Data source used in AS-ALPS

Input data
Genome NCBI RefSeq mRNA other transcript data total
version No. of data version No. of data data source
H.sapiens GRCh38 36787 NCBI genome 106 93120 Ensembl rel. 78 129907
M.musculus GRCm38 27427 NCBI genome 104 53552 Ensembl rel. 78 80979
D.melanogaster BDGP5 30264 NCBI RefSeq rel.71 26950 Ensembl rel. 78 57214
C.elegans WBcel235 27356 NCBI RefSeq rel.71 30927 Ensembl rel. 78 58283
A.thaliana TAIR 10 35173 NCBI RefSeq rel.71 35386 Ensembl Genome rel.28 70559
O.sativa IRGSP-1.0 28392 NCBI RefSeq rel.71 42132 Ensembl Genome rel.28 70524
version total AS isoforms
Swiss-Prot Release 2015/02 58326

Database for annotaion
PDB InterPro KEGG GEO
Feb. 2, 2015 Version 51.0 Jul. 22, 2015 GSE30611
PeptideAtlas
H.sapiens M.musculus D.melanogaster C.elegans
Mar., 2015 Dec., 2014 Aug., 2012 Sep., 2013

H.sapiens
  No. %
AS variant clusters 13138  
AS variant clusters annotated with PDB data 7002 53.3 %
Unique AS regions 38719  
Unique AS regions annotated with PDB data 15825 40.9 %
  N-ter. middle C-ter. total
deletion 584815.1 % 937824.2 % 6601.7 % 1588641.0 %
insertion 5541.4 % 25536.6 % 1310.3 % 32388.4 %
substitution 33908.8 % 10532.7 % 1515239.1 % 1959550.6 %
total 979225.3 % 1298433.5 % 1594341.2 % 38719100.0 %

M.musculus
  No. %
AS variant clusters 8633  
AS variant clusters annotated with PDB data 3969 46.0 %
Unique AS regions 17596  
Unique AS regions annotated with PDB data 6424 36.5 %
  N-ter. middle C-ter. total
deletion 207411.8 % 448825.5 % 3662.1 % 692839.4 %
insertion 4952.8 % 16029.1 % 530.3 % 215012.2 %
substitution 14378.2 % 5443.1 % 653737.2 % 851848.4 %
total 400622.8 % 663437.7 % 695639.5 % 17596100.0 %

D.melanogaster
  No. %
AS variant clusters 3628  
AS variant clusters annotated with PDB data 1071 29.5 %
Unique AS regions 7093  
Unique AS regions annotated with PDB data 1551 21.9 %
  N-ter. middle C-ter. total
deletion 98513.9 % 198428.0 % 1351.9 % 310443.8 %
insertion 2603.7 % 87912.4 % 1812.6 % 132018.6 %
substitution 91812.9 % 2583.6 % 149321.0 % 266937.6 %
total 216330.5 % 312144.0 % 180925.5 % 7093100.0 %

C.elegans
  No. %
AS variant clusters 4002  
AS variant clusters annotated with PDB data 1112 27.8 %
Unique AS regions 6584  
Unique AS regions annotated with PDB data 1484 22.5 %
  N-ter. middle C-ter. total
deletion 231435.1 % 144021.9 % 360.5 % 379057.6 %
insertion 1131.7 % 3956.0 % 70.1 % 5157.8 %
substitution 89613.6 % 1692.6 % 121418.4 % 227934.6 %
total 332350.5 % 200430.4 % 125719.1 % 6584100.0 %

A.thaliana
  No. %
AS variant clusters 4278  
AS variant clusters annotated with PDB data 1662 38.8 %
Unique AS regions 5706  
Unique AS regions annotated with PDB data 2053 36.0 %
  N-ter. middle C-ter. total
deletion 68412.0 % 157727.6 % 480.8 % 230940.5 %
insertion 1442.5 % 81414.3 % 200.4 % 97817.1 %
substitution 4928.6 % 2895.1 % 163828.7 % 241942.4 %
total 132023.1 % 268047.0 % 170629.9 % 5706100.0 %

O.sativa
  No. %
AS variant clusters 5075  
AS variant clusters annotated with PDB data 1773 34.9 %
Unique AS regions 6951  
Unique AS regions annotated with PDB data 2128 30.6 %
  N-ter. middle C-ter. total
deletion 4206.0 % 69310.0 % 530.8 % 116616.8 %
insertion 4516.5 % 5918.5 % 450.6 % 108715.6 %
substitution 71610.3 % 122217.6 % 276039.7 % 469867.6 %
total 158722.8 % 250636.1 % 285841.1 % 6951100.0 %

Swiss-Prot
  No. %
AS variant clusters 20504  
AS variant clusters annotated with PDB data 9156 44.7 %
Unique AS regions 38160  
Unique AS regions annotated with PDB data 13762 36.1 %
  N-ter. middle C-ter. total
deletion 580015.2 % 1076928.2 % 10012.6 % 1757046.0 %
insertion 6801.8 % 26216.9 % 1080.3 % 34098.9 %
substitution 399310.5 % 24176.3 % 1077128.2 % 1718145.0 %
total 1047327.4 % 1580741.4 % 1188031.1 % 38160100.0 %