GFF3 Format
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:
Any tool that requires information about gene position for analysis such as:
Mapping RNA-seq (Tophat, HTSeq)
Genome Browsers (IGV, Gbrowse, UCSC)
SNP feature (SNPeff) ?