Table 1 RT-PCR validation results for tissue and disease-specific splice isoforms. The experiments are categorized into three groups viz. tissue specific isoforms predicted via ESTs related to non-normalized libraries (1 to 4), tissue specific isoforms predicted only via ESTs derived from normalized libraries (5 to 16) and disease-specific isoforms (17 to 20). For some of the variants represented by normalized libraries, standard PCR did not reveal the isoforms. However, five of these isoforms were detected using refined PCR conditions. The experiments frequently validated the isoforms and the tissue type, but the predicted specificity was rarely verified.
From: Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing
Isoform | Gene | Chr. | Unigene | EST Evidence | ESTs | Cycles | Isoform | Specificity | Comment (Most sensitive PCR) | Norm. Level |
|---|---|---|---|---|---|---|---|---|---|---|
1 | Unknown | 11 | Hs.112250 | testis | 3 | 39 | + | + | Â | Â |
2 | ISGF3G | 14 | Hs.1706 | stomach | 10 | 39 | + | - | Ubiquitous | Â |
3 | MRPL42 | 12 | Hs.112110 | stomach-lymph | 5 | 39 | + | - | Ubiquitous | Â |
4 | SGN3 | 17 | Hs.6076 | testis | 3 | 39 | - | ? | Â | Â |
5 | PC326 | 13 | Hs.279882 | testis | 9 | 39 | + | + | testis [36] | Rot-5 |
6 | LMO7 | 13 | Hs.5978 | brain | 5 | 39 | + | - | brain, testis, eye(?) [18] | Â |
7 | HRD1 | 8 | Hs.274122 | brain | 3 | 39 | + | - | brain, eye, thymus, salivary gland, kidney | Â |
8 | Unknown | 1 | Hs.24119 | pancreas | 4 | 39 | + | - | approx. 10 tissues | Cot-20 |
9 | BCLG | 12 | Hs.11962 | testis | 4 | 39,78 | ?,+ | +,+ | Â | Cot-5 |
10 | RBPMS | 8 | Hs.80248 | placenta | 4 | 39,78 | ?,+ | -,- | Ubiquitous | Â |
11 | SCML1 | X | Hs.109655 | testis | 12 | 39,78 | ?,+ | +,- | approx. 6 tissues | Rot-5 |
12 | WNK1 | 12 | Hs.432900 | kidney | 3 | 39,78 | ?,+ | +,- | Digestive system [28] | Cot-25 |
13 | NY-CO-10 | 5 | Hs.23557 | testis | 3 | 39,78 | -,+ | ?,+ | Â | Cot-5 |
14 | Unknown | 11 | Hs.169100 | testis | 3 | 39,78 | -,- | ?,? | Â | Rot-5 |
15 | Unknown | 16 | Hs.48396 | breast | 4 | 39,78 | -,- | ?,? | Â | Cot-230 |
16 | CIDE-A | 18 | Hs.249129 | breast | 4 | 39,78 | -,- | ?,? | Â | Cot-230 |
17 | KCNAB2 | 1 | Hs.298184 | tumor | 29 | 39 | + | - | Ubiquitous | Â |
18 | SNRP70 | 19 | Hs.174051 | stomach ascites | 25/26 | 39 | + | - | Ubiquitous | Â |
19 | RAB1 | 14 | Hs.227327 | tumor | 39/95 | 39 | + | - | fetal(kidney, thymus, liver, spleen), ovary [19] | Â |
20 | Unknown | 7 | Hs.272688 | tumor | 12 | 39,78 | -,- | ?,? | relevant tumor sample not in set | Â |