Table 1 Summary of ETASs in the six elite varieties.

From: Analysis of elite variety tag SNPs reveals an important allele in upland rice

Total ETASs

Protein-altering ETASs a

Guichao2 2598

 

 Intergenic region 2217

 

Promoter region 80

 

 Gene region 381

 

UTR region 94

 

CDS region 88

48 non-synonymous ETASs

Intron region 199

3 ETASs disrupt splice donors/acceptors

IR64 18695

 

 Intergenic region 14884

 

Promoter region 583

 

 Gene region 3811

 

UTR region 865

 

CDS region 929

2 ETASs disrupt start codons

2 ETASs disrupt stop codons

17 ETASs produce premature stop codons

496 non-synonymous ETASs

Intron region 2017

3 ETASs disrupt splice donors/acceptors

Minghui63 11411

 

 Intergenic region 9545

 

Promoter region 278

 

 Gene region 1866

 

UTR region 437

 

CDS region 408

2 ETASs disrupt start codons

5 ETASs produce premature stop codons

252 non-synonymous ETASs

Intron region 1021

3 ETASs disrupt splice donors/acceptors

IRAT104 24652

 

 Intergenic region 20183

 

Promoter region 758

 

 Gene region 4468

 

UTR region 1021

 

CDS region 1230

3 ETASs disrupt start codons

2 ETASs disrupt stop codons

15 ETASs produce premature stop codons

753 non-synonymous ETASs

Intron region 2217

5 ETASs disrupt splice donors/acceptors

Koshihikari 914

 

 Intergenic region 717

 

Promoter region 22

 

 Gene region 197

 

UTR region 36

 

CDS region 69

1 ETAS disrupts the start codon

21 non-synonymous ETASs

Intron region 92

 

Chujing27 2639

 

 Intergenic region 2096

 

Promoter region 57

 

 Gene region 543

 

UTR region 109

 

CDS region 161

1 ETAS disrupts the start codon

1 ETAS causes a premature stop codon

82 non-synonymous ETASs

Intron region 273

2 ETASs disrupt splice donors/acceptors

  1. aprotein-altering ETASs refers to the ETASs that result in premature stop codons, disrupt start/stop codons or splice donor/acceptor sites or are non-synonymous mutations.