T T T T A T T T T A T C A T T A T T T T C T A T T T T A T T T A T T T C C T T T G T A G T T A G C A G A C T T T T G G G A A T A A A T A A G A C A T G G A T T A C T T T T T C G T C T T T T C C A T C C A A T T T A T T C T G G A T T C C A T C A C T A A T T T T A T T T T T T T C G T T T G T G G T T A T A C C G T G C A T A T G G G A A A A T G T T G T T G A A C A A A A G T C T A T A T T A A A T A T T A T C C G A G A T A T A A A A C C C A A A A A G C C T T T A T G G G A T T T A A T T C T A T C A G T G G C A G C G G T A C T T T T T C T A T T G C T A T G G G T T A A G T T T T G T C A A C A T A T G T T A G G A T T A C C T T T T G A A A A T G T T A C A A T T T C A T A T G T A G A A A A A T T A A A A T G G T T T T T T C A T C T T A C C G T G T T A G C A T T T G C T G A G G A A T T T C T T A T T A G A T C A T T C T T G C A A A A A C G C T T A A T G G A A G T T T T A G G A C C A G T T T T A A G T A T T T T G A T G A G T T C T T T T G T T T T T G C T T T T G T T T T A C A T G C A T C C G A A A T A C C A T T T A T A A A T C T A A T T A T T A G A T T T C C A T T G G G A A T T G T T A T T G G T T T T C T T T A T T A T A T T A G A A G A A A C A T A T T T T C G C C T T T T T T T A C T C A T T T A A T A T A T G A T T T T A C A A T A C T A A T A G G A G T G A T G T A G
M
K
S
K
A
K
Y
L
L
I
T
F
N
V
F
I
L
S
L
F
S I L F I S F V V S R L L G I N K T W I T F S S F P S N L F W I P S L I L F F S F V V I P C I W E N V V E Q K S I L N I I R D I K P K K P L W D L I L S V A A V L F L L L W V K F C Q H M L G L P F E N V T I S Y V E K L K W F F H L T V L A F A E E F L I R S F L Q K R L M E V L G P V L S I L M S S F V F A F V L H A S E I P F I N L I I R F P L G I V I G F L Y Y I R R N I F S P F F T H L I Y D F T I L I G V M * |
Maingene=or0395; Extension FAILED; Comments=For manual analysis, pseudo, failed extension, extended gene length>100aa and between 70% length of second shortest homolog and 90% the length of the second longest homolog | |
| or0397, or0397 - or0399 | 404420 | 404839 | pseudogene |
A
T
G
T
C
T
G
A
A
C
C
G
C
T
T
T
T
T
A
C
T G G T A A G T A T T T T G C A G C T T A T G C T G A A G A A C T G T C A G A G A A A A A G T C T C T G T T A G G T T T T G T T C A T C C T T C T T T T C G A T T T C C T C A T A A A G G T G A A A T A G T A A T A A G T A A G G A A G G G C T A A T A T T G A C C A A T T T A G A A G A A A T A A A G T T T A A T G A G C T T T C A A A A A T A A G T C T C C A T T A T G A T T C T C T T T A T A A T C G T T T T T G G G C T G G T G G A A T A G T T G G T C A G T A T C C A C G T C T T G C C T T T T T A T G T C G T G G A G A A C C C T T A G T G C T T G A A T T T A C C A A G A A T G G T A C G A G G A A A A G A T T A T A C C T T T T A A T T A A C T G G C G T T T C T T T A C A G G A T T T A C T G A T A A C C G A C T T G T T T A T G A G G T A A T G A T T C A A T T T T T G A A T C C A G A G G T A C T A T G A
M
S
E
P
L
F
T
G
K
Y
F
A
A
Y
A
E
E
L
S
E
K K S L L G F V H P S F R F P H K G E I V I S K E G L I L T N L E E I K F N E L S K I S L H Y D S L Y N R F W A G G I V G Q Y P R L A F L C R G E P L V L E F T K N G T R K R L Y L L I N W R F F T G F T D N R L V Y E V M I Q F L N P E V L * |
Maingene=or0397; Extension FAILED; Comments=Pseudogene, failed extension, extended gene length>100aa and < 50% the length of the second shortest homolog | |
| or0399 - or0400 | 406629 | 406694 | pseudogene, missed gene |
A
T
C
G
C
A
A
G
G
T
T
A
T
T
A
C
A
G
C
A
T G G T T T A C T G C A G G G C A G T T A T A T A C C T T C A A G A G A G C A A C G G G A A
I
A
R
L
L
Q
H
G
L
L
Q
G
S
Y
I
P
S
R
E
Q
R E |
Comments=Pseudogene, start/stop is absent. Found common hit with non-adjoining gene: or0236 | |
| or0402, or0402 - or0403 | 409603 | 410823 | complement (join (409603..410550, 410550..410684, 410684..410734, 410734..410823)) | pseudogene |
A
T
G
G
A
T
A
A
A
A
A
T
A
A
C
T
A
C
T
A
C G A A A C A G T C A A A A A C A T G G C T A T C G A A A A A G T C T T A A A C C A A T A C T G C T C T G C T C A A G A T C C T T C C C C C C C T G T T T T A A A G A A A C T C C T T G A A G A T T T A C T T G A T T G G T T T A T T C T T A A C C G T G A A A T C T A T C T C A T G A A A A A T G A T A A T G A T A A A G G T A A C G G C T T T T A C A A C A G A A A A C T T G C T A C T C A T G T A G G T A A C T T A G A A A T A T C T G T C C C A A G A A C T C G T A C A G G T G A G T T T A G G C C T A A C A T C C T C C C T C A A A C C T T T A A A A G G G T T G A T G A A T C A T A T A C T G A A C T T C T T A T G T C C C T T G T T A T T A A T G G T T A C T C A G A A T C T T C T C T C C T A A A C A C C C T C A A A A A C C T T C A A C T G C C T T A C T C T G A A C A G G A A C T C A A T A A G A T T A A A A A T G A C C T T A A A A G C G A A T T G G A T C T T T T T A A A C A A A G A G A A T T G C C T G A A G C T G T C T T T G C T C T A A T A A T T G A T G C C T A C C A T T G T G A A A T T A A A G A T G G C T C A A A A G T T A A A A A A G C T G C C T G T T A C A T A G T C C T T G G T A T T G A C A T G G A A G G C A A A A A A G A T A T C T T T G G C T T G T A C A C C T T C T T C G G C A A A G A A A A C A G A G C C G A C T G G A A T A A A G T C T T C G A A G A T C T A G T A A A C C G T G G A C T T A A A A A A G T T T T A A T A G T T G T C A G T G A T G A T T T C C C A G G T A T A A T T G A A A C A G T C A A G G C T G T A T A T C C T T A T G C T G A C C A C C A G C T C T G T T T T G T C C A T C T T C A A A G A A A T A T T C G T A A A T C C A T G A C C A A A G C C G A T G C T G C A G A A T T C A A C A A A G A A C T C A A C A A A A T A A A G C T C T C T T C T T C A T T T G A T G A G G C T T T A G A A A A A T T T C A A A A T C T T T G T A A T A T A T T C A A A G A G A G A T A C A G C C G T T A T A T G A A T C T C C T T A T G G A A A A A G C A G A G T A T T A T T T A G C C T T T A C T A A A T A T C C T G A A T C C T T A A G A A A A C A T A T T T A T A C C A C T A A T G T T G T A G A A A G T G T C A A C A G C C T G A T T G A G A A A A T C C G C A T A A A A A C G G G T G G A T A T T T C A A T T C C G T T G A G G T C C T T G A A A T T A A T A T T T A T C T C C A G A G A A A A A A T T T A A A A C A G A C A A A A T G G A G A A A A C C G G T T C C A A T G A T A A A T G G C C A T A T C T A T G A A A T A C A A C A A C T T T T C C A G T T A C G T T A C T T T A A C C A G A C A C A A A A T T C T T G A
M
D
K
N
N
Y
Y
E
T
V
K
N
M
A
I
E
K
V
L
N
Q Y C S A Q D P S P P V L K K L L E D L L D W F I L N R E I Y L M K N D N D K G N G F Y N R K L A T H V G N L E I S V P R T R T G E F R P N I L P Q T F K R V D E S Y T E L L M S L V I N G Y S E S S L L N T L K N L Q L P Y S E Q E L N K I K N D L K S E L D L F K Q R E L P E A V F A L I I D A Y H C E I K D G S K V K K A A C Y I V L G I D M E G K K D I F G L Y T F F G K E N R A D W N K V F E D L V N R G L K K V L I V V S D D F P G I I E T V K A V Y P Y A D H Q L C F V H L Q R N I R K S M T K A D A A E F N K E L N K I K L S S S F D E A L E K F Q N L C N I F K E R Y S R Y M N L L M E K A E Y Y L A F T K Y P E S L R K H I Y T T N V V E S V N S L I E K I R I K T G G Y F N S V E V L E I N I Y L Q R K N L K Q T K W R K P V P M I N G H I Y E I Q Q L F Q L R Y F N Q T Q N S * |
Maingene=or0402; Extension SUCCEEDED with start of type START; Comments=Pseudogene, >1 frameshifts |
| or0428 - or0429 | 432304 | 432622 | join (432304..432384, 432387..432458, 432460..432507, 432507..432533, 432535..432561, 432560..432622) | pseudogene, missed gene |
a
t
g
g
g
t
t
g
t
c
a
c
t
t
c
a
g
a
g
t
t c a c t t t a g t g a c t t a t c c t t g a g a c c t c c c c g g g t a a g a a c g a t a a c t t t c a t c t c a t a t c t g c c a g a t t t a c t g t a t g g g a t t c g g g t a g t g t t g g a c t t c g t t t t g t t a c g c a a a c t c a t c c a t c c c a a t c a g c c t c t t a t c t g g t t c t t g t t c a t c a g a c c g a g a t t t t g c c t t a a g g c t t c c t t c a g a t t c c a c c t c a c g a t g a c a c c c t t g c t c t t g g c t a g t g g t t c c c c c a c t a c c a a g c c c a c a g c g g a c t t t c a c c g c c t a g c t a t c g c c c a t g c c g g g c g c a c a t a a
M
G
C
H
F
R
V
H
F
S
D
L
S
L
R
P
P
R
V
R
T I T F I S Y L P D L L Y G I R V V L D F V L L R K L I H P N Q P L I W F L F I R P R F C L K A S F R F H L T M T P L L L A S G S P T T K P T A D F H R L A I A H A G R T * |
Comments=Pseudogene, >1 frameshift are present |
| or0428 - or0429, or0429 | 432650 | 436177 | pseudogene |
A
T
G
G
C
T
A
A
A
G
T
A
A
T
G
A
A
G
A
C
C A T G G A T G G T A A C A C A G C T G C T G C C C A T G T G G C T T A T G C T T T T A C G G A A G T A G C T G C G A T T T A C C C T A T A A C T C C A T C G T C T C C A A T G G C A G A A G T A G T A G A C C A A T G G A G T G C A C A T G G A A G A A A A A A C A T A T T T G G T C A G C C G G T A A G A G T A A T T G A A A T G C A G T C G G A A G C C G G T G C T G C A G G A G C T G T T C A T G G G T C A C T A G C A G C A G G C G C T C T C A C A A C A A C A T T C A C T G C A T C A C A A G G A C T T C T T T T A A T G A T T C C C A A C A T G T A T A A A A T T G C A G G G G A A C T T T T A C C T G G G G T A T T C C A T G T A A G T G C A C G T G C C G T T G C A A C C C A T G C T C T T T C A A T T T T C G G T G A C C A T T C T G A C G T T A T G G C A T G C C G T C A G A C A G G C T T T G C T C T G C T T G C T T C T G G C A G T G T A C A G G A A G T A A T G G A T T T A G C A A G C G T T G C A C A C C T T T C T G C T A T T A A A G G A A G A G T G C C C T T C T T G C A C T T T T T T G A C G G A T T T A G A A C A T C G C A T G A A G T A C A A A A A A T C G A A G T T T T A G A T T A C G A A G A C C T C A A A A A A C T T G T A G A T T A T G A A G C T T T A A A A G C C T T C A G A C A A A G A G C A C T A A A T C C A G A A C A T C C T G T A A C A A G G G G T A C A G C G C A A A A T C C A G A T A T A T T C T T C C A A G G A A G A G A A G C T G C C A A T A G A T T C T A C A A T G C T A T A C C T G A A A T C G T A G A A T A T T A C A T G A A T G A A A T A A A C A A A T T A A C A G G C A G A G A A T A C A A A T T A T T C A A C T A C T A C G G A G C A C C A G A T G C A G A A A G A A T A A T A A T A G C A A T G G G T T C T G T G A C A G A A A C T A T T G A A G A A A C A G T T G A T T A C T T G A T G A A A A A A G G A G A A A A A G T A G G A G T A G T C A A G G T A C A T C T T T A C A G G C C T T T C T C T G T A A A A C A T T T C T T G G A A G C G A T A C C G A A G A C T G T T A A G A A A A T A G C A G T A C T C G A T A G A A C A A A A G A A C C C G G T T C A A T T G G T G A A C C T T T G T A T G A A G A T G T A A A A A C A G C T T T C T T T G A C A G T G A A T T G C G T C C A G T C A T T G T T G G A G G T C G T T A T G G T C T T G G C T C A A A A G A T A C T A C A C C T G C A C A A A T C A T T G C T G T A T T T G A C A A C C T C A A A G C T G A T G A G C C A A A A G A C C A C T T C A C A A T A G G A A T A A T T G A T G A C G T A A C C T T T A C A T C A C T T C C T G T A G G A G A A G A A G T C G A T A C A A T A C C A G A A G G A A C A A C C A G C T G C A A A T T C T G G G G A T T C G G T T C T G A T G G T A C A G T A G G T G C A A A C A A G A G T G C T A T A A A G A T C A T A G G T G A C A A C A C A G A T T T A T A C G T G C A A G C A T A T T T C T C T T A T G A C T C A A A G A A A T C A G G C G G T G T G A C A G T A T C T C A C T T A A G A T T C G G C A A A A A A C C A A T A A G G T C A A C A T A T T T G A T A A A C A A A G C A G A C T T T A T T G C T T G C C A T A A G C A G T C T T A C G T T T A C A A C T A T G A C A T A T T A G C A G G A T T A A A A G A T G G T G G T A C T T T C C T C C T A A A C T G C A A T T G G A A A G T T G A A G A A T T A G A C A A A A A A T T G C C T G C T T C A A T C A A A A G A T A T T T A G C T A A A C A C A A C A T C A A C T T C T A C A T C A T C A A C G C T G T A G A C A T C G C A A A A G A A A T A G G T T T A G G C G G A A G A A T C A A C A T G A T A A T G C A A T C T G C T T T C T T C A A A C T C A C A A A C A T A A T A C C A A T T G A A G A G G C A G T A A A A C A C T T A A A A G A A G C T A T C G T A A A A G A A T A C G G A C A T A A A G G C G A A A A G A T A G T A C A G A T G A A C T A C G A G G C T G T A G A T A G A G G T A T A A A T T C T T T A G T C A A A G T A G A A G T T C C T G C T T C T T G G G C A G A T G C T G A A G A T G A A C C A A A A G A A G A A A G G C A A G C A C C T G A T T T T G T G A A G A A T G T T G C C G A T G T A A T G A A T A G A T T G G A A G G A G A C A A G C T T C C T G T T A G T G C T T T C C T T G G A A G A G A A G A T G G A A C C T T C C C A C C A G G C A C A G C A G C T T A T G A A A A A C G T G G A A T T G C T G T T G A C G T A C C T G A G T G G C A G A T A G A C A A C T G T A T C C A A T G T A A C C A A T G T G C A T T T G T A T G T C C T C A C G C C G C A A T A A G A C C A T T C C T T C T T A C T G A A G A A G A A G T T A A A A A T G C A C C C G A A G G C T T T A A A G T T A A A A A G G C T A T C G G A A A A G G C T T T G A A G G A T T A T A C T A C A G A A T T C A G G T T A G C G T T C T T G A T T G T A C A G G T T G C G G C G T T T G T G C A A A T G A A T G C C C T G C A A A A G A A A A A G C G C T T G T T A T G A A A C C T T T A G A A A C A C A A A T G G A A G A A G C A A A G A A C T G G G A A T A C G C A A T G A C T T T A T C A C C A A A A G A A A A C C C A A T G A A C A A A G A A A C A G T A A A G G G A A G T C A A T T T G A A A C A C C A T T G C T T G A A T T C T C A G G C G C T T G T G C A G G A T G C G G T G A A A C A C C T T A T G C A A A A C T T G T A A C C C A A T T A T T T G G C G A T A G A A T G A T G A T A G C A A A T G C T A C A G G T T G T T C T T C A A T T T G G G G A G C A A G T G C G C C A T C T A C A C C T T A C T G C A C A A A T C A T G A A G G G A A A G G A C C T G C T T G G G C A A A T T C T C T C T T T G A G G A C A A T G C A G A A T T T G G T C T T G G T A T G G C A T T A G C T G T A A A A C A G C A A A G A G A A A A A T T A G C T G A T A T A G T A A A A G A A C T G T T A G A A C T T A A C A T T A C A G C A G A A C T C A A A G A A G C T T T A C A A T T C T G G C T T G A T A A C A T G A T G G A C G G C A A A A A A T C A A A A G A A G C C A C A A T T A A A C T G T T A C C G A T A C T T C A A A A T T A C A A A G C A G A A G A C G C A A A A G T A A A A G A G C T T A T T A A C G A A A T A C T T G A A A G A A A A G A C T A T C T C A T T A A G A A G T C T C A A T G G A T A T T T G G T G G C G A T G G T T G G G C A T A C G A T A T A G G C T A T G G T G G A T T A G A C C A T G T C C T T G C T T C G G G A G A A G A T A T A A A T G T T T T A G T A T T C G A C A C A G A A G T T T A C T C A A A T A C T G G C G G A C A A T C C T C A A A A G C A A C A C C A G T A G G A G C A G T A G C A C A A T T T G C T G C A G C T G G T A A A C C A A T C G G C A A G A A A G A C T T A G G A A G A A T G G C A A T G A C A T A T G G C T A T G T A T A T G T A G C A C A A G T T G C A A T G G G A G C A A G C C A G A C A C A A T T A A T A A A A G C G C T A G T A G A A G C A G A A A G C T A T C C A G G G C C A T C T C T C A T C A T T G C G T A T G C T C C A T G T A T C G C C C A T G G A A T A A A G C A A G G T A T G A G C T G T A G T C A A T T A G A A G A A A A G A A G G C C G T A G A G G C A G G A T A T T G G G T T C T C T A T A G A T A C A A T C C G C T T C T T A A G A A A G A A G G C A A G A A T C C A T T C A T A C T C G A C T C C A A G C C A C C A A A A C T C T C T G T C A A A G A T T T C T T A C A A G G T G A A G T C A G A T T C T C A G C T C T T G A A A A G A C T T T C C C T G A A A A A G C A C A G A A G C T C T T T G A A G A A G C T G A G A A G C A A G C T C A A G A G A G G T A T A A A A T C T A C G A A A A A T T G G C A A A A G A T G A A T A A
M
A
K
V
M
K
T
M
D
G
N
T
A
A
A
H
V
A
Y
A
F T E V A A I Y P I T P S S P M A E V V D Q W S A H G R K N I F G Q P V R V I E M Q S E A G A A G A V H G S L A A G A L T T T F T A S Q G L L L M I P N M Y K I A G E L L P G V F H V S A R A V A T H A L S I F G D H S D V M A C R Q T G F A L L A S G S V Q E V M D L A S V A H L S A I K G R V P F L H F F D G F R T S H E V Q K I E V L D Y E D L K K L V D Y E A L K A F R Q R A L N P E H P V T R G T A Q N P D I F F Q G R E A A N R F Y N A I P E I V E Y Y M N E I N K L T G R E Y K L F N Y Y G A P D A E R I I I A M G S V T E T I E E T V D Y L M K K G E K V G V V K V H L Y R P F S V K H F L E A I P K T V K K I A V L D R T K E P G S I G E P L Y E D V K T A F F D S E L R P V I V G G R Y G L G S K D T T P A Q I I A V F D N L K A D E P K D H F T I G I I D D V T F T S L P V G E E V D T I P E G T T S C K F W G F G S D G T V G A N K S A I K I I G D N T D L Y V Q A Y F S Y D S K K S G G V T V S H L R F G K K P I R S T Y L I N K A D F I A C H K Q S Y V Y N Y D I L A G L K D G G T F L L N C N W K V E E L D K K L P A S I K R Y L A K H N I N F Y I I N A V D I A K E I G L G G R I N M I M Q S A F F K L T N I I P I E E A V K H L K E A I V K E Y G H K G E K I V Q M N Y E A V D R G I N S L V K V E V P A S W A D A E D E P K E E R Q A P D F V K N V A D V M N R L E G D K L P V S A F L G R E D G T F P P G T A A Y E K R G I A V D V P E W Q I D N C I Q C N Q C A F V C P H A A I R P F L L T E E E V K N A P E G F K V K K A I G K G F E G L Y Y R I Q V S V L D C T G C G V C A N E C P A K E K A L V M K P L E T Q M E E A K N W E Y A M T L S P K E N P M N K E T V K G S Q F E T P L L E F S G A C A G C G E T P Y A K L V T Q L F G D R M M I A N A T G C S S I W G A S A P S T P Y C T N H E G K G P A W A N S L F E D N A E F G L G M A L A V K Q Q R E K L A D I V K E L L E L N I T A E L K E A L Q F W L D N M M D G K K S K E A T I K L L P I L Q N Y K A E D A K V K E L I N E I L E R K D Y L I K K S Q W I F G G D G W A Y D I G Y G G L D H V L A S G E D I N V L V F D T E V Y S N T G G Q S S K A T P V G A V A Q F A A A G K P I G K K D L G R M A M T Y G Y V Y V A Q V A M G A S Q T Q L I K A L V E A E S Y P G P S L I I A Y A P C I A H G I K Q G M S C S Q L E E K K A V E A G Y W V L Y R Y N P L L K K E G K N P F I L D S K P P K L S V K D F L Q G E V R F S A L E K T F P E K A Q K L F E E A E K Q A Q E R Y K I Y E K L A K D E * |
Maingene=or0429; Extension FAILED; Comments=Pseudogene, multiple frameshifts/stopcodons | |
| or0432 - or0433 | 438150 | 438464 | pseudogene, missed gene |
A
A
A
T
T
A
T
C
T
C
T
C
T
C
A
G
A
T
A
A
T T A C G C T A A T G T C C A A T C T T T T T T T G A A G A A G A T A A A C C T A A G A T T A T T A A A C T C T T T G A G T C T T T T G T T G A T T T A T C T G A A C T T A T T C C G C C T T C T T T T T A C G T C C A T T A T T A T T T C C A C T A C C T A T A G G G A A T T A G T C T T G A A T C T A T G C T T A C T G C T C T C A T T A T C C A A A A A A T T C T C T C T A T C C C T A C T A T T C A A C T G C T C G T T T A T A T C C T T G G T C T A T C T A A A G A A C T G A G A G A G C T T T G T G G C T T C T C A A G A G T T C C T A A T G C T T C T C A A T T C T G T T G C A A T A G T T A G
K
L
S
L
S
D
N
Y
A
N
V
Q
S
F
F
E
E
D
K
P
K I I K L F E S F V D L S E L I P P S F Y V H Y Y F H Y L * G I S L E S M L T A L I I Q K I L S I P T I Q L L V Y I L G L S K E L R E L C G F S R V P N A S Q F C C N S * |
Comments=Pseudogene, start/stop is absent. Found common hit with non-adjoining gene: or0981 | |
| or0449, or0450 | 456165 | 456894 | join (456165..456641, 456640..456894) | putative pseudogene |
a
t
g
t
c
g
a
t
g
c
t
g
c
t
a
c
c
t
g
a
g a a a a a a c c g c t g t a t g a g c t t g c c t t a a g g a a a a t g g a a g a a t t g a t a a a g a c a g g g c a g t g g a a a g a g g g c a g c a a g c t c c c t t c t g a a t c a c a g c t t g c c a a a c a a t t t g g t a t t a g t c g a g c t a c t t t a a g a g a a g c a a t g a g a a t t t t a g a a g a t g a a g g a c t t a t a g t g a a a c a g c a a g g g g t a g g a a c t t t t g t a a g g a g a a a a c c c c t t a t a a a g a g t g g c t t g g a a g a g t t a t t t a g t g t t a c c a c t t t a a t t g a a a g g c a a g g g a t g g t a c c t g g t a c a a a a g a t t t t a c t g t a t a t a a a t t g c c t g c t a c a g a a a a t g a g g c a a a t c a c t t a a a a t t g a a a c c a g g a g a t a t t a t a t a t a a a g t a g a a a g g g t a a g a a c a g c a g a t g a g g t c c c g g t t g t g t a t t g c a t t g a c a g g t t a c c t c g a a g c a t t g t a g g c g a a t c t t t c t c g g g a t t t g a a c a a t c t g t g t t t t c t t a c c t t g a a a g t g a a c a c t c t a t t a c a a t a a c c t a t g c a g t t t c t a a t a t a a g a g t t a t a a a a c a t g a c c c t g t a g t t g a g a a a a a a c t a a t g a t g g a c a a a a a t g a t t c a a t t c t t t t g t t a g a a c a g g t g c a t t a c g a t g a a a a c a a t a c g c c a a t c c t t t a t t c t t c t a a c t a t t t t a a t g c t t c t a a a t t c g a c t t c t a t a t t a t a c g c a a a a g a a t a t t a t g a
M
S
M
L
L
P
E
K
K
P
L
Y
E
L
A
L
R
K
M
E
E L I K T G Q W K E G S K L P S E S Q L A K Q F G I S R A T L R E A M R I L E D E G L I V K Q Q G V G T F V R R K P L I K S G L E E L F S V T T L I E R Q G M V P G T K D F T V Y K L P A T E N E A N H L K L K P G D I I Y K V E R V R T A D E V P V V Y C I D R L P R S I V G E S F S G F E Q S V F S Y L E S E H S I T I T Y A V S N I R V I K H D P V V E K K L M M D K N D S I L L L E Q V H Y D E N N T P I L Y S S N Y F N A S K F D F Y I I R K R I L * |
Comments=For manual analysis, pseudo or ribosomal slippage, gene with one frameshift, more than 80% of the length of the second shortest homolog |
| or0460, or0460 - or0461 | 467270 | 469189 | pseudogene |
A
T
G
A
A
T
C
T
T
A
C
G
C
A
G
A
A
A
A
T
A C T A T C T T C T C A C C T C A T C G A A G G A G A A A T G G T G A A A G G T C A A G A A A T A G C C A T T A A A A T T G A C C A A A C T T T G A C T C A A G A C T C C A C T G G T A C A A T G G C G T A C C T A C A G T T A G A A G C T C T T G G A A T A G A T A G G G T A A A A A C T G A A C T T T C G G T T G C T T A C A T T G A C C A C A A T A C A T T G C A G C A A G G T C C T G A A A A T G C T G A T G A C C A C A A A T A C A T C C A G A C T G T T G C A G C A A A A T A C G G C A T A T A T T T T T C A A G A C C G G G C A A T G G A A T T T G C C A T C A G G T A C A T C T C G A A A G A T T C G G A A G G C C T G G G A A A A C T C T T T T A G G T T C T G A T A G C C A T A C G C C A A C A G C A G G T G G G T T A G G A A T G T T A G C T A T A G G A G C A G G T G G A T T A G A T G T T G C T T T G G C T A T G G C G G G A G A G C C T T A C A G G A T T A T T A T G C C T T C C A T T G T C A A T G T A A G G C T T A C T G G G A A A C T T A G A C C T T G G G T A T C G G C A A A G G A T G T A A T A T T G G A G C T T T T A A G G A G A C T G A C T G T A A A G G G T G G C G T T G G G A A G A T T T T T G A A T A T T C A G G G G A T G G G G T A A A A A C C C T A T C A G T G C C C G A A A G A G C C A C A A T T G C T A A T A T G G G C G C G G A A T T A G G G G C T A C T A C A T C A A T T T T T C C A T C G G A T G A A A G G A C G T A T G A A T T T T T A A A A G C C C A A G G A A G A G A A G A G G T A T T T G T G C C T T T G G C T G C C G A T G A A G A T G C A G A A T A C G A T G A G G T C A T T G A A A T A A A C C T T G A T G A A C T G G A A C C T T T A G T A G C A C T T C C T C A T A G C C C T G A T A A T G T T G T A A A A G T T A A A G A C G C A G G A A G G C C A A A A G T T G A C C A A G T T G C T A T A G G G T C C T G C A C A A A T T C C T C T T A T G C T G A T T T G A T G A A A G T T G C T T C C A T A T T G A G A G G C A A G G T T A T T C T A G A A C A T G T A A G T C T T G T A A T T G C T C C A G G T T C A A G A C A A G T T C T T A A C A T G C T T G C A A A A A A T G G T G C A C T T T C A G A C C T G A T A T C G G C A G G T G C A A G A A T A C T C G A A A G C G C T T G T G G C C C C T G T A T T G G T A T G G G G C A A G C C C C T G C A A C A G G T G C A A T T T C G A T T A G A A C C T T T A A T A G A A A C T T T T A C G G C A G A A G T G G T A C A A A G T C G G C A T C A G T A T A C C T A G T A A G C C C T G A A G T T G C T G C T G C T G C A G C T T T G A C A G G G T A T T T A A T A G A T C C G A G A G A G T T A G G G G A A G C A C C T G A A G T A C C T T A T G T G G A G A A A T T T G A A A T T A A T G A C A A T A T G A T T A T A A A A C C G C C A G A G G A T A G G G A A A A G G T G G A G A T A A T A A A A G G A C C T A A T A T A A A G C C A T T C C C T C T C A A T A C A C C T C T T T C T G A T A T A G A A A A G A G G G T A C T T A T T A A A G T A G G A G A T G A C A T A A C T A C A G A C C A T A T A A T G C C T T C A A A T G C T A A G T T G T T G C C C T T A A G G T C T A A T A T C C C T G A A C T T G C T A A A C A T T G C T T C G A A A T A A T A G A T G A A A A C T T T T C T A A G A G A G C G A T T G A A T G G G G C G G T G G C A T A A T T G T C G G A G G A A G C A A T T A C G G A C A A G G C T C C A G C C G A G A G C A C G C A G C A T T G G C T C C G C T T C A A C T G G G A G T A A A G G C T G T C A T A G C A A A G T C A T T T G C G A G A A T A C A C A A A G C A A A C C T T A T A A A T A G T G G A A T T C T T C C T C T T A C T T T T G T A G A T G A A A A A G A T T A T G A A G A C A T T G A G G T T G G G G A T G T T T T A A A G A T A G A A A A T G C T G T A G A A C A A G T A A G A A G T G G T A A A A A A A T C A T A A T A G T A A A T G T C A C A A A A G G A A A A A C A T T T G A A G T A A C T C T T G A T G T T T C G G A T A G A A A C A G A G A G A T A T T A A T A G C A G G C G G T A T G A T A A A T T T T G T A A A A A G T A A A A A G A A A T A A
M
N
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T
Q
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I
L
S
S
H
L
I
E
G
E
M
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G
Q E I A I K I D Q T L T Q D S T G T M A Y L Q L E A L G I D R V K T E L S V A Y I D H N T L Q Q G P E N A D D H K Y I Q T V A A K Y G I Y F S R P G N G I C H Q V H L E R F G R P G K T L L G S D S H T P T A G G L G M L A I G A G G L D V A L A M A G E P Y R I I M P S I V N V R L T G K L R P W V S A K D V I L E L L R R L T V K G G V G K I F E Y S G D G V K T L S V P E R A T I A N M G A E L G A T T S I F P S D E R T Y E F L K A Q G R E E V F V P L A A D E D A E Y D E V I E I N L D E L E P L V A L P H S P D N V V K V K D A G R P K V D Q V A I G S C T N S S Y A D L M K V A S I L R G K V I L E H V S L V I A P G S R Q V L N M L A K N G A L S D L I S A G A R I L E S A C G P C I G M G Q A P A T G A I S I R T F N R N F Y G R S G T K S A S V Y L V S P E V A A A A A L T G Y L I D P R E L G E A P E V P Y V E K F E I N D N M I I K P P E D R E K V E I I K G P N I K P F P L N T P L S D I E K R V L I K V G D D I T T D H I M P S N A K L L P L R S N I P E L A K H C F E I I D E N F S K R A I E W G G G I I V G G S N Y G Q G S S R E H A A L A P L Q L G V K A V I A K S F A R I H K A N L I N S G I L P L T F V D E K D Y E D I E V G D V L K I E N A V E Q V R S G K K I I I V N V T K G K T F E V T L D V S D R N R E I L I A G G M I N F V K S K K K * |
Maingene=or0460; Extension FAILED; Comments=Pseudogene, multiple frameshifts/stopcodons | |
| or0473 - or0474 | 485164 | 485412 | pseudogene, missed gene |
A
C
T
C
G
A
A
A
G
G
G
C
A
C
T
T
A
T
A
T
T C A T C C C A G A G C C T T C A A T A G T A A A T A C T A C A A A T T G C G T G A A A A A G C C G G T T T A G A A A A A G A T A A G A A T C T T C A T G C A T T A A G A T A T A C T T T T G C T G C A C G A T T A T T A G A A G C G G G A G T A C A G T T A A A A G T T G T A C A A A A A C T T T T C G G A C A T A C T C A A A T A T C T A C T A C A G C A G A T A T A T A T T C T C A T G T G T T G C T A G A G G T A A A A A G A G A T T C T G T T A A A A A T T A G
T
R
K
G
T
Y
I
H
P
R
A
F
N
S
K
Y
Y
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E K A G L E K D K N L H A L R Y T F A A R L L E A G V Q L K V V Q K L F G H T Q I S T T A D I Y S H V L L E V K R D S V K N * |
Comments=Pseudogene, start/stop is absent | |
| or0473 - or0474, or0474 | 485389 | 485544 | pseudogene |
A
T
G
A
A
T
A
T
A
A
G
T
G
C
C
C
T
T
T
C
G A G T G T A A A A G A G G T A G T A A A A A G G A T A A A A C C A T C T G T G A A T G A A A A A A T A A A C A A T A T C A C A G T G T T G A G C A T A G G A A A A G T G A C A C C G A T A T A T A G A A T T T T G A G G G C A A T A A A A T A T G A A A A T A T A A T A T A A
M
N
I
S
A
L
S
S
V
K
E
V
V
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S
V
N E K I N N I T V L S I G K V T P I Y R I L R A I K Y E N I I * |
Maingene=or0474; Extension FAILED; Comments=Pseudogene, failed extension, extended gene length<=100aa and < 70% the length of the second shortest homolog | |
| or0511 - or0512 | 519673 | 519819 | pseudogene, missed gene |
T
T
A
T
A
C
C
A
A
G
T
T
A
C
T
G
C
T
T
C
T A C C C A A G A A A T A T C T T C T G C A A C A G A G G A A C A A A A A A C T G C A A T A G A A G A A A T A T C A A A A T C C G C A C A A G A T T C G A G C A A T A T T G C A A A T A C A T T G A T G A G T A C A A T A A A T A A A T T T A A A A T T T A A
L
Y
Q
V
T
A
S
T
Q
E
I
S
S
A
T
E
E
Q
K
T
A I E E I S K S A Q D S S N I A N T L M S T I N K F K I * |
Comments=Pseudogene, start/stop is absent. Found common hit with non-adjoining gene: or0431 | |
| or0521 - or0522 | 527460 | 527701 | join (527460..527483, 527485..527529, 527531..527575, 527575..527613, 527615..527701) | pseudogene, missed gene |
g
t
g
c
c
g
g
g
a
a
a
c
t
t
a
a
g
g
a
g
a c c g c a g a c g a a g g c g g g g c c g a a g c c a a g g a g g g c g g a g g c g g g c a c c g a g a c a g g g a t g t c g a a t g t g c c c g g a a c c c c g c c t g a g t c a g a g g g t c g a g c t t t a g t t t a g t c t g t g a t g t c a c c t g g a g c g a c g a t g c a a a a t g c c a a t a a a a a g g a a c t t t g t c t a a g a c a g a g a a t g c a t c a t t t t g a g g c g t t c t t t t t t g t g a a a a t t g t a t g a
V
P
G
N
L
R
R
P
Q
T
K
A
G
P
K
P
R
R
A
E
A G T E T G M S N V P G T P P E S E G R A L V * S V M S P G A T M Q N A N K K E L C L R Q R M H H F E A F F F V K I V * |
Comments=Pseudogene, >1 frameshift are present |
| or0526, or0526 - or0527 | 534839 | 535697 | join (534839..535507, 535509..535697) | putative pseudogene |
a
t
g
a
a
a
a
t
t
a
a
c
a
a
a
a
c
t
a
a
c a t a c t a a a t t t a a t t t t a a t a g t c a t t t t t g t c a t t g c a t t a a t a g t g g c t a t g g t g a c t t t t g g g a a g a a t t t a a c t a t a c t a a t t a a c a g t c c c g a t a a a t t t a g g g a g t g g a t a c a c a g t t t t g g g a a a c t t g g t a t t a t t g t a t t t a t a g g a g t t c a a a t a c t t c a a g t g a t c g t a t t t g t c a t a c c a g g a g a a g t a g t g c a a a t t g c a g g a g g a t a c c t c t a c g g g g c t t t t t t a g g c a c t t t g t a c t c t g t a a t a g g c a t t a c a a t a g g t t c t c t a a t t t g t t t t c t g a t t g c c a g g g t t t t a g g c t a t a a t t t t g t g a g a a g c a t t g t t t c a g a a g a a a a g c t t a a a a a g t t t g a t t a t a t t a t a a a c a a t c c t a a a g g a g a a a c t a t t c t t t t t t t g t t g t t t t t t a t a c c t g g a a t g c c t a a a g a t g c c c t t t c c t a c a t t g c a g g a a t t a c a c c g g t t a a g t t t t a c a a t t t t t t c a t c a t t a c t c t t t t t g c g a g a c t t c c a g g c a t a t t t t t t t c t g c c t a t a t a g g g g c a a a t t t g g g g a a t a a a a a t t a c t t t a t g g c a g g a a t t g t c g c a a t t a t c g c a g t a t t a t t a t t t t t a a t a g g a g t t a a t a a a a a a g a c a t t a t t a t g g a a a a g t t a a a a a a c t t t a a a a a a g t a a a a t t t g g a g t a g c t g g a c a g a a a a t t t t a g c g g a t t t g t t t t g t a a a g c t a a t g a t t t c a t a a a a t t g t t t c t t t g t g c t a t a a t g t t a a t a t a t a a t g a a t t c a g g g g g g a a t t a t a t g t a c t t a t t a a a a g g t g g g a a a a t c c t g a c a a t g g c c g g c a a a a t t t a t g a
M
K
I
N
K
T
N
I
L
N
L
I
L
I
V
I
F
V
I
A
L I V A M V T F G K N L T I L I N S P D K F R E W I H S F G K L G I I V F I G V Q I L Q V I V F V I P G E V V Q I A G G Y L Y G A F L G T L Y S V I G I T I G S L I C F L I A R V L G Y N F V R S I V S E E K L K K F D Y I I N N P K G E T I L F L L F F I P G M P K D A L S Y I A G I T P V K F Y N F F I I T L F A R L P G I F F S A Y I G A N L G N K N Y F M A G I V A I I A V L L F L I G V N K K D I I M E K L K N F K K V K F G V A G Q K I L A D L F C K A N D F I K L F L C A I M L I Y N E F R G E L Y V L I K R W E N P D N G R Q N L * |
Maingene=or0526; Extension SUCCEEDED with start of type START; Comments=For manual analysis, pseudo or ribosomal slippage, gene with one frameshift, more than 80% of the length of the second shortest homolog |
| or0554 - or0555 | 562161 | 562372 | join (562161..562307, 562307..562372) | pseudogene, missed gene |
t
t
g
c
a
t
a
a
g
g
a
g
t
g
a
c
t
t
g
t
t a c a a a g c g g c a a c a a a a c t t a g c a a g a c c g a g g g t g g a g g c a g g g c c g t a g c c a c g g a t g g c g g a g g c g g g c a c t a a g a c a a g g a t g t c g a a t g t g c c c g g t a c c c t g c c g g a a c c c g a a g g t c g a a g t t t a g t t t t g t c g c t t t g g a a c a t c g g a g t g a c g a t g c a a a a t a t c t c c t t t g a a t a t t t t t a g
L
H
K
E
*
L
V
T
K
R
Q
Q
N
L
A
R
P
R
V
E
A G P * P R M A E A G T K T R M S N V P G T L P E P E G R S L V L S L W N I G V T M Q N I S F E Y F * |
Comments=Pseudogene, >1 in frame stop codons |
| or0579 - or0580 | 589094 | 589314 | join (589094..589189, 589192..589314) | pseudogene, missed gene |
t
t
g
c
a
t
a
a
g
g
a
g
c
g
a
c
t
t
g
t
t a c a a a g c g g t a a c a a a a c t t a g c a a g a c c g a g g g t g g a g g c a g g g c c g a a g c c a a g g a t g g c g g a g g c g g g c a c c a a g g c a t g g a t g c c g a t t g t g c c c g g t a c c c t g c c g g a a c c t g a a g g t c g a g c t t t a g t t t t g t c g c t t t g a a a c a t c g g a g c g a c g a t g t a a a a t a t c t c c t t t g t a t a t t t t t a c a a t t a a
L
H
K
E
R
L
V
T
K
R
*
Q
N
L
A
R
P
R
V
E
A G P K P R M A E A G T K A W M P I V P G T L P E P E G R A L V L S L * N I G A T M * N I S F V Y F Y N * |
Comments=Pseudogene, >1 in frame stop codons |
| or0601, or0602 | 613112 | 613707 | pseudogene |
T
T
G
A
A
A
A
T
A
A
T
A
A
T
A
G
C
A
A
C
C C A C A A T C C T C A C A A A A C T G A A G A A A T A A A A A A T T T T T T T A A A G G C T A T C C T G T T G A A A T T T A T T C T A T G G C A G A C T T G G G T A T A A A A G A A G A C A T A G A A G A G A C A G G A G A T A C G A T T G A A G A A A A T G C T C T T A T C A A G G C T C G T T T T T T A A A A G A A A A A G T T G A T G G A A T T G T T A T A G C T G A C G A T A C A G G A T T G T T T G T G G A G C A T T T A A A T G G A C A A C C T G G A G T A T A T T C A G C A A G A T T T G C T G G T G A A A A T G C T A C C T A T G A A G A T A A C A A C A A A A A T T A T T A A A A C T A T T A G A G G G T G T T C C T T A C G A A A A A A G A A A A G C T T A T T T T A A G A C A G T A A T A G C A G T G G T A G A A A G G G A A A A A G A A A C T T T A T T A G A A G G T A A A T T A G A A G G G C A C A T T T T A G A T C A T C C T C G A G G G A A A A A T G G T T T T G G A T A T G A C C C A G T T T T T T A T G T C G A T A A T T T A G G A A A G A G T T T G G C A G A A C T T A C T A T G G A A G A A A A A A A T A A G A T A A G T C A T A G A G C T G A T G C T C T T A T G A A G T T A A A A A A T T A T A T T T T A A A A C G T C T G G A G G A A A A A T A A
L
K
I
I
I
A
T
H
N
P
H
K
T
E
E
I
K
N
F
F
K G Y P V E I Y S M A D L G I K E D I E E T G D T I E E N A L I K A R F L K E K V D G I V I A D D T G L F V E H L N G Q P G V Y S A R F A G E N A T Y E D N N K N Y * N Y * R V F L T K K E K L I L R Q * * Q W * K G K K K L Y * K V N * K G T F * I I L E G K M V L D M T Q F F M S I I * E R V W Q N L L W K K K I R * V I E L M L L * S * K I I F * N V W R K N |
Comments=Pseudogene, TAA stop codon seen in alignment | |
| or0606 - or0607 | 619693 | 619827 | pseudogene, missed gene |
T
T
G
G
C
A
T
T
A
A
T
G
A
A
G
A
T
G
G
T
G G T T A A C G A A G T A T C T A C A C G A A A A G C T G A A G A A A T C A C T T A T A A A C T C T G T G A T A C T G A A T T T T C A A A A T C T A C A A T T T C T G A G C T T T G T A A A A A T C T T G A T C C T A T T G T T T A G
L
A
L
M
K
M
V
V
N
E
V
S
T
R
K
A
E
E
I
T
Y K L C D T E F S K S T I S E L C K N L D P I V * |
Comments=Pseudogene, good start found, extended gene length<=100aa and < 70% the length of the second shortest homolog | |
| or0613 - or0614 | 627721 | 627861 | pseudogene, missed gene |
C
A
T
T
C
A
T
T
T
A
G
C
A
G
T
A
A
A
G
G
A T G T C C T T A T G A T A A T G C A T G T A T A G A A T C C T T T C A T A C T T C T T T A A A G A A A G A A T A A G T A A A T A T A G T T A C T T A C T A T A C T A T A A G G A T T T A T A A A T G G G G C A A T A A A G G T A A T A G A T A A
H
S
F
S
S
K
G
C
P
Y
D
N
A
C
I
E
S
F
H
T
S L K K E * V N I V T Y Y T I R I Y K W G N K G N R * |
Comments=Pseudogene, start/stop is absent. Found common hit with non-adjoining gene: or2129 | |
| or0619 - or0620 | 633628 | 633849 | pseudogene, missed gene |
T
G
T
A
A
A
A
C
T
T
T
T
G
A
A
C
T
C
G
T
A A A A G G G A A A G T G C C A C T T A T A C A T G T C A T C A C A A A T T A T G T T G T G A T G A A T G A T A A T G C A A A C G C A C T T T T G A G T T T T G G A G C A T C A C C T G C A A T G G C A A T G T T G C A A G A A G A G G C A T A T G A T T T T A C C G C G A T T T C A A A T G C C A T G T A C A T A A A T A T A A A A T A C C T G C T A T C C T T A A C C A G G G A A G A T G T G C A G C T A T A A
C
K
T
F
E
L
V
K
G
K
V
P
L
I
H
V
I
T
N
Y
V V M N D N A N A L L S F G A S P A M A M L Q E E A Y D F T A I S N A M Y I N I K Y L L S L T R E D V Q L * |
Comments=Pseudogene, start/stop is absent. Found common hit with non-adjoining gene: or0617 | |
| or0633 - or0634 | 649647 | 649943 | pseudogene, missed gene |
A
T
T
G
T
A
C
T
C
T
T
T
T
A
C
T
T
T
T
A
T A G C A A T A G A G A C A G A T T A G A A A T A T C A T T T A A A C A A A A T C T A A T T G A T T C A A T A A A C A G C T T T T T A G A C G A A T A T C A A A A C A T A T T T A A A G A C A T A G A G G A A A T A A A A C A A C A T A T A A A A G A G A A G C C A G A T A T A A A A T C G A T A A T A A A T C A G C T A A T A A A T G A A A T A A A A A A A G T A G G G A G A A A G A T G T A T C T A A T A A T A G A C G A G T A T G A C C A T T T T G C C A A T G A T A T A A T A G C G A T G G G A G A C A A T G A A T T A T T A A A A C T A T C T T T A T T A T G A
I
V
L
F
Y
F
Y
S
N
R
D
R
L
E
I
S
F
K
Q
N
L I D S I N S F L D E Y Q N I F K D I E E I K Q H I K E K P D I K S I I N Q L I N E I K K V G R K M Y L I I D E Y D H F A N D I I A M G D N E L L K L S L L * |
Comments=Pseudogene, non-canonical start found, extended gene length <= 80% the length of the second shortest homolog. Found common hit with non-adjoining gene: or0635 | |
| or0637, or0637 - or0638 | 655561 | 656161 | join (655561..655743, 655743..655976, 655976..656161) | pseudogene |
a
t
g
a
a
a
g
c
a
a
a
a
g
a
a
c
t
t
t
t
a g a a c t a c t g c g g a t a t c a a g a t c a a c a c t a a c c a a g t a t g t t a a a g a a g g c a a a a t a a g a g t a a c a g t t a t g c c a a a c g g a t t t t a c g a t t a t a a t g a a g a a g a t g t g t a t a a a a t c t t t a t g a a a g a a g t t g a a a g a a a g a c t t a t a t t t a c g c t a g a g t t t c a a c a c a a a a g c a g a a a a a g g a t t t a g a a a a t c a a a t t g a g t t a t t a a a a t a g t t t t g t t t t a g c a a t g g t t a t a a a a t a c a t a g a g t a t t c a g t g a t a t a g c c a g t g a a a t c a g t t t t g a a a a a a g a a a a g a t t t c t t t a a a a t g c t c g a t g a t a t t c t t g c t g g c a g a g t a g a a a g a g t t g t t a t a a c t t a t a a a g a t a g a t t g a a c a g a g t t g t a t t t g g a c t t t t t a a a a a t t t a t t t a a a a a a t t t a a c a c t g a a a t a g t a g t t a t g t c a g a a g t g g g t g a c g a a a a a c t t g a t g c t c a g g a a a t a t t t g a a g a a a t c g t a a a t t t t a t t c a c t a t t a c a a c a t g a a g t t a t a c a g c a a a a g a a a a a t t a a a a a a a t a a a a g a a a t a t t g g a g a a t g g a a g a t g g a a a a g g t a g
M
K
A
K
E
L
L
E
L
L
R
I
S
R
S
T
L
T
K
Y
V K E G K I R V T V M P N G F Y D Y N E E D V Y K I F M K E V E R K T Y I Y A R V S T Q K Q K K D L E N Q I E L L K * F C F S N G Y K I H R V F S D I A S E I S F E K R K D F F K M L D D I L A G R V E R V V I T Y K D R L N R V V F G L F K N L F K K F N T E I V V M S E V G D E K L D A Q E I F E E I V N F I H Y Y N M K L Y S K R K I K K I K E I L E N G R W K R * |
Maingene=or0637; Extension SUCCEEDED with start of type START; Comments=Pseudogene, >1 frameshifts |
| or0638 - or0639, or0639 | 657412 | 658425 | pseudogene |
A
A
A
T
A
C
C
T
A
C
T
T
T
C
T
C
A
T
A
A
A A A A G T A T T T A T T G A A C T T T T A A G A A G T T T T G T C A A A A A A G A T T G G G T A A G T G A A A T A G A C G A A T C T A A A G T A A T A C G A A T A A A C A A A T C C T T C A T A T T A C A A G A T T T T A A A A A T A A A G A G G C T G A T T T G G T T T A T C A A G T A A A A T T G A A G G A T A A A G A A G T T T T C T T T T A T A T A T T G T T G G A A T T A C A A T C A A A A G T T G A T T T T C A A A T G C C A T A C A G A T T G T T A T T G T A T A T A A T T G A A G T G T G G A G A G A A A T T C T T A A A G A T A C A T C A T T A A A C C A G C A A A A A A G G A A G G A C T A T A A A T T A C C A G C G A T T A T T C C T A T C G T G T T G T A T A A T G G T G T T A A T A G A T G G A C T G C T T C T T T G A G C T T T A A A G A A A C G A T A G A T T C A T A T C A A T T A T T T G G A G A A A A T A T A A T A G A T T T C A A G T A T A T T C T A A T T G A C G T A A A C A G A T A T A A T G A A G A A G A A C T T T T A C A G C T G T C A A A T T T G A T A A G C A G T A T A T T T C T A T T G G A T A G A A A A A T A G A C A A G G A A G A G C T G A C A G A A A A A T G G G G G A A A T T A G C A G A T G T T T T A A A G G A C A T A T C G G A A G A A G A A T T C A T A A T A C T T A G A A A T T G G C T T T T C T C A G T T G T A T C G A G A T T T T T A C C A G A G G A T A A A G A A A A A G A G A T A A A A G A A A T T T T A G T A C A A A G T G A G G G G G T G G A A G A G A T G A T T T C A A A T T T A G A A C G A A G C T T A A G A G A A G A G T T T A G G A A A A C G A G A A G A G A A G G A T T A A A A G A A G G A C T T A A A A A A G G G A A G T T G G A A G G C T T A A A A A T A G G A A A A A T G G A A G G G A G A A T G G A A G G C A A A A T A G A A G G A A T A C G C A T G G T A G T G T T T G A G C A A C T C A A G G A A A A A T T C A C A G A T A T T C C A G C A G A A T A T T T G G A A G G T A T T G C A A A A T T G G A T G A T A A A A C T T T A C T T C A G T T A G C A A A A G A C A T T T T A A A G A T A G A G A A A T T A G A A G A G T T G A A G A A A T A T A T A T A A
K
Y
L
L
S
H
K
K
V
F
I
E
L
L
R
S
F
V
K
K
D W V S E I D E S K V I R I N K S F I L Q D F K N K E A D L V Y Q V K L K D K E V F F Y I L L E L Q S K V D F Q M P Y R L L L Y I I E V W R E I L K D T S L N Q Q K R K D Y K L P A I I P I V L Y N G V N R W T A S L S F K E T I D S Y Q L F G E N I I D F K Y I L I D V N R Y N E E E L L Q L S N L I S S I F L L D R K I D K E E L T E K W G K L A D V L K D I S E E E F I I L R N W L F S V V S R F L P E D K E K E I K E I L V Q S E G V E E M I S N L E R S L R E E F R K T R R E G L K E G L K K G K L E G L K I G K M E G R M E G K I E G I R M V V F E Q L K E K F T D I P A E Y L E G I A K L D D K T L L Q L A K D I L K I E K L E E L K K Y I * |
Maingene=or0639; Extension SUCCEEDED with start of type ALNSTART; Comments=Pseudogene, extend to start of alignment | |
| or0644 - or0645, or0645 | 663790 | 664002 | pseudogene |
T
T
G
G
G
A
A
G
T
A
A
G
C
A
T
G
C
T
A
C
T A A A A A T G T T G G A T T T C C A A T A C T A G G A G A A A A T G T A T T A G T A G G G G C A G G T G C A A A A T T A T T A G G T C C G A T A A A G A T T G G A A A C A A T G T T A T T A T T G G T G C A A A T G C T G T A G T T A T A A A T G A T G T A C C A G A T A A T T G T A T A G C A G T T G G T G T T C C A G C A A A A A T A A T A C C T A A A A A T A A T T T G G G G G A T T A A
L
G
S
K
H
A
T
K
N
V
G
F
P
I
L
G
E
N
V
L
V G A G A K L L G P I K I G N N V I I G A N A V V I N D V P D N C I A V G V P A K I I P K N N L G D * |
Maingene=or0645; Extension FAILED; Comments=Pseudogene, failed extension, extended gene length<=100aa and < 70% the length of the second shortest homolog | |
| or0655 | 677204 | 677545 | pseudogene |
T
T
G
C
T
T
G
A
A
A
G
A
A
A
T
T
A
C
T
G
G A T A C A G G A T A T T A A G G T A T A T A C A A A T T T T G T A G A A G G G A T A G A A T T T G A A G G T C A T G T A T G C A C T T T T G A T A A C G A T G G T G A A A T C A T T G A G C T G G A G T A T A A T C C T T G C A A A T T T T A C T T C G G A A T G A A T C C G G A T T A T T T T A A T A A A T T G C C T T A T T T G A T A G A T A A A G A C A A T G A T G G T T T T A C A T A T T G C A G A A G A T G C A A G G T T A T T T T T T C T G A A A C T G A G G G G C A T A G A G A A T G T G G C A A A G A A G T T A T A C T G C C A G A G T A T A T A C T T G T T C G A A T A A G G A G A T G G A A A A A T G A C G A G G T T A G A T C C G A T T A A
L
L
E
R
N
Y
W
I
Q
D
I
K
V
Y
T
N
F
V
E
G
I E F E G H V C T F D N D G E I I E L E Y N P C K F Y F G M N P D Y F N K L P Y L I D K D N D G F T Y C R R C K V I F S E T E G H R E C G K E V I L P E Y I L V R I R R W K N D E V R S D * |
Maingene=or0655; Extension FAILED; Comments=Pseudogene, failed extension, extended gene length>100aa and < 50% the length of the second shortest homolog | |
| or0656 - or0657 | 682471 | 682853 | complement (join (682471..682611, 682613..682696, 682695..682853)) | pseudogene, missed gene |
A
T
T
A
A
C
G
A
A
A
G
T
G
A
A
G
A
G
A
G
A A A A C C T A A A G C C T T T G C C T G C G T T G G A T A A G T A T C A A A A A T T T C T G A T A G A A A G A T G A G G A A G T A C A T A A G G C T A A G G C T T C T T G T C G T A G A T G A A G T A G G G T A T T T G C C T T T A G A C A A C C T T G G A G T A A A T C T T T T T T T T T A G C T G A T A A A C G C A C A G T A T G A G A G A A G A A G C A T A A T A C T T A C A A G C A A T A G A G T A T T T G A G G A A T A T G G T A A A T T A A G G G G G A A G C C A A T T C T T G C A A C T G C G T T T T T G G A T A G A T T G C C G T A C C A T G C C T A T A T A A T T A A C A T A A G A A G T A A C A A T T A C C G T T T A A A G G A T A G G T T A A A G A C T A G T C T T T A T T A T G T T A A A A C T G T A A G C C T A A A T T A A
I
N
E
S
E
E
R
K
P
K
A
F
A
C
V
G
*
V
S
K
I S D R K M R K Y I R L R L L V V D E V G Y L P L D N L G V N L F F * L I N A Q Y E R R S I I L T S N R V F E E Y G K L R G K P I L A T A F L D R L P Y H A Y I I N I R S N N Y R L K D R L K T S L Y Y V K T V S L N * |
Comments=Pseudogene, abnormal start as well as frameshift |
| or0659 - or0660 | 687934 | 688029 | pseudogene, missed gene |
T
A
T
T
A
A
G
T
T
A
C
A
A
C
A
G
G
T
A
A
A A C T T C A A A T G G T A A A A T G T A T G T T A G A A T T G T C G G T G C A A A A G A A G A T G C C C A A A A A A A G G G C C G T G G T G A T T A A
Y
*
V
T
T
G
K
T
S
N
G
K
M
Y
V
R
I
V
G
A
K E D A Q K K G R G D * |
Comments=Pseudogene, start/stop is absent | |
| or0682 - or0683 | 710064 | 710293 | join (710064..710171, 710171..710293) | pseudogene, missed gene |
a
t
g
a
a
a
g
g
a
g
a
c
g
t
t
a
t
t
g
t
g a a a a t a a g t t t t t t g g g a g c t a c t a a a g a a g t t a c a g g c t c a t g c t a t t t a g t t g a g a c g g a a a a a a c t a a a t t t c t t g t a g a t t g c c g t a t g t t t c a g g g g g g a g a a g t t g a a g a c g a g t t a a a c t a t c a a g a a t t t a t t t t t g a t g t a a g t g a g a t a a a c a a t a t a a a t g a a a g t t t a a t g a a a t t g t a t a g a g a a c t t t t g g a t t a g
M
K
G
D
V
I
V
K
I
S
F
L
G
A
T
K
E
V
T
G
S C Y L V E T E K T K F L V D C R M F Q G G E V E D E L N Y Q E F I F D V S E I N N I N E S L M K L Y R E L L D * |
Comments=Pseudogene, gene with one frameshift, less than 80% of the length of the second shortest homolog |
| or0699 - or0700 | 726834 | 727152 | complement (join (726834..726896, 726895..726921, 726923..726949, 726949..726996, 726998..727069, 727072..727152)) | pseudogene, missed gene |
A
T
G
G
G
T
T
G
T
C
A
C
T
T
C
A
G
A
G
T
T C A C T T T A G T G A C T T A T C C T T G A G A C C T C C C C G G G T A A G A A C G A T A A C T T T C A T C T C A T A T C T G C C A G A T T T A C T G T A T G G G A T T C G G G T A G T G T T G G A C T T C G T T T T G T T A C G C A A A C T C A T C C A T C C C A A T C A G C C T C T T A T C T G G T T C T T G T T C A T C A G A C C G A G A T T T T G C C T T A A G G C T T C C T T C A G A T T C C A C C T C A C G A T G A C A C C C T T G C T C T T G G C T A G T G G T T C C C C C A C T A C C A A G C C C A C A G C G G A C T T T C A C C G C C T A G C T A T C G C C C A T G C C G G G C G C A C A T A A
M
G
C
H
F
R
V
H
F
S
D
L
S
L
R
P
P
R
V
R
T I T F I S Y L P D L L Y G I R V V L D F V L L R K L I H P N Q P L I W F L F I R P R F C L K A S F R F H L T M T P L L L A S G S P T T K P T A D F H R L A I A H A G R T * |
Comments=Pseudogene, >1 frameshift are present |
| or0700 - or0701 | 728666 | 728737 | pseudogene, missed gene |
C
T
G
A
A
T
A
A
T
T
A
T
T
T
T
A
T
T
C
A
G C G T C C T C T C A C A C C A C C G T A C G T A C C G T T C G G T A T A C G G C G G T T C A T T A G G
L
N
N
Y
F
I
Q
R
P
L
T
P
P
Y
V
P
F
G
I
R
R F I R |
Comments=Pseudogene, non-canonical start found, extended gene length <= 80% the length of the second shortest homolog | |
| or0701, or0702 | 728734 | 729616 | complement (join (728734..729276, 729278..729616)) | pseudogene |
A
T
G
C
A
A
G
C
A
G
A
A
A
T
A
T
T
A
A
A
A G C T A T T C A A A C A A T T T C A A A C C C T T T T T T A G A C T A T T T T T T T A T A G C T G T A A C T A T G T T G G G A A G T T C A G G A T T T T A T T T T A T T T T T A T C C C C C T T T T T T A C T G G T G T G T A G A T A A A A G A T T T G G T C T A A A A T T G G G A C T C A T A T T G A T A A G C T C T A T C T A T G T A A A C A C T G T T T T A A A A G A G A T A A C A A A A A T A G C A A G A C C T A T A G G A T A T C C A G G A A T A A G G T C T A T T T T T A C A C A A T C G G C A G G A G G A T A T T C T T T C C C A A G T G G C C A T G C A C A A G G T T C T A C A A C T G T T T G G G G A A C T T T A A T G G T A C A C T A T A A A A A A A A A T G G C T G T G G T A T G T A G G A A T C G C C A T C G T A T T A C T C G T A T C A T T T T C G C G A A T G T A T T T A G G T G T C C A C T G G C C G A T A G A T A T T A T T G G C G G A A T A T T G A T A G C T G T T T T A A T A A T A A T T T T A A G T G A A C T T A T T G A T A G C A T C G T G A A A G A A A G C A A T T T T A A C A T A A G T T T A T C T T T T A A A G T T A T T T T G T C A A T T T T A A T C C C T G C G C T T T T T A T A T T A A T T T T C C C T C A C A A G G A T A T T T A T G A A T A C A T G G G T T T A A T T T C T G G T A C T T T A A T A G G T T A T T T T A T A G A C A A A G A A A A A T T T G A T T T T A C T G T C C A T G C T C C T C T T C A A A A G C A A A T T T T G A A G T T A C T A A T T G G C A T A A T T G T A T T T T T T G T A C T T A A A G A G G G A T T A A A A T T T G T G T T G C C T T C T G G A A A T A T T T T T A A C G C T A T A A G G T A T G C A A T T T G C G G A C T G T G G C T T T C T C T T G G T G C A C C T T A T G T A T T C A A T C T T T T T A A A T T A A A C G A T A A A A C A A T A A A G G C A T C G A G T A G G A G C T G A
M
Q
A
E
I
L
K
A
I
Q
T
I
S
N
P
F
L
D
Y
F
F I A V T M L G S S G F Y F I F I P L F Y W C V D K R F G L K L G L I L I S S I Y V N T V L K E I T K I A R P I G Y P G I R S I F T Q S A G G Y S F P S G H A Q G S T T V W G T L M V H Y K K K W L W Y V G I A I V L L V S F S R M Y L G V H W P I D I I G G I L I A V L I I I L S E L I D S I V K E S N F N I S L S F K V I L S I L I P A L F I L I F P H K D I Y E Y M G L I S G T L I G Y F I D K E K F D F T V H A P L Q K Q I L K L L I G I I V F F V L K E G L K F V L P S G N I F N A I R Y A I C G L W L S L G A P Y V F N L F K L N D K T I K A S S R S * |
Comments=Pseudogene, both frameshift and stopcodon in gene |
| or0752, or0752 - or0753 | 779710 | 781143 | pseudogene |
A
T
G
A
A
T
A
A
A
A
T
A
A
C
A
A
T
T
G
A
T A A A A A T A A A A A T G T G C C T T T A T A T A T T C A A T T G T A C A G T C A A A T A A A A A G A T T T A T A G A G A A T G G C A G C C T G C C A G G T G G A T A T A A A C T C C C C A C T A T A A G A A G C C T T G C A A A G G A G T T G G G G G T A A A C A A T A T T A C A G T G A T T A A T G C T T A T A A G C T T T T A G A G C A A A A T G G A T A T A T A T A T A C T A A A G T A G G A A G T G G T A C T T A C G T T T G T G A A G A T A T A A A A A A A G A A G A G G A C C T T G A T G A A A G C T T T A A A T T A A C A G A C C A A G G A G A A A T T C C C T T A A A G A A A G G A A T T A T A A A T T T T G C T T C T T C A T C T C T T A A T C C A G A G C T T T T T C C A G T G G A G G A T T T T G G A G A T T T A A T C A A T A G A G T A T T G A G A A G A G A T G G A G G A T A T G C T T T T G A G T A T C A A G A C A C A A G A G G A T A T A A A C C A T T A A G A G A A T C T A T A A A A G A A T T T G T A A A G A A A G A T G A A A T A T T T A C T T A T G T T G A A A A T A T A C A G G T A A T T T C T G G G G G A C A G C A A G G T A T A G A T G T A G T A T C G A A A G C G C T A A T A A A T T T T G A A G A T A G C A T A A T T G T T G A A A G A C C C A C C T A T T C G T G G G C T T T A G C C T C T T T T G A A T C G A G A G G A G C A G A G A T T T T A G A A G T G G A T T T A A A A A A A G A T G G A A T A A A T T T A G A G G A A T T G G A G G A T A A G T T A A A G A A A T T T A A G C C A A A G T T C A T A T A T A C A A T A C C C A A T T T T C A C A A T C C C A C C G G C A T T G T T T A C A G T G A G G A A A A A A A G A A G A A A C T A A T A G A G T T G G C G G A A A A A T A T G A A A C T T A T A T T T T A G A A G A T G A T T T T G C C A G T G A T T T A A G T T T T A C T G A A G A A A A G A T A T T G C C A C T T A A A G C T T A T G A T A A A T A T G A C A G A G T C A T T T A T A T A A A A A G C T T C T C A A A A A T A T A C A T G C C G G G T T T G A G G T T A G G T T T T A T A A T T G C T C C A G A A A G G C T A G T A A G T A G T T T C C T A A A A G C C A A A T A T G T G A C A G A T T T A T C T A C T T C A G G T T T G A T G C A A A G A G C C T T T G A T T T A T A T C T T A G A G A A A A T A T T T G G A A A A A T C A T A T T G A A G A A A T A A A A C A A G T A A T G A A A A A A A G A T T T G A A A A G A T G G G T A A T G G A C T T C A G A T G T T A A A A A A T T A T G T A G A A T T T G A A T A T C C T A A A G G G G G T T T T T A C T A C T G G T T A A G A C T T A A A G A C A A T A T T T C T G C T A A A A A T T T A T A T T C T A A A T G T T T A G A G A A A A A T T T A C T T A T A G T C C C A G G A G A C A T G T T T T T T G C A A T A A A A A A A G A G A C C A A T T T T A T A A G A T T A A G T T T T G C C T C T T G T G A G T T G G A G G A G A T A G A T A A G G G G A T A G A T A T A C T G A A A G A G G T T T T A G A A G G A G A A T C T A A T G A A A A C G G C A T A T A T C T T C C T A T A A T A T A A
M
N
K
I
T
I
D
K
N
K
N
V
P
L
Y
I
Q
L
Y
S
Q I K R F I E N G S L P G G Y K L P T I R S L A K E L G V N N I T V I N A Y K L L E Q N G Y I Y T K V G S G T Y V C E D I K K E E D L D E S F K L T D Q G E I P L K K G I I N F A S S S L N P E L F P V E D F G D L I N R V L R R D G G Y A F E Y Q D T R G Y K P L R E S I K E F V K K D E I F T Y V E N I Q V I S G G Q Q G I D V V S K A L I N F E D S I I V E R P T Y S W A L A S F E S R G A E I L E V D L K K D G I N L E E L E D K L K K F K P K F I Y T I P N F H N P T G I V Y S E E K K K K L I E L A E K Y E T Y I L E D D F A S D L S F T E E K I L P L K A Y D K Y D R V I Y I K S F S K I Y M P G L R L G F I I A P E R L V S S F L K A K Y V T D L S T S G L M Q R A F D L Y L R E N I W K N H I E E I K Q V M K K R F E K M G N G L Q M L K N Y V E F E Y P K G G F Y Y W L R L K D N I S A K N L Y S K C L E K N L L I V P G D M F F A I K K E T N F I R L S F A S C E L E E I D K G I D I L K E V L E G E S N E N G I Y L P I I * |
Maingene=or0752; Extension FAILED; Comments=Pseudogene, multiple frameshifts/stopcodons | |
| or0760, or0760 - or0761 | 787158 | 787340 | pseudogene |
T
T
G
A
T
A
G
A
A
T
T
A
A
A
T
G
G
T
G
T
T T C A A A G T C T T A C A A C A A A G G C A A A G T A A A A G C T G T T G A C A A T A T T G A T C T T A T T G T A A A T G C T G G T G A A A T A T T T G G A T T T T T A G G C C C T A A C G G T G C T G G A A A A A C T A C T A C C A T A A A A A T G A T A G T C T G G A A G C A T T G G C G T T A T A A T G C A A T A C A C T A A
L
I
E
L
N
G
V
S
K
S
Y
N
K
G
K
V
K
A
V
D
N I D L I V N A G E I F G F L G P N G A G K T T T I K M I V W K H W R Y N A I H * |
Maingene=or0760; Extension FAILED; Comments=Pseudogene, failed extension, extended gene length<=100aa and < 70% the length of the second shortest homolog | |
| or0760 - or0761 | 787351 | 787512 | pseudogene, missed gene |
T
T
G
T
A
T
G
A
C
A
A
A
T
T
G
G
G
C
T
T
A A A A G A A A T A A C G A T A A A A A G T G G C C C T T A T A A A G A C A T A G G T T C A C C C A C A A G A G A T T T A A C T C C T G A A G A G A A A A A G A T A T T G C A G T G A G T T A T A G G A G T G T A T A G T A C G A C T A G A T A T T T T G T A T T A T T T G T T A T G T G A
L
Y
D
K
L
G
L
K
E
I
T
I
K
S
G
P
Y
K
D
I
G S P T R D L T P E E K K I L Q * V I G V Y S T T R Y F V L F V M * |
Comments=Pseudogene, TGA/TAG stop codon, no start found, extending to start of BlastX alignment | |
| or0764 | 788936 | 789124 | putative pseudogene |
A
T
G
T
G
G
G
A
C
A
A
G
T
A
C
A
A
G
G
A
T A T A G G A A T A A G A G T A G T G T A T A C A C T C G T T A G A G A T A A A A A A C T C A T G A A T A T A G T A G C G G T T T C T C C A A G A G A T G A T G A T T A T T G T T A C T C A G T A G C A G A G A A G A G A A G A A G A A A A T A C G G G A A T G A T T T A T T T A C C A A A G G A T T C G A A A A G T T A G A A A G T G A A T A A
M
W
D
K
Y
K
D
I
G
I
R
V
V
Y
T
L
V
R
D
K
K L M N I V A V S P R D D D Y C Y S V A E K R R R K Y G N D L F T K G F E K L E S E * |
Maingene=or0764; Extension FAILED; Comments=For manual analysis, pseudo, failed extension, extended gene length<=100aa and < 90% the length of the second longest homolog | |
| or0825 - RNA_56 | 843969 | 844130 | pseudogene, missed gene |
T
T
G
G
T
T
C
A
A
G
A
G
A
A
C
T
G
T
T
G
G C A A A G G G G A T T A A A T T C C A T C G C A A G A T A T A A A G A G T T A G A T G A T A A A A A T T T T G C A G A A T A C T A T T T A A T A G G G A C A A T G T T A A G T A T A C T T A T A G C T C T T T T T G G A G G T T T A G C G A T A A A A G C C A T A T T A A A A A T A T A A
L
V
Q
E
N
C
W
Q
R
G
L
N
S
I
A
R
Y
K
E
L
D D K N F A E Y Y L I G T M L S I L I A L F G G L A I K A I L K I * |
Comments=Pseudogene, good start found, extended gene length<=100aa and < 70% the length of the second shortest homolog | |
| or0827 - or0828 | 845708 | 845944 | pseudogene, missed gene |
A
T
G
A
C
T
G
A
A
A
A
G
C
T
T
T
T
T
T
A
T G A A A A T A A C T A T G T T A C C T A G T T T G A T G C C A A C A T C A T A G A T A A A A G G A A A A C C C A C G A T A A A T G G G A G T T A G T G T T A G A T A A A A C T T A T T T C T A T C C T G A A A G T G G T A G A C A A C C G A G T G A T A C A G G G A T A A T T G A T G G C T T T A A A G T T T A C A A A G T A T A T G A G G A A A A T G A T G T A A T A T A C C A T G T A G T A G A T A A A T G T G T C A A A A T T A C T T G A
M
T
E
K
L
F
Y
E
N
N
Y
V
T
*
F
D
A
N
I
I
D K R K T H D K W E L V L D K T Y F Y P E S G R Q P S D T G I I D G F K V Y K V Y E E N D V I Y H V V D K C V K I T * |
Comments=Pseudogene, TGA/TAG stop codon, start with Good alignment found, extended gene less than 80% the length of second shortest homolog with e-value less than e-05 | |
| or0830 - or0831 | 847368 | 847491 | join (847368..847397, 847399..847491) | pseudogene, missed gene |
t
t
g
c
a
t
a
a
g
g
a
g
t
g
a
c
t
t
g
t
t a c a a a g c g a a a a c a a a a c t t a g c a a g a c c g a g g g t g g a g g c a g g g c c g a a g c c a a g g a t g g c g g a g g c g g g c a c c t t a a g g c a t g g a t g c c a c c t g a c g t a g
L
H
K
E
*
L
V
T
K
R
K
Q
N
L
A
R
P
R
V
E
A G P K P R M A E A G T L R H G C H L T * |
Comments=Pseudogene, gene with one frameshift, less than 80% of the length of the second shortest homolog |
| or0839 - or0840, or0840 | 857819 | 857953 | pseudogene |
A
T
G
G
A
G
A
A
T
T
T
T
T
T
G
A
A
A
G
T
T G C A G A A C T G A G A A A A A A T A T A A G C T T A A A A G G A A A A G A A A G T G C A G A A A A A T A T A G T T A T G A T A A A A T G A T T A A A G A A A T A C A A C A G A T T T A T C A T A C C T T G A A G G G A A G A T A A
M
E
N
F
L
K
V
A
E
L
R
K
N
I
S
L
K
G
K
E
S A E K Y S Y D K M I K E I Q Q I Y H T L K G R * |
Maingene=or0840; Extension FAILED; Comments=Pseudogene, failed extension, extended gene length<=100aa and < 70% the length of the second shortest homolog | |
| or0856 - or0857 | 874575 | 874799 | pseudogene, missed gene |
A
T
T
T
T
A
C
A
A
T
T
A
A
A
C
A
C
T
G
C
C C T T G A G G C A G T T T T T T A G C A A T T T T A C G A T T A T C T A A A A A A T A G A C C A T A C A A C G T A T A C T T G T C A T T T T T T G G T G T T A G A T T T C C T A A A G G T A A T G A G A T A A A A A C T A T T A T C G A T C C A G A T A T A G T G G T A A A A A A G A A C T A C T T T A T T T T A C A A T A T T T T A A T G G T A A A A T T A T A T T G A T A A A T T T T T T A C A G A G G A G C T G A
I
L
Q
L
N
T
A
L
E
A
V
F
*
Q
F
Y
D
Y
L
K
N R P Y N V Y L S F F G V R F P K G N E I K T I I D P D I V V K K N Y F I L Q Y F N G K I I L I N F L Q R S * |
Comments=Pseudogene, TGA/TAG stop codon, no start found, extending to start of BlastX alignment. Found common hit with non-adjoining gene: or0051 | |
| or0870 - or0871, or0871 | 887603 | 888154 | putative pseudogene |
A
T
C
C
G
C
T
T
T
T
A
T
T
T
T
T
T
C
A
T
A A T T C T T A G G A G G T G T G T A T T T A T T A A C A A A G A G C T G C A G G T C A A T G A G G A A A T A A G A G A C A A A G A G G T A A G G T T G A T A G A C C A A G A T G G A A A G C A A A T T G G C A T A A T G T C G G C A A A G G A A G C T T A T A A A A T T G C T C A A G A G C G A C A T C T T G A T T T G G T T A A G A T T G C C C C T C A A G C C A A T C C G C C C G T G T G C A A A T T G A T G G A T T T T G G T A A G T A C A G G T A C G A G C T T A G T A A G A G G G A G A A A G A G G C A A A G A A A A A G C A A A A G G T G A T A A A T G T T A A A G A A A T A A G A A T G T C T C C A A A T A T T G A A G A T C A T G A T T T T G G A G T A A A G T T G A G A A G T G C T A T T A A A T T T T T A A A A G A A G G T G A C A A G G T A A A A G T T A C T A T A A G A T T T A G A G G A A G A G A A G C T G T T C A T A C T T C A C T G G C A G A A G A C C T T T T A A A G A G G T T T G C A G A A G A G C T T G A T G A G T A T G G C G C T A T A G A A A A A G C T C C T A A T A T G G A G G G T A G G A A T T T A A T A A T G G T A T T A A C A C C A A G A A A A T A G
I
R
F
Y
F
F
I
I
L
R
R
C
V
F
I
N
K
E
L
Q
V N E E I R D K E V R L I D Q D G K Q I G I M S A K E A Y K I A Q E R H L D L V K I A P Q A N P P V C K L M D F G K Y R Y E L S K R E K E A K K K Q K V I N V K E I R M S P N I E D H D F G V K L R S A I K F L K E G D K V K V T I R F R G R E A V H T S L A E D L L K R F A E E L D E Y G A I E K A P N M E G R N L I M V L T P R K * |
Maingene=or0871; Extension SUCCEEDED with start of type NONCANSTART; Comments=For manual analysis, pseudo or non-canonical start codon, extended gene length > 80% the length of the second shortest homolog | |
| or0884 - or0885 | 903241 | 903360 | pseudogene, missed gene |
A
A
T
A
A
A
G
A
A
G
G
A
C
A
T
A
G
A
G
C
A A A T A T T T T A A A C C C T T A T T A C A A C A A G G T A G G A G T A G G A A T A G T G A A A A A T A A A G A G G A C A A T G G C A T A A T A G T G G T A G A A A T G T T T A T A A A A G A T T A A
N
K
E
G
H
R
A
N
I
L
N
P
Y
Y
N
K
V
G
V
G
I V K N K E D N G I I V V E M F I K D * |
Comments=Pseudogene, start/stop is absent | |
| or0897, or0897 - or0898 | 915514 | 916185 | putative pseudogene |
A
T
G
G
C
T
T
T
T
T
C
T
A
A
A
A
A
G
A
T
G A T A G G A C A G C A A G A A A T A G T G C C A G G C C C T G T A G A G C C A G G G C A A C T T C C A G A A C C T A C A G A G A T A G C T T G C A T T G A A G T G A C T A A A G T G T A T G A T G C T T G T T C G C A A A G A A T A T G T T T A G A T A A T A T A C C A C C T A T T A C T T T T G T A C C T T C T G T A T T G A A T T T A A C T C C C A G C T T T G G A G A A A T A A C A A A T A T T A C T G T A T C A C T T G T T A C A C C T C C T G G T T T T G T T A T A A C T C C A C T T C C G G A T A G G C C A G G A T T T G C G A G G G T A G A A G C A A C T T T T C A A G T G A C T T A T G A T A T T G T G A T T A A C T A T C C A G A T G G A A C T A C A C A A A C A T T G C C A G G A A A T A T T A C T A C T T T C A A C A A A G A T A T T G T A C T T T A C G T A C C A G A C C C A A A T G T A G C A A T A A T G A A A T A C G A G G C G T T A G C A G A G G G C T T G T A C G G A A A G G T T A A T C T A G G A G T T A C T A C C A C T G T A G A A G T G A T A A T T G G G G T A T G G A T T G T G A T A A A A T C C G C A G T A G A T G T G C A A T T A T T A G T T C C G T C T T A C G G T T T C T G C C C T A C T C C A G C A G C T T G C G A G G A G T T C G T A A C A G A T G T G T G T G A A A T T T T C A A T C A G A A G C C T T T C C C A T C T T T T G A T C C G C C T C A A A T G C A T C A A A A T C C T T A T T A A
M
A
F
S
K
K
M
I
G
Q
Q
E
I
V
P
G
P
V
E
P
G Q L P E P T E I A C I E V T K V Y D A C S Q R I C L D N I P P I T F V P S V L N L T P S F G E I T N I T V S L V T P P G F V I T P L P D R P G F A R V E A T F Q V T Y D I V I N Y P D G T T Q T L P G N I T T F N K D I V L Y V P D P N V A I M K Y E A L A E G L Y G K V N L G V T T T V E V I I G V W I V I K S A V D V Q L L V P S Y G F C P T P A A C E E F V T D V C E I F N Q K P F P S F D P P Q M H Q N P Y * |
Maingene=or0897; Extension FAILED; Comments=For manual analysis, pseudo, failed extension, extended gene length>100aa and between 70% length of second shortest homolog and 90% the length of the second longest homolog | |
| or0897 - or0898 | 916210 | 916528 | complement (join (916210..916272, 916271..916297, 916299..916325, 916325..916372, 916374..916445, 916448..916528)) | pseudogene, missed gene |
A
T
G
G
G
T
T
G
T
C
A
C
T
T
C
A
G
A
T
T
T T A C T C C C A T G A C T T A T C C T T G A G A C C T C C C C G G G T A A G A A C G A T A A C T T T C A T C T C A T A T C T G C C A G A T T T A C T A T A T G G G A T T C G G G T A G T G T T G G A C T T C G T T T T G T T A C G C A A A C T C A T C C A T C C C A A T C A G C C T C T T A T C T G G T T C T T G T T C A T C A G A C C G A G A T T T T G C C T T A A G G C T T C C T T C A G A T T C C A C C T C A C G A T G A C A C C C T T G C T C T T G G C T A G T G G T T C C C C C A C T A C C A A G C C C A C A G C G G A C T T T C A C C G C C T A G C T A T C G C C C A T G C C G G G C G C A C A T A A
M
G
C
H
F
R
F
Y
S
H
D
L
S
L
R
P
P
R
V
R
T I T F I S Y L P D L L Y G I R V V L D F V L L R K L I H P N Q P L I W F L F I R P R F C L K A S F R F H L T M T P L L L A S G S P T T K P T A D F H R L A I A H A G R T * |
Comments=Pseudogene, >1 frameshift are present |
| or0909 - or0910, or0910 | 927748 | 929823 | putative pseudogene |
A
T
A
T
A
T
C
C
A
A
C
C
A
T
A
T
C
T
G
T
A A A G A G A A G A A T T C T T T T T T T A C T T T T T T T A T C T T C T A T A G T A G T T T T T G G A C T T A T A C T C A G A C T T T T T T G G A T A C A G G T A G T A A A A A G T G A A G A T T A T C A A A A G A T G G C A C T T C C T C A A T G G A C T T T A G A A G T A T C T G T T A G T G G T A A A A G G G G A A A T A T A T T T G A T A G A A A T G G C A A A G T A T T A G C A G A A A A T A T A A G T G T T A A T A A A A T A A G T G T T A T C C C T A A A G A A A T A C C T G A T T C T C A A A G A G A A G C A G T A G C T G A A G C T T T A G C C C A A A T A T T A A A T T T A G A T A A A G G A A A A G T T C T T C A A A A G A T T T C T A A T A A A A A C T T A C A A G A A G T G T T A A T T G C T A A A C A A G T T G A T G A C G A A A A G G T A G C A G A G A T A A G A A A G C T T A A T A T A G A T G G A A T A A T A A T T T C T G A G G A C A T G A A A A G A T T C T A T C C C A A T A A T A C T C T T G C A T C A C A T G T C T T G G G T T T T A C T G G A A T T G A C A A C C A G G G T T T A G A T G G C G T T G A A T T A G C A T T T G A C A A C T T T T T A A G A G G T A T T C C G G G A A G A A T T T T T A C T C C A A T G G A T G C T A T A G G T A G A A A G A T G G A T G T G G G A G A G G A A G A G T A T T T T G A A C C T C T T C C A G G T T A T A A C G T A G T G C T T A C A A T A G A T G A A A C T A T T C A G C A T T T T G C A G A A A A G G C T C T T A A C C A A G C G A T G G T T C A T T C T A A G C C T T C A A A A G G A G C A G T A G C C A T T G T T A T G G A C C C C A A A A C A G G G G A A A T A T T G G C T T T G G C T A A T A G A C C A A A T T T T A A T C C T A A T A A T C C T T T T G A A G G A C C G C A G G A A G A A T G G T A T A A A G T T T G G C G A A A T A A A G C T A T T T C T G A T T C T T A T G A A C C T G G T T C T G T T T T T A A G A C A A T T A C T G C T T C T G C A G C T T T A G A A G A A A A A C T T G T A G G T C T T A A T G A A C A G T T T T A T T G T C C G G G C T A T A C T A T A G T T T C T G G A C A T A G A A T A A A T T G C T G G G C T A C C C A T G G C A G T G A A A A T T T T G T T C A A G G T G T T C A A A A T T C T T G C A A C G C A G T T T T T G T G A C G T T A G G A C A A A G G C T A G G A G T A G A A A A A C T C T A T A A A T A C A T A C A T G A T T T T G G A T T T G G A C A A A G G A C A G G A A T A C T T C T T C C T G G T G A A G C T C C A G G T C T T G T A T T G G C A G A A A G T A G T G T T G G G C C T G T T G A G T T A G C C A C T A A T T C T T T T G G G C A A G G T A T T G C T G T G A C G C C T C T T C A G A T G A T T A C T G C T G T C T C C G C A A T A G C C A A T G G A G G A A A A T T G A T G C A A C C T C T A A T T G T G A A A T C A A T T G T A G A T T C A A A T G G A A A A G T A G T G A A G G A A T T T A A A C C A A A A G T A G T G A G G C A A G T C A T T T C T G A A C A G A C C T C T T C T A C A A T G A G A G A A A T A C T A A A A A G T G T A G T G T C A G A G G G A A C A G G C A A A G C A G G A T A T A T T G A A G G A T T T G A T G T A G C T G G A A A G A C T G G T A C T A C A G A A A A A T A T A T G C C A G G C A A A T A T G T G G C A T C T T T T A T A G G T T T T G C A C C A G C G G A G G A T C C A A A A G T T A T T G T G T T G G T G G T A A T A G A T G A G C C T A A T A A T C C G G A A A C C C A T T T T G G A A G C C A A T T G G C T G C A C C T G T A G T A A A G A G T A T T T T A G A A G A T A C C T T A A G A T A T T T G G A A G T A C A G C C A A G A G G A A T A G A A A A A C C T G C A T C A G T T G T A G T A C C G G A T G T G A G G A A T A T G A A A C T T T A T G A A G C A G A A A A C A T T A T T T T A T C G A A T A A G C T T A A C T T T A T T A T A G A A G G A A A T G G A G A T A C T G T T T T T G A C C A A A T G C C T A A A C C A G G A G C A A T T G T A G A A G A A A A C A C A C A A G T T A T T T T G T A C T T A A A T G C T G A A A A A A T A C A A G A G G T A G T A G T T C C T G A T T T A A C T G G T A A A A G C G T A A A A G A A G C T A C A G A A A T T T T A A A T T C T T T G G G G C T T A A A A T A A G A A T A A A A G G C A G C G G T T T T G C T G T G A A T C A A A G T C C G A A A G A A G G C A C G A T T T T G A A A A A A G G C G A A A C T G T A G A A G T G G A G T T T A G G C C T A A G G A A A A A T A A
I
Y
P
T
I
S
V
K
R
R
I
L
F
L
L
F
L
S
S
I
V V F G L I L R L F W I Q V V K S E D Y Q K M A L P Q W T L E V S V S G K R G N I F D R N G K V L A E N I S V N K I S V I P K E I P D S Q R E A V A E A L A Q I L N L D K G K V L Q K I S N K N L Q E V L I A K Q V D D E K V A E I R K L N I D G I I I S E D M K R F Y P N N T L A S H V L G F T G I D N Q G L D G V E L A F D N F L R G I P G R I F T P M D A I G R K M D V G E E E Y F E P L P G Y N V V L T I D E T I Q H F A E K A L N Q A M V H S K P S K G A V A I V M D P K T G E I L A L A N R P N F N P N N P F E G P Q E E W Y K V W R N K A I S D S Y E P G S V F K T I T A S A A L E E K L V G L N E Q F Y C P G Y T I V S G H R I N C W A T H G S E N F V Q G V Q N S C N A V F V T L G Q R L G V E K L Y K Y I H D F G F G Q R T G I L L P G E A P G L V L A E S S V G P V E L A T N S F G Q G I A V T P L Q M I T A V S A I A N G G K L M Q P L I V K S I V D S N G K V V K E F K P K V V R Q V I S E Q T S S T M R E I L K S V V S E G T G K A G Y I E G F D V A G K T G T T E K Y M P G K Y V A S F I G F A P A E D P K V I V L V V I D E P N N P E T H F G S Q L A A P V V K S I L E D T L R Y L E V Q P R G I E K P A S V V V P D V R N M K L Y E A E N I I L S N K L N F I I E G N G D T V F D Q M P K P G A I V E E N T Q V I L Y L N A E K I Q E V V V P D L T G K S V K E A T E I L N S L G L K I R I K G S G F A V N Q S P K E G T I L K K G E T V E V E F R P K E K * |
Maingene=or0910; Extension SUCCEEDED with start of type NONCANSTART; Comments=For manual analysis, pseudo or non-canonical start codon, extended gene length > 80% the length of the second shortest homolog | |
| or0946 - or0947 | 963817 | 963966 | pseudogene, missed gene |
A
T
G
G
A
A
C
T
G
C
A
A
G
G
A
A
T
A
G
G
G G A T G T A A C A G C A A G C T T T G G A G T A A C T G A A T A T A G G G A T A C T G A T A C C A T T G A C A T A G T T C T T A T T C G A G T A G A C A A C A T G C T T T A T G A A G C A A A G G G T G A A G G A A G A A A T T G T G T A A A A A G C G A A T A A
M
E
L
Q
G
I
G
D
V
T
A
S
F
G
V
T
E
Y
R
D
T D T I D I V L I R V D N M L Y E A K G E G R N C V K S E * |
Comments=Pseudogene, good start found, extended gene length<=100aa and < 70% the length of the second shortest homolog | |
| or0948 - or0949 | 965758 | 966042 | join (965758..965925, 965928..965960, 965959..966042) | pseudogene, missed gene |
t
a
t
t
t
t
c
c
g
a
a
a
a
t
t
g
g
g
t
a
t g a a g t a t a t a a g a a g a a t a a a a a a a a t t g c g a a g c a a a g t t c a a a a t a g c c a a a g t a g a a a a a t t t c t a a g a t t t a t a g a g g a a a a a a t a t t a a a a g a c a a a t g g t c g c c a g a t g c a g t a g t a g g t t a t t t g c a g a a g g a g t t c t g g g a a a a a a a a g a a a c a g t t t g t a c t a a g a c a c t g t g t a a t a g a c t t c c a a g a a g a a t t t t a a g a t a t a a g a c a c c a g a a g a a t t c t t t t t g c a a g a g a t a g c t c a a g c t a t t a a c t a g
Y
F
P
K
I
G
Y
E
V
Y
K
K
N
K
K
N
C
E
A
K
F K I A K V E K F L R F I E E K I L K D K W S P D A V V G Y L Q K E F W E K K E T V C T K T L C N R L P R R I L R Y K T P E E F F L Q E I A Q A I N * |
Comments=Pseudogene, start/stop is absent. Found common hit with non-adjoining gene: or0623 |
| or0953 - or0954 | 972859 | 973128 | pseudogene, missed gene |
A
A
T
A
A
A
G
T
A
A
C
T
A
A
G
G
C
A
A
T
A C A A G T T T T A G A A G A G G G G T T T A A A G A T G C G A T A G C G G T C T T A G A A C T T C C T G A A C C T T A T C G G A G A A G G C T T C G T A C T A C T A A T A T G T T A G A A C G G T T A A A T G A A G A A A T T C G T T G A T G T G A A A G A G T A A T A A G G A T A T T T C C C A G T C G A G A A T C T T C T A T T T G C C T A A T T G G A T C C T C A T T A A T G G A A C A A G A T G A A A A A T G G G C C T C A G G A A G A G A G T A T T T G G A C A C G A C T G A G T A T T T T G A G T A G
N
K
V
T
K
A
I
Q
V
L
E
E
G
F
K
D
A
I
A
V
L E L P E P Y R R R L R T T N M L E R L N E E I R * C E R V I R I F P S R E S S I C L I G S S L M E Q D E K W A S G R E Y L D T T E Y F E * |
Comments=Pseudogene, start/stop is absent | |
| or0960, or0961 | 981906 | 982632 | join (981906..982331, 982330..982632) | putative pseudogene |
a
t
g
a
a
a
c
t
a
a
a
a
a
t
t
a
t
t
g
t
g c c a a t t a c t t c a g a g g t a t t t a a t g a g g a a g t t a a a a a g g a a a t c a a a c a c t a t g t a g a t c c t g a t g a t t a t g t t g a t g t t g a a a a t t t g a a t t a t g g t c c g g c g t c c a t c g a g t g t g a a t a t g a t g a a g c t a t g g c t g t a c c a g a t a t c t t a a a t a a g g t a a a g a a a g c t c a a g a a g a a g g a t t t g a g g g t a t a g t t a t t g a t t g t t t t g g g g a t c c g g g g g t a c a t g c t g c a c g g g a a c t t g t t g a t a t a c c c g t t t g c g g t g g t t t t g a a c c t t c t a t g c a a a t t g c t t t a g g a c t t g g t c a a a a c a t t g g t g c t g t t a c a g t t t t g c c c a a t g t t a t t c c a a t g c t a c a c g a t t t a g t t g c c a a g a t g g g a a t a g a a a a g c g a a t a a a a g c a c t a c g a t a t a t t a a c a t t c c a g t a t t a g a t t t g g g c g a t a a g a a a a a a t t a g a a g a t g c c t t a t t c a a g g a a a g c t t a g a t g c a a t t c a a a a a g a a a a t g t t c a t g t t a t t g t a t t a g g t t g t a c t g g c a t g a t g g g a g t g g c t a a t a a t c t a a t g a a c a g g t t a a a a g a a g c t g g t t a t g a t g t t c c a g t a a t a g a c c c g g c c t t t g c t g c g g t a a g a a t g g t t a a a a c t t a t a t a c g c a t g g g a t t g a a g c a t a g c c g g t t g a c t t a c a t g a c t c c t c c t g c a a a a c c a t a t a c t t g g t g g g g a a a a t a g
M
K
L
K
I
I
V
P
I
T
S
E
V
F
N
E
E
V
K
K
E I K H Y V D P D D Y V D V E N L N Y G P A S I E C E Y D E A M A V P D I L N K V K K A Q E E G F E G I V I D C F G D P G V H A A R E L V D I P V C G G F E P S M Q I A L G L G Q N I G A V T V L P N V I P M L H D L V A K M G I E K R I K A L R Y I N I P V L D L G D K K K L E D A L F K E S L D A I Q K E N V H V I V L G C T G M M G V A N N L M N R L K E A G Y D V P V I D P A F A A V R M V K T Y I R M G L K H S R L T Y M T P P A K P Y T W W G K * |
Comments=For manual analysis, pseudo or ribosomal slippage, gene with one frameshift, more than 80% of the length of the second shortest homolog |
| or0961 - or0962 | 982714 | 983162 | complement (join (982714..982968, 982968..983138)) | pseudogene, missed gene |
C
A
A
A
T
T
A
A
A
G
A
A
G
T
C
T
T
A
A
G
T G C C A T T G A C T T A A T A G T A A T T G G A A T A A G C A G A A T T A T A G A T A C A G G T A T A T T T G T A A T T A C T A G T G T T G C T A C A A C T G A A A A A T T T T G T C T T G C A G T T G T G C T C T C A T A T A T T C T A G C A A G A T T A G C T T G T G C T T T T G C G G C A A T T T C T T A T G C A G A A T T G G C A T A C A T A T T T C C A A T T A T A G G T T C T A C C T A T A A C T A C A T C T A T A T G C T A A T G A A A A A A C T T A T T G C T T G G A C A A T A G G A T A G G A C T T A A T G C T T G A T T A C G T A T T T G C T C T T C T G G C A A T C T C T T T G G G C T G G T T T G T T T A T T A T T T C A C T A A C C T A A A T A T T A G T G C T G C T T T T A A A G C A T T T G T A C T T C T C T T T T T T G T C T T A G T C G A T A A A C C A C A T G T A A A A C C A G C T A A T T G G T A A
Q
I
K
E
V
L
S
A
I
D
L
I
V
I
G
I
S
R
I
I
D T G I F V I T S V A T T E K F C L A V V L S Y I L A R L A C A F A A I S Y A E L A Y I F P I I G S T Y N Y I Y M L M K K L I A W T I G * D L M L D Y V F A L L A I S L G W F V Y Y F T N L N I S A A F K A F V L L F F V L V D K P H V K P A N W * |
Comments=Pseudogene, start/stop is absent |
| or0993 - or0995, or0995 | 1014246 | 1014695 | join (1014246..1014326, 1014326..1014403, 1014402..1014695) | pseudogene |
a
t
g
a
g
c
c
t
c
a
t
t
a
t
g
a
t
t
a
c
a g g c g g t g c a a g g t c t g g c a a a a g t g a a t t t g c t g a a a a a t t g g c a t t g g a a a a g g a a g a g g a c a g c g t c c t t t a t a t a g c t a c t t c t a t t c c t t t t g a c g a a g a a a t g a a a a a a a g g a t c a a a a g g c a t a a a a a a a a g a g a c c a g c t t c a t g g c a g a c a a a a g t t t a t a a a a a t c t a a a c a a g g t a a t a g t g g a a a g c a a t g c a a a a g t t g t a t t a g t t g a c t g t c t t a c a g t t a t g a t t a c t a a t c t t t t a a t a g a a g t c g a t t t g a c t t g g c a a a a t a a t t t a a c t g c t t t t a t g a t a t a t g c a g a c t g c g g c a t t c a a a g a a t g c c t a a t g c t c a t t t g g a t a g c t t c a a a a t t g c t t t c t t t t g c a a a c a t t g t a a a a t t t t c a t a g a g a a a c t g g t a t t c a a a t c t t t a a t a a t a a a a a t t a t t t a a
M
S
L
I
M
I
T
G
G
A
R
S
G
K
S
E
F
A
E
K
L A L E K E E D S V L Y I A T S I P F D E E M K K R I K R H K K K R P A S W Q T K V Y K N L N K V I V E S N A K V V L V D C L T V M I T N L L I E V D L T W Q N N L T A F M I Y A D C G I Q R M P N A H L D S F K I A F F C K H C K I F I E K L V F K S L I I K I I * |
Maingene=or0995; Extension SUCCEEDED with start of type START; Comments=Pseudogene, >1 frameshifts |
| or1001, or1001 - or1002 | 1020741 | 1021384 | join (1020741..1020920, 1020920..1021099, 1021099..1021236, 1021236..1021289, 1021289..1021384) | pseudogene |
t
t
g
a
a
t
g
t
t
a
a
a
g
c
a
g
t
t
a
t
t t t c g a t t t a g a t g t a a c g c t a a t a g a t t c a a a a a a a g a t a t t g t t a t a g c t g c a a a t a a g g c a t t t a g t g a a t t t a a t c t t c c a a c t t t a c c t g a a a a a a c a t t a g c a t t t t t a a c t g c t a a c g g t g c t g a a g c a g t t a t a a a g t g t g g t t t g a g g g a a a a a a a t a t g c a t t t g t t t g a t a g a g t a t t c g g c a g a t t t g a a a a g a t t t a t g g c g a g t c c t g t a c t a a t t a t a c t t c t t t a t t t c c a g g a g t a a g a g a a a c t t t a a a c t t t t t a a a a g a a a g g a a a a t t a a t a t t g g a a t t g c t a c t c t t a a a t g c a g a a t t a t a a c a g a a a a g a t t t t a a a a c a t t t t a g a a t t g a g a a a t a t t t t t c a g c t g t a t t g t g c t t a g a a g a t g t c a a a a a t a t a a a a c c t c a t c c a g a a a t a a t a g a g a a g c t a t t g c a a a a a a t a a a t a a t g t t t c a g a g t a a a c t t t a t a c a t t g g g g g t t c t g a a g t t g a g g t t t t g t g t g g a a a a a a t g c a g g a g t t t a t a c t g t g c t g g t a a c a t a t g g a a c a g g a g a t t t a c a g t c t a t c g t t g c t c t g c a g c c a g a t t t t g t a a t t a c c g a c t t a a c a a a a t t a a t t g t t t t a g t a t c t t a g
L
N
V
K
A
V
I
F
D
L
D
V
T
L
I
D
S
K
K
D
I V I A A N K A F S E F N L P T L P E K T L A F L T A N G A E A V I K C G L R E K N M H L F D R V F G R F E K I Y G E S C T N Y T S L F P G V R E T L N F L K E R K I N I G I A T L K C R I I T E K I L K H F R I E K Y F S A V L C L E D V K N I K P H P E I I E K L L Q K I N N V S E * T L Y I G G S E V E V L C G K N A G V Y T V L V T Y G T G D L Q S I V A L Q P D F V I T D L T K L I V L V S * |
Maingene=or1001; Extension SUCCEEDED with start of type START; Comments=Pseudogene, >1 frameshifts |
| or1015, or1015 - or1016 | 1033437 | 1034231 | putative pseudogene |
T
T
G
G
G
C
A
G
C
T
T
T
A
T
T
T
G
G
T
G
C C C T T T T T G G T G T G C C C A A A T T T C A C T A T T T C A C T T T C A C A C T A G T T T C T A T G A C G A T G A T T C T T T A G A T G T C A A T G A C G C T A A A T C T G C T G C C G A G T T T A A A G A T T T G T A C G A T T C T A A A A C T T T A A T C C C T T C T C T T A A G G A A T T C T T T A A T T T A C A T C C T A T T T T C T C T T A T A G A T A C T T C T T A G G T G A C G C C G G G T T T G A T T C T T T T G A T A A T T A T A A A T A C T T G T T C T C A A A G C T T G G C A T A A T A C C T A T T A T C C C T A T T A A C C C T C G A A A T T C T A A A A A C T T A C T T C A A C C T A C T T T T A A C T C T G A T G G T A T C C C T A C C T G T C C C C G T G A C C C T T C T C T T A A A A T G T C C T A T G A T G G T A T C G T T C G G G A A A A A G G T A G A A C T A C C A G A A T T A A A T G G C T T T G C C C T A T G T C C A A A A A A G T T A G A C T A A A T G G T A A A A C T A C T T A T A T T C T T G A A T G T G A T A A C C C T T G T A C C T C T T C T A A A T G T G G C A G A A T A T T C T A T A C T A C C C T T G A T A T T G A T T T T A G A A A A A A T A C T G T T G T C C C T C G T A A C T C T A A A A A G T G G T C C A A A C T T T A T G A A A A A C G C C C T A T T A T T G A A A A A T C T A T T T C T C T T T T A A A A A G T T C T A T C G C T G T T G A T A G C T T T A A A C T C A T A A A T A C C A G G T C A A T C A A A G C T G A T G T T T T T C T T G G G G C T A T C A C T C A G C A T A T T G G T T T A A T T A T T A C T G C A A A G C T T G G T A C T T T T G A A C A T C C T T T A T C T T T G A A A A A A C T T T T G G C T T G A
L
G
S
F
I
W
C
P
F
W
C
A
Q
I
S
L
F
H
F
H
T S F Y D D D S L D V N D A K S A A E F K D L Y D S K T L I P S L K E F F N L H P I F S Y R Y F L G D A G F D S F D N Y K Y L F S K L G I I P I I P I N |