Genome-wide Study of NAGNAG Alternative
Splicing in Arabidopsis
Yanjing Shi1, Guangli Sha2, Xiaoyong Sun3*
1College of Chemical Engineering, Qingdao University of Science & Technology, Qingdao, Shandong, P.R. China;
2Qingdao Agricultural Academy, Qingdao, Shandong, P.R. China;
3McDermott Center for Human Growth and Development, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
* Correspondence: ;
Supplemental Data
Supplemental legends
Supplemental Fig. S1 Examples for NAGNAG+ acceptor and NAGNAG++ acceptor. chr1:3505016-3505019 is not only a NAGNAG+ acceptor resulting in the tri-nucleotides difference between AT1G10600.1 and AT1G10600.3, but also a NAGNAG++ acceptor resulting in multiple region differences between AT1G10600.2 and AT1G10600.3
Supplemental Fig. S2 Distance distribution of genome-wide alternative acceptor sites. X represents the distance between two alternative acceptor sites; Y represents the number of alternative acceptor sites. Based on the expression level at each alternative acceptor site, we marked the site as high-expression group (solid line), or low-expression group (dashed line)
Supplemental Fig. S3 WebLogo for 30 bp flanking sequence of 3' acceptor site at the NAGNAG acceptor (group 2A) based on expression levels. Position 31 and 34 at x-axis are two alternative splicing sites
Supplemental Fig. S4 WebLogo for 7 bp and 30 bp flanking sequence of the NAGNAG motifs (group 2B) based on expression levels. The two figures (top) are from high_1.low_2 group, and the two figures (bottom) are from low_1.high_2 group
Supplemental Fig. S5 WebLogo for 30 bp flanking sequence of 5' donor site at the NAGNAG acceptor (group 2A) based on expression levels. Position 31 in x-axis is the 5' splice site
Supplemental Fig. S6 Length distribution for exons (a) and introns (b).
Supplemental Fig. S7 Expression distribution of the genes containing NAGNAG acceptor (solid line) versus other genes (dashed line)
Supplemental Table S1 Amino acid insertion/deletion events between two NAGNAG+ isoforms
Supplemental Information S1 Five RNA-Seq datasets from NCBI Sequence Read Archive
Supplemental Table S1 Single amino acid insertion/deletion events between two NAGNAG+ isoforms
Table S1. Single amino acid insertion/deletion events between two NAGNAG+ isoforms
Amino Acid / Data 1 / Data 2 / Data 3 / Data 4 / Data 5 / cDNA/ESTQ / 58 / 42 / 48 / 39 / 53 / 82
S / 22 / 14 / 21 / 11 / 21 / 43
K / 20 / 9 / 18 / 11 / 21 / 33
A / 18 / 14 / 16 / 10 / 20 / 29
E / 19 / 10 / 11 / 12 / 15 / 34
V / 11 / 5 / 8 / 5 / 10 / 17
R / 9 / 3 / 5 / 5 / 6 / 20
L / 3 / 0 / 3 / 1 / 3 / 6
G / 2 / 0 / 2 / 0 / 2 / 7
D / 2 / 1 / 1 / 1 / 2 / 3
H / 2 / 2 / 1 / 2 / 2 / 1
P / 1 / 1 / 2 / 1 / 2 / 2
M / 2 / 0 / 2 / 1 / 2 / 2
N / 1 / 1 / 1 / 0 / 1 / 3
T / 1 / 0 / 0 / 0 / 1 / 4
F / 0 / 0 / 1 / 1 / 1 / 2
C / 1 / 0 / 1 / 0 / 1 / 1
W / 1 / 0 / 0 / 0 / 0 / 1
I / 0 / 0 / 0 / 0 / 0 / 1
Supplemental Information S1 Five RNA-Seq datasets from NCBI Sequence Read Archive
ecotype / Canary Islands (Can-0), Columbia (Col-0) / Columbia (Col-0) / Columbia (Col-0) / Columbia (Col-0) / Columbia (Col-0)
plants / 11-day-old seedling, 10-day-old root, stage 12 floral bud / Mixed stage of floral tissue, 3-week-old leaf / 4-week-old Meristem and younger leaves, 4-week-old oldest 4 to 6 leaves / leaf / 5-week-old plants
Notes / no / wild type and mutant lines / agro-transfected with pHTR13:HTR13::GFP (At5g10390) for the tagged H3.1 line and with pHTR5:HTR5::GFP (At4g40040) for the tagged H3.3 line, using the destination vector pMDC107 / 24 hr after Botrytis cinerea infection / infected with Pst (avrPphB), sprayed with 1 mM Salicylic Acid (SA), infected with P. syringae DC3000
Sample number / 6 / 6 / 4 / 1 / 13
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