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Table 1 Alternative 3′ ends for Olfr1507 and Olfr15 revealed in silico, and their subsequent experimental validation

From: Alternative polyadenylation produces multiple 3’ untranslated regions of odorant receptor mRNAs in mouse olfactory sensory neurons

  RNA-Seq RL-PAT
Gene PolyA site 3’end position (nt after stop) Matching canonical PAS (nt after stop)b Cleavage position (nt after stop) Nb of clones sequenced PolyA tail length (nt, mean ± SEM) Matching canonical PAS (nt after stop)e
Olfr1507 XS Not detected Not relevant 92 2 19 ± 8 None
114 2 17 ± 3
S 1193–1273a AAUAAA (1263, 1281) 1283 7 44 ± 18 AAUAAA (1263, 1281)
1290 1 11
1294 1 39
M 2593 AUUAAA (2628) 2653 1 86 AUUAAA (2628)
L 4013 AAUAAA (4076) 4093 1 16 AAUAAA (4076)
4109 2 16 ± 1
4112 1 46
XL 4943 AAUAAA (5049)c No RL-PAT confirmationd Not relevant
Olfr15 S 902 AAUAAA (901) 924 2 87 ± 1 AAUAAA (901)
931 1 26
936 1 19
M1 2462 AUUAAA (2487), AAUAAA (2529) No RL-PAT confirmationd Not relevant
M2 2742 AAUAAA (2665, 2675, 2685, 2806, 2798, 2806, 2814, 2822), AUUAAA (2790) 2816 1 22 AAUAAA (2798, 2806, 2814, 2822), AUUAAA (2790)
2820 1 28
2824 1 31
2836 1 48
L 4762-4837a AUUAAA (4717) No RL-PAT confirmationd Not relevant
  1. aThe 3’ ends distant of less than 100 nt were merged as a single polyA site. bFor each putative polyA site, predicted canonical PAS matching in a [− 100;+ 100] window from the RNA-Seq-deduced 3′ end are indicated. cNote that for Olfr1507 3’XL isoform, the closest canonical PAS is slightly outside the 100-nt precision window. The cleavage site and polyA tail length were experimentally mapped using RL-PAT on adult male OM, further confirming the polyA site usage for most of the 3’UTR isoforms. dXL site of Olfr1507, M1 and L sites of Olfr15 could not be confirmed by RL-PAT because no specific forward primer could be designed due to repeat sequences upstream of these polyA sites. eFor each confirmed polyA site, predicted canonical PAS matching in a [− 100;0] window from the identified cleavage sites are indicated