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Table 1 Summary of the experimental assay for validating computationally inferred human tandem donors.

From: Comparative analysis of sequence features involved in the recognition of tandem splice sites

Ensemble gene (ENSG00000#) Gene name Region PTC Transcript coverage (distal/proximal) Analyzed tissues Confirmed donors (distal/proximal)
172613 RAD9A; RAD9 homolog CDS + 3/17 Kidney; Leukocytes (+/+); (+/+)
175605 ZNF32, zinc finger protein 32 CDS + 14/2 Heart; Leukocytes (+/+); (+/+)
104859 SFRS16; arginine/serine-rich splicing factor 16 CDS + 9/7 Leukocytes; Spleen (+/+); (+/+)
161574 CCL15, small inducible cytokine A15 precursor CDS + 35/6 Colon (+/+)
177646 ACAD-9, Acyl-CoA Dehydrogenase Family, mitochondrial Precursor CDS + 13/8 Brain; Heart (+/+); (+/-)
148459 PDSS1, Trans-Prenyltransferase CDS + 6/2 Small intestine (+/+)
180198 RCC1, regulator of chromosome condensation 5'UTR + 4/2 Small intestine; Testis (+/+); (-/+)
170581 STAT2, signal transducer and activator of transcription 2 CDS + 8/1 Brain; Thymus (+/-); (+/-)
102878 HSF4, heat shock transcription factor 4 CDS + 6/1 Colona, Braina (-/+); (-/+)
090061 CCNK, cyclin K CDS + 17/1 Leukocytes (+/-)
137502 RAB30, Ras-related Protein RAB-30 CDS + 1/7 Leukocytes (-/+); (-/+)
134987 WDR36, WD-Repeat Prtoeine 36 CDS + 1/4 Leukocytes (-/+)
157911 PEX10, peroxisome assembly protein 10 CDS + 3/18 Brain (-/+)
049656 CLPTM1L, cisplatin resistance related protein CRR9p CDS + 2/32 Ovary; Small Intestine (-/+); (-/+)
  1. A5EΔ4 splicing exons were selected according to both transcript coverage, concordance of tissues inferred from cDNA-libraries of A5EΔ4 genes, and commercially available samples. RT-PCR primers were targeted to flanking exons, assayed, and sequenced. In the last column, "+" indicates that the tested A5EΔ4 splicing exon was detected to be present in both splice variants of the corresponding samples, separately for each tested tissue (a bolded "+" indicates the major form). In all, 7/14 A5EΔ4 splicing exons were verified in panels of nine normal tissues. In the fourth column (PTC), "+" indicates the presence of a premature termination codon.a Additional retention-type intron [see Additional File 1]