Experimental Validation of Predicted Alternatively Spliced Exons
|
Gene |
Alt exona |
PCR confirmedb |
Type of alternative confirmedc |
Gene description |
|---|---|---|---|---|
| FGF11 | 2 | Yes | Skip | Fibroblast growth factor 11 |
| EFNA5 | 4 | Yes | Skip | Ephrin-A5 |
| NCOA1 | 8 | Yes | Skip | Steroid nuclear receptor coactivator |
| PAM | 22 | Yes | Skip | Protein associated with Myc mRNA |
| GOLGA4 | 9 | Yes | Skip | Golgi autoantigen, golgin subfamily a, 4 |
| NPR2 | 9 | Yes | Skip | Natriuretic peptide receptor B/guanylate cyclase B |
| VLDLR | 9 | Yes | Int Retd | Very low density lipoprotein receptor |
| BAZ1A | 12 | Yes | Alt 3′sse | Bromodomain adjacent to zinc finger domain protein 1A |
| SMARCD1 | 7 | Yes | Alt 3′ssf | SWI/SNF related, matrix associated, actin-dependent regulator of chromatin, subfamily d, member 1 |
| PRKCM | 15 | No | Protein kinase C, mu | |
| TIAM2 | 12 | No | T-cell lymphoma invasion and metastasis 2 | |
| MDA5 | 4 | No | Melanoma differentiation associated protein-5 | |
| RNASE3L | 15 | No | Nuclear RNase III | |
| HAT1 | 7 | No | Histone acetyltransferase 1 | |
| DICER1
|
6
|
No
|
|
Dicer1, Dcr-1 homolog (Drosophila)
|
-
↵a Serial number of exon (out of gene's exons) identified as alternative.
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↵b For each predicted exon, primers were designed from its flanking exons and RT—PCR was conducted using total RNA from 14 different tissue types: cervix, uterus, ovary, placenta, breast, colon, pancreas, liver + spleen, brain, prostate, testis, kidney, thyroid, and assorted cell-lines. Products were sequenced, and alternative splicing was searched.
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↵c Type of alternative splicing: Skip, exon-skipping; Alt 3′ss, alternative 3′ splice site (acceptor); Int Ret., intron retention.
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↵d Retention of intron 8 (size 103 nucleotides) was detected in VLDLR.
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↵e Deletion of 86 nucleotides was detected on the 3′ end of exon 12 7 of BAZ1A.
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↵f Extension of 44 nucleotides was detected on the 3′ end of exon 12 of SMARCD1.
