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Table 2 Predicted and confirmed splicing variants for Clcc1 and Pnkd

From: Postnatal developmental dynamics of cell type specification genes in Brn3a/Pou4f1 Retinal Ganglion Cells

Primer Pair fragment size, bp Predicted transcripts Confirmed splice junctions
Clcc1
 pr.1 + pr.9 208 + (26) NM_145543^ ex.1a_ex.3
 pr.2 + pr.9 181+ (26), 252 + (26) NM_145543^, NM_001177771, XM_006501416^, XM_011240107 ex.1a/1b_ex.3
 pr.3 + pr.9 220 + (26) NM_001177771, XM_006501416^, XM_011240107 ex.1b_ex.3
 pr.4 + pr.9 203 + (26) NM_001177771, NM_001177770, XM_006501416^, XM_011240107 ex.1b_ex.3
 pr.5 + pr.9 172 + (26) NM_001177771, NM_001177770, XM_006501416^, XM_011240107 ex.1b_ex.3
 pr.6 + pr.9* 293 + (26) NM_001177770, XM_011240107 none
 pr.7 + pr.9 300 + (26) NM_001177771, novel uncharacterized ex.2_ex.3
 pr.2 + pr.8* 199 + (26) 270 + (26) NM_001177771 none
 pr.3 + pr.8* 238 + (26) NM_001177771 none
 pr.4 + pr.8* 221 + (26) NM_001177771 none
 pr.6 + pr.8* 453 + (26) none none
 pr.7 + pr.8 159 + (26) NM_001177771, novel uncharacterized ex.2
 pr.10 + pr.11 432 + (26) all transcripts ex.4_ex.5_ex.6
Pnkd
 pr.1 + pr.2 246 + (26) NM_025580, NM_001039509^ ex.2_ex.3
 pr.3 + pr.4* 289 + (26) NM_025580 none
 pr.5 + pr.6 167 + (26) NM_019999^ ex.5
 pr.5 + pr.7 282 + (26) NM_019999^ ex.5_ex.6
 pr.8 + pr.9 360 + (26) all transcripts 3’-UTR
  1. Column 1 represents primer combinations, column 2 – DNA fragment size after RT-PCR. Some of the primer combinations could give rise to two different DNA fragments from two different splice variants. Column 3 shows transcript variants predicted to be recognized by the respective primer combination. Column 4 demonstrates exon-to-exon splicing junction which were experimentally confirmed by RT-PCR using respective primer combination. ^ - transcripts detected by RT-PCR. * - primer combination which gave negative result in RT-PCR. Numbers in parenthesis refer to T3 promoter extension, as required for ISH probe generation (Table should appear after “Clcc1 transcripts detected in the retina” section in “Results”)