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

Table 2 Predicted and confirmed splicing variants for Clcc1 and Pnkd

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

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”)

ISSN: 1749-8104