Pseudogenes for contig
| Features | Start | End | Frame Joins | Pseudo Tag | Seq | GenePRIMP Notes |
|---|---|---|---|---|---|---|
| or4694 - or4695, or4695 | 91482 | 92761 | complement (join (91482..91598, 91598..92761)) | putative pseudogene |
A
T
G
C
T
T
C
C
C
C
G
T
T
T
T
G
C
C
G
A
T A T T T T T C A G C A G G G A A A C C G C T G G C T T A A C T G G C T G G A G A A G C A G C C G G A A G G G T C T G T G C G T C C G G T G G T G A T T G A G T C G G T G A C A A A A A T C A T G G C G T G C G G G A C C A C G C T G A T G G G T T A C A C A C A G T G G T G T T G T T C C T C A C C G G A C T G T T G C C A C A C A A A A A A G G T C T G C T T C C G G T G T A A A A G T C G C T C C T G C C C G C A C T G C G G G G T G A A G G C T G G C G C A C A G T G G A T A C A G T A T C T G C T G A G T C T G G T T C C C G A C T G C C C G T G G C A G C A T A T T G T G T T C A C A C T T C C C T G C C A G T A C T G G T C C C T G A T A T T C C A C A A C C G G T G G T T G C T G G C A G A G A T G A G C C G T A T C G C A G C G A A T G T G A T A C T G G A A A T C T G C C G T C A G G C G G A C G T G G A G C C G G G G A T A T T C A C G G T A A T C C A C A C A T G G G G A C G A G A C C A G C A G T G G C A T C C G C A C A T A C A C C T G T C G A C A A C A G C C G G C G G T G T G A C G T C A G C T C A C A C C T G G A A A A A C C T T C A T T T T T A C G C C C G T A A G G T G A T G C G C A T G T G G C G T T A C C G G A T A A C G C G A T T A C T G T C C C G G A A A T A C C C G G A G C T G G T G A T A C C G G C T G A G C T G G C A G C A G A G G G A A G C G G C A G A C G G G A A T G G A A T C G C T T C C T G G A C A C C C A C T A C C G G C G T G G C T G G A A T G T C A A C G T A T C C C G G G T G A T G G A T A A C G C C A C G C A T G T G G C G G T G T A C T T T G G C T C T T A C C T G A A A A A G C C G C C G G T G C C A A T G G G C C G T C T G G A A C A C T A T G C C G G T C A G G A T G A A A T T G G T C T G C G T T A C A A C A G C C A C C G C A C A A A A C G G G A A G A A T A C C T G G T G A T G A G T G G C G A T G A G T T C A T G G A A A G G T T C T C G T G G C A T G T G G C G G A T A A G G G G T T C C G T A T G G T G A G G T A C T A C G G T T T C C T G A G T C C G T C G A A A C G G C G G T T A C T G G A A G A G G T G G T G T A C G T C A T A A C G G A G A C G G T G A G A A A A A C G G C G A T G C A A A T C A G G T G G A G A G G G A T G T A T C A G C G G T T A C T G A A G G T T G A C C C G C T G A A A T G C A T C C T G T G C G G A A G T C A G A T G C G G T T T A C G G G G C T G A A G C G G G G A T A C C A T C T G G C A G A G C T G A T T A T G A T G C A T G A G C C G C T G G G C C C G A A T G C A G T G T T G C G G C T G A G A G C C G C A G A G G G G A A G T T G C G T C C A T T T T A C G G G G A A C G G A G C A A A A A A A C A C C A T C C A T A C C C T T T A T C A A T C A G T G T T A T C C T G T T T A A
M
L
P
R
F
A
D
I
F
Q
Q
G
N
R
W
L
N
W
L
E
K Q P E G S V R P V V I E S V T K I M A C G T T L M G Y T Q W C C S S P D C C H T K K V C F R C K S R S C P H C G V K A G A Q W I Q Y L L S L V P D C P W Q H I V F T L P C Q Y W S L I F H N R W L L A E M S R I A A N V I L E I C R Q A D V E P G I F T V I H T W G R D Q Q W H P H I H L S T T A G G V T S A H T W K N L H F Y A R K V M R M W R Y R I T R L L S R K Y P E L V I P A E L A A E G S G R R E W N R F L D T H Y R R G W N V N V S R V M D N A T H V A V Y F G S Y L K K P P V P M G R L E H Y A G Q D E I G L R Y N S H R T K R E E Y L V M S G D E F M E R F S W H V A D K G F R M V R Y Y G F L S P S K R R L L E E V V Y V I T E T V R K T A M Q I R W R G M Y Q R L L K V D P L K C I L C G S Q M R F T G L K R G Y H L A E L I M M H E P L G P N A V L R L R A A E G K L R P F Y G E R S K K T P S I P F I N Q C Y P V * |
Maingene=or4695; 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 |
| or4694 - or4695 | 91388 | 91548 | complement (join (91388..91422, 91422..91452, 91454..91548)) | pseudogene, missed gene |
A
T
T
T
T
A
C
G
G
G
G
A
A
C
G
G
A
G
C
A
A A A A A A C A C C A T C C A T A C C C T T T A T C A A T C A G T G T T A T C C T G T T T A A T T G T C G T T T C C G T T C A T A T G G T G C A T A A G A G T G T T G A A G A A A T A T C C G T T T T G T G G T G T T T T T T T A A T C T T T T G G G G G T T T T A A T T C C T A T T G A
I
L
R
G
T
E
Q
K
N
T
I
H
T
L
Y
Q
S
V
L
S
C L I V V S V H M V H K S V E E I S V L W C F F N L L G V L I P I |
Comments=Pseudogene, abnormal start as well as frameshift |
| or4685 - or4686 | 83095 | 83208 | pseudogene, missed gene |
A
T
G
G
T
A
G
C
T
C
A
G
G
C
G
G
G
G
C
A
G G C A T T A G C C T G G C C G G T T T C C G A T G A C A C C G G T A T T C C T A C C C C C G T C T G G G C T A T C A C C A A T G A G C G T A G G A A C T C G G T G A T A G C G T T T T A A
M
V
A
Q
A
G
Q
A
L
A
W
P
V
S
D
D
T
G
I
P
T P V W A I T N E R R N S V I A F * |
Comments=Pseudogene, good start found, extended gene length<=100aa and < 70% the length of the second shortest homolog | |
| or4686 - or4687 | 85688 | 85939 | complement (join (85688..85789, 85792..85878, 85877..85939)) | pseudogene, missed gene |
G
T
G
C
G
C
G
G
T
C
G
G
A
G
T
G
G
T
C
C
C G A C A A G G G T T T A C C C G C A G T C G G G G C G T A T C T C C G C G T T A G C G C G G G C C G T C A G G G C C G C T T A C G A G C G T G T A C T G A G G A C T T C C A G C C A G A A G A C T G G C A G C G A T G A C A A T G T A G T T A C A A C A T T C A T T T A A A A G C G A T G T T G T T C C C G C C C T T C G G G C G G G G G C G G C C T C G C T T T T C A G T T A T G A G G G G T G G G T A C G G T G C T G C G T T T G T G T G G T G T T T T T A T T C C T G A
V
R
G
R
S
G
P
D
K
G
L
P
A
V
G
A
Y
L
R
V
S A G R Q G R L R A C T E D F Q P E D W Q R * Q C S Y N I H L K A M L F P P F G R G R P R F S V M R G G Y G A A F V W C F Y S * |
Comments=Pseudogene, >1 frameshift are present |
| or4694, or4694 - or4695 | 90699 | 91394 | putative pseudogene |
A
T
G
T
C
T
G
A
C
C
C
T
G
T
A
C
G
T
A
T
T A C A A A T C C C G G T G C A G A A T C G C T G G G G T A T G A T T C A G A T G G C C A T G A A A T T A T G G C C G T T G A T A T T T A T G T A A A C C C T C C A C G T G T C G A T G T C T T T C A T G G T A C C C C G C C T G C A T G G A G T T C C T T T G G G A A C A A A A C C A T C T G G G G C G G A A T C G A G T G G G T C G A T G A T T C C C C A A C C C G A A G T G A T A T C G A A A A A A G G G A C A A G G A A A T C A C A G C G T A C A A A A T C A C G C T C A G C G C G C A G C A G A A A G A G A A T G A G A A T A A G C G T A C T G A A G C C G G A A A A C G C C T C T C T G C G G C G A T T G C T G C A A G G G A A A A A G A T G A A A A C A C A C T G A A A A C A C T C C G T G C C G G A A A C G C A G A T G C C G C T G A T A T T A C A C G A C A G G A G T T C A G A C T C C T G C A G G C A G A G C T G A G A G A A T A C G G A T T C C G T A C T G A A A T C G C C G G A T A T G A T G C C C T C C G G C T G C A T A C A G A G A G C C G G A T G C T C T T T G C T G A T G C T G A T T C T C T T C G T A T A T C T C C C C G G G A G G C C A G G T C G T T A A T C G A A C A G G C T G A A A A A C G G C A G A A G G A T G C G C A A A A C G C A G A C A A G A A G G C C G C T G A T A T G C T T G C T G A A T A C G A G C G C A G A A A A G G T A T T C T G G A C A C G C G G T T G T C A G A G C T G G A A A A A A A T G G C G G G G C A G C C C T T G A T C A A T A G
M
S
D
P
V
R
I
T
N
P
G
A
E
S
L
G
Y
D
S
D
G H E I M A V D I Y V N P P R V D V F H G T P P A W S S F G N K T I W G G I E W V D D S P T R S D I E K R D K E I T A Y K I T L S A Q Q K E N E N K R T E A G K R L S A A I A A R E K D E N T L K T L R A G N A D A A D I T R Q E F R L L Q A E L R E Y G F R T E I A G Y D A L R L H T E S R M L F A D A D S L R I S P R E A R S L I E Q A E K R Q K D A Q N A D K K A A D M L A E Y E R R K G I L D T R L S E L E K N G G A A L D Q * |
Maingene=or4694; 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 | |
| or4663 - or4664 | 63239 | 63292 | pseudogene, missed gene |
T
T
G
T
G
T
T
G
T
G
G
T
G
A
G
A
A
T
A
T
C A C C T T T C A T C A G G T G G C C A A A T T T A G T G T G C C A
L
C
C
G
E
N
I
T
F
H
Q
V
A
K
F
S
V
P
|
Comments=Pseudogene, start/stop is absent | |
| or4669 - or4670 | 68530 | 68661 | pseudogene, missed gene |
G
G
C
G
T
C
G
A
C
C
G
C
G
A
T
A
T
C
A
A
T G C G G C A C T C A A C A T C C G G C A A A A A G G A A T A C T G G A A C T A A A G G C G G C G G G A C T C G T C G T C T C T G C C T A T G G A G G C C A G C G T A A A T C C G T C G C A C A G A C G G T T G C G G C C T G A
G
V
D
R
D
I
N
A
A
L
N
I
R
Q
K
G
I
L
E
L
K A A G L V V S A Y G G Q R K S V A Q T V A A * |
Comments=Pseudogene, start/stop is absent | |
| or4660 - or4662, or4662 | 62048 | 62794 | putative pseudogene |
T
T
G
T
G
C
A
G
C
G
A
A
A
T
A
C
G
C
C
G
G G C G T G G A A C C A A A G T C G G G G C T C T G C G G G C G C G C G C A C T C T G G C T G A A A T G C T G A C T C A A A A C G G C G T C C C G A T G A G C C G T T A C C G T G C C G G A C G T C T G A T G A A A T A T C T G A A C C T G A G C A G T T G T C A G C C C G G A A A A C A T C A G T A T A A A A A T G C C C G T C A G G A G C A T A C C A G C C T G C C G A A T C T G C T T G A G C G T C A G T T C G C A G T A C C G G A G C C A G A C C G G G T A T G G T G T G G A G A T A T T A C G T A T C T C T G G G C A G G A A A T C G C T G G T G C T A T C T G G C G G T T G T T A T G G A T C T T T T T G C C C G C A G G G T T A T C G G C T G G A G T C T G T C A G C G C A T G C C G A T A C C G C A C T G A T A A G C A G T G C C C T G C G G A T G G C C T A T G A G A C G C G T G G C C A A C C C C G G G A T G T C G T G T T C C A T A G C G A C C A G G G A A G C C A G T A T A C A G G C C T T A A A T A T C A A C A A C T T C T C T G G C G T T G C A G A A T A A A T C A A A G C G T C A G T C G G C G G G G A A A C T G C T G G G A T A A C A G C C C C A T G G A A C G C T T C T T C C G C A G T C T G A A A A C A G A A T G G G T G C C A A C G A A T G G T T A C G C A G G C A A G G A C G A G G C C C G G C A G C A A A T T A A T G A T T A C A T A T T G A A C T A C T A C A A C A G C G T C A G A C C T C A C C A T T A T A A C G G T G G G C T G A C G C C G G A A G A G T C A G A G A A C A G A T A C C A T T T T T A C T G T A A A A C C G T G G C C A A T A T T A C T T G A
L
C
S
E
I
R
R
A
W
N
Q
S
R
G
S
A
G
A
R
T
L A E M L T Q N G V P M S R Y R A G R L M K Y L N L S S C Q P G K H Q Y K N A R Q E H T S L P N L L E R Q F A V P E P D R V W C G D I T Y L W A G N R W C Y L A V V M D L F A R R V I G W S L S A H A D T A L I S S A L R M A Y E T R G Q P R D V V F H S D Q G S Q Y T G L K Y Q Q L L W R C R I N Q S V S R R G N C W D N S P M E R F F R S L K T E W V P T N G Y A G K D E A R Q Q I N D Y I L N Y Y N S V R P H H Y N G G L T P E E S E N R Y H F Y C K T V A N I T * |
Maingene=or4662; 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 | |
| or4628, or4628 - or4629 | 28167 | 28433 | putative pseudogene |
A
T
G
A
G
A
C
C
A
T
C
A
A
T
T
A
T
C
T
T
C G C A A C C G C C G A G T A T G T A A A G C G T C T G C G T G A A G A G T G C C T G C G G G A G A A T A A A C C C C T G C A C C G C C A T A C C C G C T T C A G A C G T C A G G A G C T G G C A C A G G A T G A G A T T A A C C C G G A C G T C C T G G C G A T G A G C G G A C A T A T T G C C A G A C G C T G C A G T G A G C A G A A G C G G G T G C G T A T C C C C G C C A T G A A A G T C A G C G A A T G G G G C C A C C T G C T C C G C G C G C T T G A A A T T G A G C G G G T C T G C C A C T G A
M
R
P
S
I
I
F
A
T
A
E
Y
V
K
R
L
R
E
E
C
L R E N K P L H R H T R F R R Q E L A Q D E I N P D V L A M S G H I A R R C S E Q K R V R I P A M K V S E W G H L L R A L E I E R V C H * |
Maingene=or4628; Extension FAILED; Comments=For manual analysis, pseudo, failed extension, extended gene length<=100aa and < 90% the length of the second longest homolog | |
| or4631 - or4632 | 30092 | 30303 | complement (join (30092..30169, 30171..30221, 30223..30303)) | pseudogene, missed gene |
T
T
G
A
C
G
C
C
A
G
C
G
G
C
A
A
A
A
A
G
T T T T G T G G C T G G T A C A T C T C T C C C C T G G A C G A C T G A A A C G G G A T G T G G T C G T G T A T G T A C C C C C G G A A A G T C C G T C T G C G G A G A A C A G G C C G C A G T G C G G C G G C A G A C A G G C A G A G A C A G C T G C G C C A T C A G G C G C A G T G G C C T T A C A C A C C G T A A G G T G T G C A G G G A G C G C C G C A T C C G G C G C G A C T G A
L
T
P
A
A
K
S
F
V
A
G
T
S
L
P
W
T
T
E
T
G C G R V C T P G K S V C G E Q A A V R R Q T G R D S C A I R R S G L T H R K V C R E R R I R R D * |
Comments=Pseudogene, >1 frameshift are present |
| or4638 - or4641, or4641 | 41598 | 41774 | putative pseudogene |
A
T
G
A
A
T
C
T
G
G
T
A
G
A
C
G
C
C
T
T
T G T C A A A A A A G T A A T A T C C G G G C C A T A T A A A G A A T A T G G A A A A T G G T G G A T A G A T G T T G A A T A C A T T T C A T G G G G C G T T C C C G G G A A A A C A A G A C T G A T G T T T G A G T C A A A G G A G C A G G C A C T G G A A G T T A A A G A A G G G T A C A A A T T T T T A A C G T G A
M
N
L
V
D
A
F
V
K
K
V
I
S
G
P
Y
K
E
Y
G
K W W I D V E Y I S W G V P G K T R L M F E S K E Q A L E V K E G Y K F L T * |
Maingene=or4641; Extension FAILED; Comments=For manual analysis, pseudo, failed extension, extended gene length<=100aa and < 90% the length of the second longest homolog | |
| or4660, or4660 - or4662 | 61498 | 61782 | pseudogene |
A
T
G
G
C
C
T
G
G
G
C
T
G
T
C
C
T
G
T
C
A C T G T T G C A G T T C A T T C T G G T T C A G G T T C T G G T C A G A A C A A A T G A C G G T G G T C G T A A A G C C G T C C G G G A A T A T A T C G T C A T T A A C G A T G A G C T T C G C G A C A A T C T T T C C G G A A T G C C G C A T G C A G A G T G G G G G C A T C A C A T T G A T G C C A T A A T C C G G C A G G A G A A G C G C C G T A T C C G G G A C C A G A T T C T G G A A A T G T A T A T C C G G A A T G A A G T T G A C C G A A G A G A A G C G A T T C T T T T T A T C C C G C C A G G G G A G T T A C G G T C A T G A
M
A
W
A
V
L
S
L
L
Q
F
I
L
V
Q
V
L
V
R
T
N D G G R K A V R E Y I V I N D E L R D N L S G M P H A E W G H H I D A I I R Q E K R R I R D Q I L E M Y I R N E V D R R E A I L F I P P G E L R S * |
Maingene=or4660; Extension FAILED; Comments=Pseudogene, failed extension, extended gene length<=100aa and < 70% the length of the second shortest homolog For manual analysis, Examine as broken gene, potential fragments are | |
| or4624 - or4625 | 25466 | 25884 | complement (join (25466..25552, 25552..25644, 25643..25777, 25777..25884)) | pseudogene, missed gene |
C
T
G
C
G
C
C
A
T
C
A
G
G
C
G
C
A
G
T
G
G C C T T A C A C A C C G T C A G G T G T G C A G G G A G C G C C G T T T C C G G C G C G A C A G G G G C G G C G C G A C C G G A A C G G T C G C T G C A A G C C T G G T T T T T T C A G A C A T C G G A C C G T A G C G G C A G C C C G A A A C C G C G C C A G C G G G T T C G G C G G A G A C T G G C G G G T G C G C C A G C A G C T G C C T G T C G G A G T C G G G C C T G A C G A C C G G A T G C C G C C A G G C A G C C G G G A G C C G A A G G T G T G T C C C C G C C T C C G G A A A T C A G A A C A A C A G A A A C G A C A T A A C A G A A A A A T G C C T C A C A C C A T G A C G G G C A G G A A G G G C A G C G C C G C A G G C G C G G G C C C T C C T G C A T T T C A G G C A G G C G T A A G C C T G C C A G G G T T T T C C G G C G G C C T G G C A G G C C A T A C C C C C G C C G G A G C G G G G G A G T A A
L
R
H
Q
A
Q
W
P
Y
T
P
S
G
V
Q
G
A
P
F
P
A R Q G R R D R N G R C K P G F F R H R T V A A A R N R A S G F G G D W R V R Q Q L P V G V G P D D R M P P G S R E P K V C P R L R K S E Q Q K R H N R K M P H T M T G R K G S A A G A G P P A F Q A G V S L P G F S G G L A G H T P A G A G E * |
Comments=Pseudogene, abnormal start as well as frameshift |
| or4627, or4627 - or4628 | 27639 | 28073 | putative pseudogene |
A
T
G
A
C
T
G
T
C
A
G
C
A
G
C
A
C
G
A
T
T T C C G T T T T T T G C C G C G A C G G G G T G T T C C G T A C T G T T T A C T G C C A C C T G C A C G G T G A G C C G A C C T G G A A C G G T C G C A T C C T G C A T A C C C A C T A T G C C A C C G G T C A G C A G G C C G A A G C C C T G G T T G A A C A C G G T G A T A T C C G T T G C C T C G G T C C C C G T T G C G A C A A A C C C G C C G G G C A T A C G C T T C A G A A C C C G G T G G A C G G T G T G A C G G C T T A T T A C G G A C G T G A C A G T G G T T T C C G G A T G G A C A G T G A A G C G C G T G A G T A C C G T T C T T T C A T G G A G G C C A T C G C C A C G G A A A G C A C T G A A G A G G T G C G C T T T C A T T A T G T G T T C A T C G A C G G C T A C T G G A A G G T G A T G T A C C G C A C G C C G G A A G G C T G G A A G A T G A A G T C G C T C G C G C T G G C A C T G C G C C G C T G T C C G A A A T G A
M
T
V
S
S
T
I
S
V
F
C
R
D
G
V
F
R
T
V
Y
C H L H G E P T W N G R I L H T H Y A T G Q Q A E A L V E H G D I R C L G P R C D K P A G H T L Q N P V D G V T A Y Y G R D S G F R M D S E A R E Y R S F M E A I A T E S T E E V R F H Y V F I D G Y W K V M Y R T P E G W K M K S L A L A L R R C P K * |
Maingene=or4627; 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 | |
| or4627 - or4628, or4628 | 28167 | 28433 | putative pseudogene |
A
T
G
A
G
A
C
C
A
T
C
A
A
T
T
A
T
C
T
T
C G C A A C C G C C G A G T A T G T A A A G C G T C T G C G T G A A G A G T G C C T G C G G G A G A A T A A A C C C C T G C A C C G C C A T A C C C G C T T C A G A C G T C A G G A G C T G G C A C A G G A T G A G A T T A A C C C G G A C G T C C T G G C G A T G A G C G G A C A T A T T G C C A G A C G C T G C A G T G A G C A G A A G C G G G T G C G T A T C C C C G C C A T G A A A G T C A G C G A A T G G G G C C A C C T G C T C C G C G C G C T T G A A A T T G A G C G G G T C T G C C A C T G A
M
R
P
S
I
I
F
A
T
A
E
Y
V
K
R
L
R
E
E
C
L R E N K P L H R H T R F R R Q E L A Q D E I N P D V L A M S G H I A R R C S E Q K R V R I P A M K V S E W G H L L R A L E I E R V C H * |
Maingene=or4628; Extension FAILED; Comments=For manual analysis, pseudo, failed extension, extended gene length<=100aa and < 90% the length of the second longest homolog | |
| or4617 - or4618 | 19423 | 19504 | join (19423..19437, 19436..19504) | pseudogene, missed gene |
A
T
G
C
G
T
G
A
A
A
A
C
C
C
G
C
G
G
C
T
T G C A G C G A C C G T T C C G G T C G C G C C G C C C C T G T C G C G C C G T G A C C T G C G C T C C C T G C A C A C C T G A
M
R
E
N
P
R
L
A
A
T
V
P
V
A
P
P
L
S
R
R
D L R S L H T * |
Comments=Pseudogene, gene with one frameshift, less than 80% of the length of the second shortest homolog |
| or4623, or4623 - or4624 | 23905 | 24501 | putative pseudogene |
A
T
G
A
T
G
A
A
A
T
C
A
G
A
C
G
A
A
C
A
A T A T C A G G T T C C C G T G T G G A T G C G A C C T C T G T T G C C G T T G C T C T G C A A T A C C G G T G G T A A T G A T C C G G A G G A A C T G C T G A A T G A T A C A G A A A C C A C C G C C A G T G C G A A T A T T G T C C G T T A T G T A C T G A T A G T T G C A G T G C G G T C G C A G A T T G A T C T G C T G C A G C T A C T G T A C A G G A A A G G A C T G T T G C G C A C A G A G A T A C C A G G T G G C T T T T C A C C G G A A G A A G C G C A G G A A C T C C T G G A T A A T C T G G T G C G C A G C C A T A T C A G C A A G G C G C T G T C G G G T G A G C G A A T G G C A G C C C G T G A C A G A A A T G C C G A T C T G A C C T G G A T T C G C C A G C A A C T G G T C G A T G C C G C C T G G T T T G T C C G T G C C A C A C T G G A A G C G C A T A G G A T G G G C G T C G G A A A T G A G A G T C C C T C T G C T C C G C C G G A G A C A A T G C C G G A C A T A C A G A C A C G G G A A C T G G T T A T G T T G A T C A A G C G A C T G G C A T C A T C G C T G A A A G C G G T G A A A C C C G A C A G T A G C G T G G T G C G T G A A G C G C A G G A C T G G C T G T G C G A C A G A A A A C T T G T G G A T A T C A C A G A T A T T C T C C G G T G A
M
M
K
S
D
E
Q
Y
Q
V
P
V
W
M
R
P
L
L
P
L
L C N T G G N D P E E L L N D T E T T A S A N I V R Y V L I V A V R S Q I D L L Q L L Y R K G L L R T E I P G G F S P E E A Q E L L D N L V R S H I S K A L S G E R M A A R D R N A D L T W I R Q Q L V D A A W F V R A T L E A H R M G V G N E S P S A P P E T M P D I Q T R E L V M L I K R L A S S L K A V K P D S S V V R E A Q D W L C D R K L V D I T D I L R * |
Maingene=or4623; 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 | |
| or4617, or4617 - or4618 | 18906 | 19097 | putative pseudogene |
A
T
G
A
A
T
A
T
C
A
G
C
A
C
A
G
A
A
A
C
C C G C G A A A T T C T G C G C A A T T A C A A A G C C G T G A T T A A T G C G C G G C G T C G T G A A A T G G G G C A G A A A C C G C T C A C C A C T G C G C A G A T T G T T G A T G A A A T C T G C G A T T T T G T G G C G A A T C A G C A G G C G G T T T T C C T C G G T G G T C A C T A T A T C C T T C A G G G C A G C A G A A A C C G G T G A
M
N
I
S
T
E
T
R
E
I
L
R
N
Y
K
A
V
I
N
A
R R R E M G Q K P L T T A Q I V D E I C D F V A N Q Q A V F L G G H Y I L Q G S R N R * |
Maingene=or4617; Extension FAILED; Comments=For manual analysis, pseudo, failed extension, extended gene length<=100aa and < 90% the length of the second longest homolog | |
| or4599 - or4600 | 6426 | 6617 | putative pseudogene, missed gene |
A
T
A
A
T
A
A
G
T
A
G
C
C
A
T
A
T
A
G
A
A A C G C A G T T A A A T T A C C G G A G A G C C G T T T C C G T C A T A T C C G A C T T T C T G A A A T A T C A C A A C T T T C C G G A A G T G T A C C A C G C T G A G A A A A T C A T C A T A T C A C T G T T T T C C G C C C C T G C G C G G C G C A T C A C A G G T C A G G G A G A T G A C A C A A C A T A T A G T G T C A T T A G T A G C T G A
I
I
S
S
H
I
E
T
Q
L
N
Y
R
R
A
V
S
V
I
S
D F L K Y H N F P E V Y H A E K I I I S L F S A P A R R I T G Q G D D T T Y S V I S S * |
Comments=For manual analysis, pseudo or non-canonical start codon, extended gene length > 80% the length of the second shortest homolog | |
| or4610 - or4611 | 15116 | 15322 | pseudogene, missed gene |
G
T
G
G
A
A
T
A
C
C
G
C
A
G
C
C
G
T
C
G
T C T T T C T G A C G G C A A G G T T A T G C C G C G A A A G C G G C T T G A A G G G C G T T C A T C A G A A A A G G G C G A C G G G C T G G C G T A C A C T G T C A C C G A C G C C A G C C G G G A G C G G T A A A A G C G C C C G T C C C G T G C C C G C C G G A C G C G G G A C A C T G A C C A C A G G C A G C G T T T A T G C C G C G C C G C G T C A G C C G G C G C A G T A
V
E
Y
R
S
R
R
L
S
D
G
K
V
M
P
R
K
R
L
E
G R S S E K G D G L A Y T V T D A S R E R * K R P S R A R R T R D T D H R Q R L C R A A S A G A V |
Comments=Pseudogene, TAA stop codon in frame | |
| or4614 - or4615, or4615 | 17836 | 18440 | join (17836..17931, 17931..18440) | putative pseudogene |
G
T
G
A
T
T
T
T
C
C
G
G
T
C
G
T
T
C
G
C
C C G C T C A G G T T T C G C G G T C T C A C C C T G C A A C T C C C G C C A G C C G T G T G C G T C A G G C T G C G G C T T C C C T T G C G C C C C T T G C A T C C C C G C C T T A T C G C C C G G C T T T T A T G G A G G C A C G G C A C C G C C C G G T G T C G C G G A A T A T G T G A A C A A C G G A G G A A A T C C C A T G C A G T A T G C G A A A C C T G T C A C T C T G A A T G T T G A A G A G T G C G A T C G T C T G T C T T T T C T G C C T T A C C T G T T T G G C C T G G A T T T T C T G T A T G C C G A A G C G T C T G T G T A C G C G C T G G C G A A A C A A A T G A T G C C G G A A T A T G A A G G C G G C T T C T G G C A C T T C A T C C G C C T G C C G G A C G G T G G C G G T T A C A T G A T G C C G G A T G G C G A C C G T T T C C A C A T G G T G A A C G G T G C A A A C T G G T T T G A C C G T A C C G T G A G T G C T G A T G C C G C A G G C A T C A T C C T T A C C T C T C T T G T G A T T A A C C G C C A G T T G T G G C T G T A C C A C G A C A G C G G T G A T G C A G G A C T G A C C C A G C T T T A C C G G A T G C G C G A T G C G C A G T T G T G G C G T C A C A T C G A A T T T C A C C C C G A A T G C A A C G C G A T T T A C G C G G C T C T G G A C T G A
V
I
F
R
S
F
A
R
S
G
F
A
V
S
P
C
N
S
R
Q
P C A S G C G F P C A P C I P A L S P G F Y G G T A P P G V A E Y V N N G G N P M Q Y A K P V T L N V E E C D R L S F L P Y L F G L D F L Y A E A S V Y A L A K Q M M P E Y E G G F W H F I R L P D G G G Y M M P D G D R F H M V N G A N W F D R T V S A D A A G I I L T S L V I N R Q L W L Y H D S G D A G L T Q L Y R M R D A Q L W R H I E F H P E C N A I Y A A L D * |
Maingene=or4615; 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 |
| or4595 - or4596 | 2440 | 2583 | putative pseudogene, missed gene |
A
T
G
A
A
G
T
A
C
A
G
C
C
C
C
G
G
G
A
A
T G G C T C C G G G C T G A T T C A G G T T C T G A T T C G C T G T C A G C C C G C G T G G T G G C T G G C C T G G C T C A T T T C C T G T C G T C A G G C G T T C A A C T C C C G A C T G C A G A T T A T G G C A C G C T G C A A G A A C A C C T G A
M
K
Y
S
P
G
N
G
S
G
L
I
Q
V
L
I
R
C
Q
P
A W W L A W L I S C R Q A F N S R L Q I M A R C K N T * |
Comments=For manual analysis, pseudo, good start found, extended gene length<=100aa and < 90% the length of the second longest homolog | |
| or4595, or4595 - or4596 | 843 | 2426 | putative pseudogene |
A
T
G
G
A
T
A
T
C
T
C
G
C
T
T
C
T
C
A
G
T A C C A C C C G T G A C C C T G A A C A G C T T C G C G C T C T G G C A A T T G C C A T G G T G C A A A A A G C C A T G G C T G A G A G C C A G A A T C T T G C A A A T G T G G T G C A G G A A A A A G A C C G G A A T A T T G C A G A A C T T C A G A A C C G T A T C C G C A T C C T G G A A G A G C A G A T G A A G C T C G C A C G C C A G C A G C G T T T T G G T A A A A A A T G C G A A T C G C T G G C C G G G A T G C A A C G T T C C C T G T T T G A A G A G G A T G T T G A C G C G G A T A T C G C A G A A A T C T C G G C G C A T C T G G A C A A A C T G C T T C C T C A G A C C G G G G A C G A A G A A A A A A C A A C A A C A C G T C C T G T T C G T A A G C C C T T G C C T T C A C A T C T T C C C C G T G C T G A A A A G G T T A T C C C G C C A G C T G A G G A A C G T T G T C C T G A C T G T G A T G C C C C C C T G C A C T T C A T T C G C G A T G A A G T C A G C G A G A A G C T G G A A T A T A T C C C C G C A C A G G T T G T G G T C C A C C G C T A T A T C C G C C C G C A G T A C A G C T G T C C C T G C T G T G A G A A A G T G T T C A G C G G A A A A A T G C C G G C A C A T A T C T T T C C G A A A A G T G C T G T T G A G C C A T C G G T C A T C G C A C A G G T T G T C A T C A G C A A A T A T A C C G A C C A T C T G C C C C T G T A T C G C C A G C A G C A C A T T T T C T C C C G A A T G G G T G T G G A G C T C C C C G T C A G T A C A A T G G C G G A T A T G G T C G G T G T T G C T G G C G C T G C A C T G G C C C C G C T G G C A A A A T T G T T A C G C C A C G A G C T T C T G A C A C G G G A T G T T A T T C A T G C T G A T G A A A C G T C C C T G A G G C T C C T T G A T A C C C G G A A A G G T G G T A A A T C C T G C T C C G G C T G G C T G T G G G C T T A C G T C A G C G G T G A A A G A A G C G G T C C G C C G G T C G T C T G T T T T G A C T C G C A G A C C G G G C G G G C C C T C A G A T A T C C T G A G G C C T G G T T G C A G G G C T G G C A T G G C G G T A C G C T G G T G A G T G A C G G G T A C A A C G T G T A C A A A T C T C T G G C G G A T A A T C A C C C A G G T A T C A C A T C T G C C T G T T G C T G G A G C C A C G C A A G G C G C G G C T T C G C A A A T C T G T A C A A G G C C A G C A G G G A G C C C C G T G C A G C C A T G G C G C T G A G A A A A A T C G C C G G T C T T T A C C G T A T T G A G A A G C T C A T C C G C G A T C G T C C T G T G G A A A A A A T A C G G C A A T G G C G A C A A C G G T A T T C C C G G C C G A T A G T G A A T G A C C T G T T T G C C T G G C T T G A A G A G C A G G A G C C G T G C T G T C C G C C C G A C G G A C C A C T A A A T A A A G C G A T T A A C T A T A T C C T G A A C C G G C G C G A T G A A C T G A G C T G C T T C C T G G G T G A C G G A G C C G T G C C C C T G G A C A A T A A T A T C T G C G A G C G T G C C A T T C G C C C G G T G G T C A T G G G G C G G A A A G C A T G G T T A T T C G C A G G T T C A C T G A T G G C C G G G A A C C G C G C G G C A C A G A T A A T G A G C C T T C T G G A A A C G G C A A A A C G T A A T G G T C T G G A G C C A C A T G C C T G G C T G A C A G A C G T C C T G G C G C G T C T G C C G G A A T G G C C A G A G G A G C G A C T G G C A G A G T T G C T G C C C C T T G A G G G A T T T A C C T T C T C C G G G T G A
M
D
I
S
L
L
S
T
T
R
D
P
E
Q
L
R
A
L
A
I
A M V Q K A M A E S Q N L A N V V Q E K D R N I A E L Q N R I R I L E E Q M K L A R Q Q R F G K K C E S L A G M Q R S L F E E D V D A D I A E I S A H L D K L L P Q T G D E E K T T T R P V R K P L P S H L P R A E K V I P P A E E R C P D C D A P L H F I R D E V S E K L E Y I P A Q V V V H R Y I R P Q Y S C P C C E K V F S G K M P A H I F P K S A V E P S V I A Q V V I S K Y T D H L P L Y R Q Q H I F S R M G V E L P V S T M A D M V G V A G A A L A P L A K L L R H E L L T R D V I H A D E T S L R L L D T R K G G K S C S G W L W A Y V S G E R S G P P V V C F D S Q T G R A L R Y P E A W L Q G W H G G T L V S D G Y N V Y K S L A D N H P G I T S A C C W S H A R R G F A N L Y K A S R E P R A A M A L R K I A G L Y R I E K L I R D R P V E K I R Q W R Q R Y S R P I V N D L F A W L E E Q E P C C P P D G P L N K A I N Y I L N R R D E L S C F L G D G A V P L D N N I C E R A I R P V V M G R K A W L F A G S L M A G N R A A Q I M S L L E T A K R N G L E P H A W L T D V L A R L P E W P E E R L A E L L P L E G F T F S G * |
Maingene=or4595; 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 | |
| Features | Start | End | Frame Joins | Pseudo Tag | Seq | GenePRIMP Notes |
Help
A pseudogene may be detected during any of the following processes:
- Gene extension: An attempt to extend a gene on one or both sides based on evidence from homologs. If the extension is successful, the modified gene may be classified as a pseudogene. If the extension is unsuccessful, the existing gene may be classified as a pseudogene.
- Gene joining: An attempt to join two or more genes into a single when there is strong evidence to suggest that these are part of a single gene. Here, the newly formed longer gene may be classified as the pseudogene.
- Gene insertion: An attempt to insert a new gene in an intergenic region where no genes have been called, but which has good hits to a conserved sequence. Here, the newly inserted gene may be classified pseudogene.
- Pseudo Tag: This column indicates the kind of process during the course of which the pseudogene was identified. "pseudogene" and "putative pseudogene" denote pseudogenes detected during "gene extension (1 above)" or "gene joining (2 above)". "pseudogene, missed gene" and "putative pseudogene, missed gene" denote pseudogenes detected during insertion of a new gene.
- Features: This column indicates the region in the genome over which the pseudogene is found. An intergenic region between genes 'g1' and 'g2' is denoted by 'g1-g2'. If the pseudogene is discovered during gene insertion, this column contains the intergenic region in which the pseudogene was found. If the pseudogene is discovered during gene joining, this column contains the candidate genes and surrounding intergenic regions that were joined to form a single gene (pseudogene). If the pseudogene is discovered during gene extension, this column contains the region over which gene extension was attempted. For example, "or0740-or0741,or0741,or0741-or0742" indicates that an attempt was made to extend 'or0741' on both ends, using both flanking intergenic regions. The column GenePRIMP Notes indicates whether extension suceeded or not. In case of successful extension, coordinates of the modified gene are reported in the Start, End, and Frame Joins columns. Otherwise, coordinates of the original gene are reported.
- GenePRIMP Notes: This column explains why the gene was classified as a 'pseudogene' or 'putative pseudogene'. In the case of gene extension, it also indicates whether the extension succeeded.
- Seq: This column contains both the nucleotide and the amino acid sequences for the pseudogene.
