Table 3. Candidate alternative conserved exons (ACEs) verified by RT-PCR experiments and subsequent sequencing or by literature and transcript-based evidence
|
ID |
Human Ensembl ID (ENSG 00000#) |
Human Exon |
Human Exon Length,bp |
Mouse Ensembl ID (ENSMUSG 00000#) |
Mouse Exon |
Gene Name |
ACESCAN Score |
Skipping in human tissues (RT- PCR) |
Skipping in mouse tissues (RT-PCR) |
Other evidence |
|
|
S1 |
091129 |
24 |
36 |
020598 |
24 |
NRCAM |
1.73 |
Ce |
Br, Te, Emb |
Ref. 1 |
|
|
S2 |
078328 |
5 |
93 |
008658 |
5 |
A2BP1 |
1.67 |
— |
Sk, Lu, Li, Te, Emb |
Ref. 2 |
|
|
S3 |
083312 |
20 |
76 |
009470 |
19 |
TNPO1 |
1.61 |
Br, Te, He, Ce, Sk, Bm, FBr |
Br |
|
|
|
S4 |
079819 |
12 |
63 |
019978 |
12 |
EPB41L2 |
1.59 |
Br, Pr, Li, Lu, Ki, Sk, Bm, Te |
Br, Ki, Li, Sk, Te, Emb, He, Lu |
|
|
|
S5 |
137764 |
17 |
27 |
032364 |
16 |
MAPKK 5 |
1.48 |
— |
Ki, Li |
Human NM_002757.2 skips 17 & 18 |
|
|
S6 |
137764 |
18 |
33 |
032364 |
17 |
MAPKK 5 |
1.38 |
— |
Ki, Li |
Human NM_002757.2 skips 17 & 18 |
|
|
S7 |
175388 |
4 |
33 |
048320 |
4 |
Q8N787 |
1.26 |
Pr, Li, Lu, Ki, Sk, Bm, Te |
Ki, Sk, Lu, Li, Te, Emb, He |
|
|
|
S8 |
156113 |
9 |
92 |
021780 |
2 |
KCNMA1 |
1.22 |
Te |
Li, Lu |
|
|
|
S9 |
182872 |
4 |
74 |
031060 |
5 |
RBM 10 |
1.05 |
Li, Lu, Te |
Br, Ki, Sk, Lu, Li, Te, Emb, He |
|
|
|
S10 |
144331 |
4 |
163 |
027016 |
3 |
ZNF533 |
1.03 |
Br, Pr, Te, He, Li, Ce, Sk, Bm, FLi, Ki, FBr |
Br, Li |
|
|
|
S11 |
130558 |
4 |
220 |
026833 |
4 |
OLFM1 |
0.99 |
FBr |
Br, Ki |
|
|
|
S12 |
155970 |
9 |
39 |
039478 |
8 |
NM_181723 |
0.95 |
Ce, FBr, Br |
Br |
|
|
|
S13 |
172660 |
8 |
35 |
020680 |
8 |
TAF15 |
0.92 |
Br, Pr |
Br, Ki, Sk, Lu |
|
|
|
S14 |
112062 |
9 |
80 |
024004 |
9 |
MAPK14 |
0.80 |
Pr, Li, Lu, Ki, Sk, Bm, Te |
Sk, Li |
|
|
|
S15 |
169045 |
5 |
139 |
007850 |
5 |
HNRNPH |
0.78 |
Br, Pr, Li, Lu, Ki, Sk, Bm, Te |
Br, Li, Te |
|
|
|
S16 |
079819 |
13 |
147 |
019978 |
13 |
EPB41L2 |
0.68 |
Br, Pr, Li, Lu, Ki, Sk, Bm, Te |
Br, Ki, Li, Sk, Te, Emb, He, Lu |
|
|
|
S17 |
114098 |
11 |
83 |
032468 |
13 |
NM_014154 |
0.67 |
Li, Lu, Ki |
Sk, Lu |
|
|
|
S18 |
169057 |
2 |
125 |
031393 |
2 |
MECP2 |
0.36 |
— |
Br, Li, Te, Ki, Lu, Bm, He |
Ref. 3 |
|
|
S19 |
149970 |
9 |
147 |
025658 |
8 |
NM_014927 |
0.21 |
Br, Pr, Li, Lu, Ki, Sk, Bm, Te |
Br, Ki, Te |
|
|
|
S20 |
122367 |
4 |
368 |
021798 |
5 |
LDB3 |
0.14 |
Te |
Br, Ki, Li, Te, Emb, He |
|
|
|
S21 |
101977 |
5 |
117 |
031139 |
3 |
MCF2 |
0.10 |
Br |
Br, Ki |
|
|
|
S22 |
060237 |
12 |
279 |
045962 |
Matched sequence in intron |
PRKWNK1 |
0.26 |
Ki, Sk, Bm |
Not Skipped |
Mouse annotation unclear |
|
|
S23 |
136531 |
3 |
92 |
026992 |
6 |
Scn3a |
0.10 |
Pr, Te, Ki, FBr |
Not Skipped |
|
|
|
S24 |
153944 |
2 |
41 |
034017 |
2 |
MSI2 |
1.75 |
Not Skipped |
Not Skipped |
|
|
|
S25 |
121964 |
5 |
92 |
036890 |
9 |
NM_024659 |
1.30 |
Not Skipped |
Not Skipped |
|
|
|
S26 |
155966 |
19 |
53 |
031189 |
5 |
FMR2 |
1.06 |
Not Skipped |
Not Skipped |
|
|
|
S27 |
182197 |
3 |
108 |
038616 |
4 |
EXT1 |
0.69 |
Not Skipped |
Not Skipped |
mRNA AK130054 (Lu): Exons 2-6 skipped |
|
|
S28 |
079739 |
7 |
116 |
025791 |
8 |
PGM1 |
0.36 |
Not Skipped |
Not Skipped |
|
|
|
S29 |
164692 |
33 |
108 |
029661 |
37 |
COL1A2 |
0.14 |
Not Skipped |
Not Skipped |
|
|
|
S30 |
117676 |
11 |
89 |
003644 |
11 |
RPS6KA1 |
0.14 |
Not Skipped |
Not Skipped |
|
|
|
C1 |
069188 |
22 |
202 |
041592 |
16 |
SDK2 |
-0.27 |
Not Skipped |
Not Skipped |
|
|
|
C2 |
073670 |
22 |
120 |
020926 |
22 |
ADAM11 |
-0.81 |
Not Skipped |
Not Skipped |
|
|
|
C3 |
183773 |
6 |
97 |
022763 |
6 |
NM_144704 |
-1.41 |
Not Skipped |
Not Skipped |
|
|
|
C4 |
143761 |
3 |
111 |
020440 |
3 |
ARF1 |
-1.62 |
Not Skipped |
Not Skipped |
|
|
|
C5 |
146904 |
4 |
403 |
029859 |
5 |
EPHA1 |
-2.01 |
Not Skipped |
Not Skipped |
|
|
|
C6 |
140859 |
6 |
112 |
031788 |
6 |
KIFC3 |
-0.99 |
Not Skipped |
Not Skipped |
|
|
|
C7 |
018236 |
13 |
176 |
000107 |
14 |
CNTN1 |
-0.71 |
Not Skipped |
Not Skipped |
|
|
|
C8 |
008405 |
12 |
104 |
020038 |
12 |
CRY1 |
-1.15 |
Not Skipped |
Not Skipped |
|
|
|
C9 |
178035 |
8 |
91 |
006666 |
8 |
IMPDH2 |
-1.15 |
Not Skipped |
Not Skipped |
|
|
|
C10 |
164070 |
7 |
245 |
025757 |
7 |
OS94_HUMAN |
-1.66 |
Not Skipped |
Not Skipped |
|
|
|
C11 |
130812 |
5 |
271 |
038742 |
6 |
ANGPTL6 |
-1.55 |
Not Skipped |
Not Skipped |
|
|
|
E1 |
166164 |
10 |
108 |
031660 |
10 |
BRD7 |
-0.98 |
EST/mRNA evidence |
Not Skipped |
BX377621 (placenta cot 25-normalized) BI860548 (mammary adenocarcinoma cell line) AV747130 (Adult Pituitary) |
|
|
E2 |
132849 |
32 |
84 |
028562 |
22 |
NM_005799 |
-0.66 |
EST/mRNA evidence |
Not Skipped |
mRNA AJ224748 (HeLa) Exon is not seen in any other mRNAs (5) or ESTs (2) |
|
|
E3 |
100395 |
3 |
134 |
022394 |
3 |
L3MBTL2 |
-0.86 |
EST/mRNA evidence |
Not Skipped |
BU171558 (melanotic melanoma) Exon is included in all other mRNAs (8) and ESTs (>40) |
|
|
E4 |
107897 |
3 |
121 |
026781 |
2 |
ACBD5 |
-0.73 |
EST/mRNA evidence |
Br, Ki, Emb |
ESTs (neuroblastoma, BM011542, BM011474); mRNAs (BC025309, neuroblastoma; AB082527, brain) |
|
|
E5 |
120992 |
6 |
74 |
025903 |
6 |
LYPLA1 |
-0.65 |
EST/mRNA evidence |
Not Skipped |
BQ434220 (embryonic carcinoma), H04075 (placenta at birth), BE246387 (leukopheresis) |
|
|
E6 |
076513 |
13 |
161 |
041870 |
13 |
ANKRD13 |
-1.24 |
EST/mRNA evidence |
Not Skipped |
AK095130 (substantia nigra) |
|
|
E7 |
103876 |
12 |
102 |
030630 |
12 |
FAH |
-1.26 |
EST/mRNA evidence |
Not Skipped |
S63549 (tyrosinemia patients), Exon included in 30 ESTs |
|
|
E8 |
120137 |
3 |
177 |
018846 |
4 |
PANK3 |
-1.03 |
EST/mRNA evidence |
Not Skipped |
U46305 (Pancreatic cancer) |
|
|
E9 |
124198 |
35 |
131 |
027682 |
35 |
ARFGEF2 |
-1.04 |
EST/mRNA evidence |
Not Skipped |
BU173319 (Retinablastoma) |
|
|
E10 |
106443 |
5 |
160 |
029629 |
6 |
PHF14 |
-1.05 |
EST/mRNA evidence |
Not Skipped |
BF816107 (adenocarcinoma) |
|
|
E11 |
170248 |
10 |
178 |
032504 |
10 |
PDCD6IP |
-1.56 |
EST/mRNA evidence |
Not Skipped |
BQ961575 (leiomyosarcoma) |
|
|
E12 |
107937 |
3 |
104 |
021149 |
3 |
GTPBP4 |
-1.58 |
EST/mRNA evidence |
Not Skipped |
AK097093 (spleen, skips exon but retains downstream intron) |
|
|
E13 |
134899 |
12 |
145 |
026048 |
12 |
ERCC5 |
-1.59 |
EST/mRNA evidence |
Not Skipped |
AA191090 (hNT neuroteratocarcinoma neurons) |
|
|
E14 |
150753 |
3 |
165 |
022234 |
3 |
CCT5 |
-1.83 |
EST/mRNA evidence |
Not Skipped |
AU143554 (retinoblastoma) |
|
|
E15 |
132170 |
6 |
451 |
000440 |
7 |
PPARG |
-1.54 |
EST/mRNA evidence |
Br, Ki, Li, Emb, Te |
BI524664 (NIH_MGC_122), CA426975 (subchondral bone) |
|
Samples S1–S30 are candidate ACEs, samples C1–C11 are low-scoring ACEs (scored <0), and samples E1–E15 are low-scoring ACEs with human EST/mRNA evidence of skipping. Abbreviations for tissues are as follows. Ce, cerebellum; Br, whole brain; FBr, fetal brain; Sk, skeletal muscle; Li, liver; Lu, lung; He, heart; Bm, bone marrow; Te, testis; Pr, prostate; Ki, kidney; FLi, fetal liver; Emb, embryonic mix.
1. Wang, B., Williams, H., Du, J. S., Terrett, J. & Kenwrick, S. (1998) Mol Cell Neurosci 10, 287-95.
2. Shibata, H., Huynh, D. P. & Pulst, S. M. (2000) Hum Mol Genet 9, 1303-13.
3. Kriaucionis, S. & Bird, A. (2004) Nucleic Acids Res. 32, 1818-23.