# organism: Drosophila melanogaster # std1 Adh std1 TFBS 32002 32006 . + . Adh std1 TATA_signal 32009 32012 . + . transcript "1" Adh std1 TSS 32033 32034 . + . transcript "1" Adh std1 prim_transcript 32034 33122 . + . transcript "1" Adh std1 exon 32034 32277 . + . transcript "1" Adh std1 start_codon 32122 32124 . + . transcript "1" Adh std1 CDS 32122 32277 . + . transcript "1" Adh std1 splice5 32277 32278 . + . transcript "1" Adh std1 splice3 32332 32333 . + . transcript "1" Adh std1 exon 32333 32452 . + . transcript "1" Adh std1 CDS 32333 32452 . + . transcript "1" Adh std1 splice5 32452 32453 . + . transcript "1" Adh std1 splice3 32571 32572 . + . transcript "1" Adh std1 exon 32572 32729 . + . transcript "1" Adh std1 CDS 32572 32729 . + . transcript "1" Adh std1 splice5 32729 32730 . + . transcript "1" Adh std1 splice3 32784 32785 . + . transcript "1" Adh std1 exon 32785 32830 . + . transcript "1" Adh std1 CDS 32785 32830 . + . transcript "1" Adh std1 splice5 32830 32831 . + . transcript "1" Adh std1 splice3 32825 32826 . + . transcript "1" Adh std1 CDS 32826 33003 . + . transcript "1" Adh std1 exon 32826 33122 . + . transcript "1" Adh std1 stop_codon 33001 33003 . + . transcript "1" Adh std1 polyA_signal 33090 33095 . + . transcript "1" Adh std1 polyA_site 33101 33102 . + . transcript "1" Adh std1 prim_transcript 38100 41973 . - . transcript "2" Adh std1 exon 38100 41973 . - . transcript "2" Adh std1 polyA_site 39620 39621 . - . transcript "2" Adh std1 polyA_signal 39685 39690 . - . transcript "2" Adh std1 stop_codon 40125 40127 . - . transcript "2" Adh std1 CDS 40125 40390 . - . transcript "2" Adh std1 start_codon 40388 40390 . - . transcript "2" Adh std1 TSS 41973 41974 . - . transcript "2" Adh std1 TATA_signal 41998 42001 . - . transcript "2" Adh std1 TFBS 42187 42193 . - . Adh std1 TFBS 42211 42216 . - .
TFBS transcription factor binding site.
TATA_signal TATA-box (TBP binding site).
TSS transcription start site (note the transcription start is in
between the <start> and <end> annotation in the gff file! Historically
the <start> is -1 and <end> is +1.
prim_transcript primary (initial, unprocessed) transcript.
exon region of genome that codes for portion of spliced mRNA (does not always CDS).
start_codon start codon (ATG).
CDS coding sequence; sequence of nucleotides that
corresponds with the sequence of amino acids in a
protein (location includes start and stop codon).
splice5 5' splice site (note the exon and intron boundary is between <start> and <end>;
the last base of the exon is <start> and the "G" of the "GT" consensus sequence is
<end> (for a gene on the forward strand).
splice3 3' splice site (note the exon and intron boundary is between <start> and <end>;
the "G" of the "AG" consensus sequence is the <start> and the first base of the exon
is the <end> (for a gene on the forward strand).
stop_codon stop codon (TAA|TGA|TAG).
polyA_signal recognition region necessary for endonuclease cleavage
of an RNA transcript.
polyA_site site on an RNA transcript to which will be added adenine
residues by post-transcriptional polyadenylation (Note the site
is in between <start> and <stop>.
Please also note that it is very important that your group (usually by
gene) together your predictions using the last column of the GFF
format. In our examples there are 2 genes predicted, transcript "1"
and transcript "2". Note also that this last column is now following
the newer GFF version 2!
A typical "gene" finding prediction for "transcript "1" " submitted by groupX should look like (Note in this example the second 3' splice off which results also in a different CDS annotation. In addition, the third exon is missed.
# groupX Adh groupX start_codon 32122 32124 . + . transcript "1" Adh groupX CDS 32122 32277 . + . transcript "1" Adh groupX splice5 32277 32278 . + . transcript "1" Adh groupX splice3 32382 32383 . + . transcript "1" Adh groupX CDS 32383 32452 . + . transcript "1" Adh groupX splice5 32452 32453 . + . transcript "1" Adh groupX splice3 32571 32572 . + . transcript "1" Adh groupX CDS 32572 32830 . + . transcript "1" Adh groupX splice5 32830 32831 . + . transcript "1" Adh groupX splice3 32825 32826 . + . transcript "1" Adh groupX CDS 32826 33003 . + . transcript "1" Adh groupX stop_codon 33001 33003 . + . transcript "1"