GFF3 Format

http://gmod.org/wiki/GFF3

Chr1    TAIR10  chromosome      1       30427671        .       .       .       ID=Chr1;Name=Chr1
Chr1    TAIR10  gene    3631    5899    .       +       .       ID=AT1G01010;Note=protein_coding_gene;Name=AT1G01010
Chr1    TAIR10  mRNA    3631    5899    .       +       .       ID=AT1G01010.1;Parent=AT1G01010;Name=AT1G01010.1;Index=1
Chr1    TAIR10  exon    3631    3913    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  five_prime_UTR  3631    3759    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  protein 3760    5630    .       +       .       ID=AT1G01010.1-Protein;Name=AT1G01010.1;Derives_from=AT1G01010.1
Chr1    TAIR10  CDS     3760    3913    .       +       0       Parent=AT1G01010.1,AT1G01010.1-Protein;
Chr1    TAIR10  exon    3996    4276    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  CDS     3996    4276    .       +       2       Parent=AT1G01010.1,AT1G01010.1-Protein;
Chr1    TAIR10  exon    4486    4605    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  CDS     4486    4605    .       +       0       Parent=AT1G01010.1,AT1G01010.1-Protein;
Chr1    TAIR10  exon    4706    5095    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  CDS     4706    5095    .       +       0       Parent=AT1G01010.1,AT1G01010.1-Protein;
Chr1    TAIR10  exon    5174    5326    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  CDS     5174    5326    .       +       0       Parent=AT1G01010.1,AT1G01010.1-Protein;
Chr1    TAIR10  exon    5439    5899    .       +       .       Parent=AT1G01010.1
Chr1    TAIR10  CDS     5439    5630    .       +       0       Parent=AT1G01010.1,AT1G01010.1-Protein;
Chr1    TAIR10  three_prime_UTR 5631    5899    .       +       .       Parent=AT1G01010.1

Applications and Tools that use it:

1. Any tool that requires information about gene position for analysis such as:

   1. Mapping RNA-seq (Tophat, HTSeq)

   2. Genome Browsers (IGV, Gbrowse, UCSC)

   3. SNP feature (SNPeff) ?