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|
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”)
