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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]