Table 1 |
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|
A summary of the 40 observed exceptions |
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|
Non- |
Alternative |
JEC21/alt boundary |
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|
Int |
conserved |
In Frame |
Presence/Absence |
Frame |
|||||
|
Gene |
# |
Boundary |
Boundaries |
JEC21 |
H99 |
R265 |
WM276 |
shift |
Comments |
|
|
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|
Conserved alternative boundary |
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|
CNA00590 |
1 |
5' |
-6 (GTGAGT) |
+/+ |
+/+ |
-/+ |
-/+ |
Yes |
cDNA supporting alternative boundary |
|
CNA03150 |
3 |
3' |
-9 (CAG) |
+/+ |
-/+ |
-/+ |
-/+ |
Yes |
|
|
CNC00370 |
9 |
5' |
+3 (GTGAGT) |
+/+ |
-/+ |
-/+ |
-/+ |
Yes |
cDNA supporting intron ret. |
|
CNC01260 |
8 |
3' |
+6 (TAG) |
+/+ |
+/+ |
-/+ |
-/+ |
Yes |
cDNA supporting alt boundary, intron ret. |
|
CND02500 |
1 |
3' |
+6 (TAG) |
+/+ |
+/+ |
-/+ |
-/+ |
Yes |
cDNA supporting out-of-frame boundary |
|
CND03170 |
8 |
5' |
+6 (GTAAGT) |
+/+ |
+/+ |
-/+ |
+/+ |
Yes |
|
|
CND03550 |
1 |
3' |
+6 (CAG) |
+/+ |
-/+ |
+/+ |
+/+ |
Yes |
Fig 2A |
|
CND03880 |
7 |
3' |
-3 (CAG) |
+/+ |
+/+ |
-/+ |
-/+ |
Yes |
|
|
CND04350 |
1 |
3' |
+9 (C/TAG) |
+/+ |
-/+ |
-/+ |
-/+ |
Yes |
|
|
CNE00380 |
3 |
3' |
+3 (C/AAG) |
+/+ |
-/+ |
-/+ |
-/+ |
No |
cDNA supporting alternative boundary |
|
CNE01370 |
3 |
3' |
+9 (CAG) |
+/+ |
+/+ |
+/+ |
-/+ |
Yes |
|
|
CNF02810 |
9 |
3' |
+9 (C/TAG) |
+/+ |
+/+ |
-/+ |
-/+ |
Yes |
|
|
CNH03260 |
8 |
3' |
+6 (TAG) |
+/+ |
-/+ |
-/+ |
-/+ |
Yes |
|
|
CNK01580 |
2 |
3' |
+6 (C/TAG) |
+/+ |
+/+ |
-/+ |
-/+ |
No |
cDNAs supporting alternative boundary |
|
Non-conserved alternative boundaries |
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|
CNA01650 |
1 |
3' |
-3 (TAG) |
+/- |
-/+ |
-/+ |
-/+ |
Yes |
|
|
CNB04950 |
6 |
5' |
+3 (GTTCAC) |
+/- |
+/- |
-/+ |
-/+ |
No |
|
|
CNC04760 |
1 |
3' |
+3 (TAG) |
+/- |
+/- |
+/+ |
-/+ |
Yes |
Fig 2B |
|
CND00770 |
1 |
3' |
-3 (CAG) |
+/- |
+/- |
+/- |
-/+ |
Yes |
|
|
CNH03490 |
7 |
3' |
-12 (CAG) |
+/- |
+/- |
-/+ |
-/+ |
Yes |
|
|
CNI02860 |
6 |
5' |
+3 (GTTCAT) |
+/- |
+/- |
+/- |
-/+ |
Yes |
|
|
CNK00690 |
2 |
3' |
+6 (CAG) |
+/+ |
-/+ |
+/- |
+/+ |
Yes |
|
|
CNL04670 |
4 |
3' |
+9 (C/TAG) |
+/- |
+/+ |
-/+ |
-/+ |
Yes |
|
|
CNL06040 |
1 |
3' |
-3 (GAG) |
+/- |
+/- |
+/+ |
-/+ |
Yes |
|
|
CNM02250 |
2 |
3' |
-9 (AAG) |
+/- |
+/- |
-/+ |
-/+ |
No |
|
|
Intronization/de-intronization |
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|
CND01950 |
3 |
3' |
No |
+/ |
-/ |
-/ |
-/ |
No |
Intronization Fig 3B (1/0 cDNAs spliced/unspliced) |
|
CNF02770 |
6 |
Both |
No |
+/ |
-/ |
-/ |
-/ |
No |
Intronization Fig 3E (1/7 cDNAs spliced/unspliced) |
|
CNG00990 |
3 |
Both |
No |
+/ |
-/ |
-/ |
-/ |
No |
Intronization Fig 3A (1/4 cDNAs spliced/unspliced) |
|
CNL03830 |
4 |
3' |
No |
+/ |
-/ |
-/ |
-/ |
No |
Intronization Fig 3D (1/7 cDNAs spliced/unspliced) |
|
CNI02050 |
4 |
Both |
No |
+/ |
-/ |
-/ |
-/ |
No |
Intronization Fig 3C (2/4 cDNAs spliced/unspliced) |
|
CNL04380 |
1 |
3' |
No |
+/ |
+/ |
-/ |
-/ |
Yes |
Direction unclear Fig 4A (1/0 cDNAs spliced/unspliced) |
|
CND00470 |
1 |
5' |
No |
+/ |
-/ |
-/ |
+/ |
No |
Convergent Fig 4B (2/0 cDNAs spliced/unspliced) |
|
More complex cases |
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|
CNB05120 |
2 |
5' |
No |
+/ |
+/ |
-/ |
+/ |
Yes |
Unclear (53 bp) |
|
CNF04220 |
1 |
Both |
No |
+/ |
+/ |
-/ |
-/ |
Yes |
Unclear (58 bp) |
|
CNI04240 |
1 |
3' |
No |
+/ |
-/ |
+/ |
+/ |
Yes |
Unclear (64 bp) |
|
CNJ02980 |
2 |
5' |
No |
+/ |
+/ |
-/ |
-/ |
Yes |
Unclear (52/53 bp) |
|
CNK02560 |
2 |
3' |
No |
+/ |
-/ |
-/ |
-/ |
Yes |
Unclear (136/137/143 bp) |
|
CNK02690 |
2 |
3' |
No |
+/ |
+/ |
-/ |
-/ |
Yes |
Unclear (57/58 bp) |
|
CNL06330 |
4 |
3' |
No |
+/ |
-/ |
+/ |
+/ |
Yes |
Unclear (62 bp) |
|
CNM00170 |
5 |
Both |
No |
+/ |
-/ |
-/ |
-/ |
Yes |
Unclear (Fig 4C), unspliced cDNA (61/64 bp) |
|
CNN00940 |
2 |
3' |
No |
+/ |
-/ |
+/ |
+/ |
Yes |
Unclear (84 bp, inframe stop) |
|
|
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|
Roy BMC Evolutionary Biology 2009 9:192 doi:10.1186/1471-2148-9-192 |
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