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 43099 NCBI genome 108 94347 Ensembl rel. 86 137446
M.musculus GRCm38 29914 NCBI genome 106 58776 Ensembl rel. 86 88690
D.melanogaster BDGP6 30430 NCBI RefSeq rel.78 30356 Ensembl rel. 86 60786
C.elegans WBcel235 28093 NCBI RefSeq rel.78 31562 Ensembl rel. 86 59655
A.thaliana TAIR 10 35173 NCBI RefSeq rel.78 35386 Ensembl Genome rel.32 70559
O.sativa IRGSP-1.0 28392 NCBI RefSeq rel.71 42132 Ensembl Genome rel.32 70524
version total AS isoforms
Swiss-Prot Release 2016/09 59368

Database for annotaion
PDB InterPro KEGG GEO
Oct. 3, 2016 Version 59.0 Dec. 17, 2016 GSE30611
PeptideAtlas
H.sapiens M.musculus D.melanogaster C.elegans
Jan., 2016 Dec., 2014 Aug., 2012 Sep., 2013

H.sapiens
  No. %
AS variant clusters 13380  
AS variant clusters annotated with PDB data 7306 54.6 %
Unique AS regions 40434  
Unique AS regions annotated with PDB data 17207 42.6 %
  N-ter. middle C-ter. total
deletion 643015.9 % 988524.4 % 6081.5 % 1692341.9 %
insertion 5501.4 % 26746.6 % 1170.3 % 33418.3 %
substitution 37199.2 % 9662.4 % 1548538.3 % 2017049.9 %
total 1069926.5 % 1352533.4 % 1621040.1 % 40434100.0 %

M.musculus
  No. %
AS variant clusters 9589  
AS variant clusters annotated with PDB data 4516 47.1 %
Unique AS regions 20208  
Unique AS regions annotated with PDB data 7573 37.5 %
  N-ter. middle C-ter. total
deletion 253512.5 % 514225.4 % 3781.9 % 805539.9 %
insertion 4712.3 % 17258.5 % 640.3 % 226011.2 %
substitution 16198.0 % 5732.8 % 770138.1 % 989349.0 %
total 462522.9 % 744036.8 % 814340.3 % 20208100.0 %

D.melanogaster
  No. %
AS variant clusters 3482  
AS variant clusters annotated with PDB data 1033 29.7 %
Unique AS regions 6697  
Unique AS regions annotated with PDB data 1473 22.0 %
  N-ter. middle C-ter. total
deletion 86112.9 % 196729.4 % 1412.1 % 296944.3 %
insertion 2063.1 % 84812.7 % 1922.9 % 124618.6 %
substitution 88213.2 % 2583.9 % 134220.0 % 248237.1 %
total 194929.1 % 307345.9 % 167525.0 % 6697100.0 %

C.elegans
  No. %
AS variant clusters 4556  
AS variant clusters annotated with PDB data 1250 27.4 %
Unique AS regions 7607  
Unique AS regions annotated with PDB data 1720 22.6 %
  N-ter. middle C-ter. total
deletion 290638.2 % 157020.6 % 360.5 % 451259.3 %
insertion 1592.1 % 4646.1 % 70.1 % 6308.3 %
substitution 99313.1 % 1772.3 % 129517.0 % 246532.4 %
total 405853.3 % 221129.1 % 133817.6 % 7607100.0 %

A.thaliana
  No. %
AS variant clusters 4278  
AS variant clusters annotated with PDB data 1703 39.8 %
Unique AS regions 5707  
Unique AS regions annotated with PDB data 2105 36.9 %
  N-ter. middle C-ter. total
deletion 69712.2 % 157127.5 % 480.8 % 231640.6 %
insertion 1322.3 % 81714.3 % 200.4 % 96917.0 %
substitution 4928.6 % 2885.0 % 164228.8 % 242242.4 %
total 132123.1 % 267646.9 % 171030.0 % 5707100.0 %

O.sativa
  No. %
AS variant clusters 5076  
AS variant clusters annotated with PDB data 1819 35.8 %
Unique AS regions 6951  
Unique AS regions annotated with PDB data 2188 31.5 %
  N-ter. middle C-ter. total
deletion 4196.0 % 69210.0 % 530.8 % 116416.7 %
insertion 4516.5 % 5918.5 % 450.6 % 108715.6 %
substitution 71910.3 % 122217.6 % 275939.7 % 470067.6 %
total 158922.9 % 250536.0 % 285741.1 % 6951100.0 %

Swiss-Prot
  No. %
AS variant clusters 20879  
AS variant clusters annotated with PDB data 9280 44.4 %
Unique AS regions 38793  
Unique AS regions annotated with PDB data 13915 35.9 %
  N-ter. middle C-ter. total
deletion 593615.3 % 1091628.1 % 10072.6 % 1785946.0 %
insertion 6881.8 % 26736.9 % 1100.3 % 34718.9 %
substitution 406710.5 % 24586.3 % 1093828.2 % 1746345.0 %
total 1069127.6 % 1604741.4 % 1205531.1 % 38793100.0 %