Example 3: Alternative Splicing

perl xGAEVAL.pl --clean_db --GFF examples/example3.gff3

Description:

This example illustrates the use of GAEVAL in evaluating alternative splicing. In addition to the standard evaluation of observed incongruent introns, this example also showcases the ability of GAEVAL to determine if an incongruent structure has previously been documented by an alternatively spliced isoform (alternative transcript of the evaluated annotation). In this example, An Arabidopsis gene locus ( At3g20080 ) encodes three transcripts showing evidence of alternative splicing.

GAEVAL Results:

Incongruency Analysis (At3g20080.1)

 1:  Incongruent Introns Detected:
 2:   7008467..7008910
 3:     Alternative Intron
 4:      Supporting evidence: 1
 5:      Documented by Local Annotation Isoforms: 1
 6:       LOCAL:At3g20080.3
 7:   7009426..7009445
 8:     Alternative Intron
 9:      Supporting evidence: 1
10:   7009740..7009818
11:     Alternatively Annotated Intron
12:      Supporting evidence: 2
13:   7010477..7010978
14:     Alternative Intron
15:      Supporting evidence: 2
16:      Documented by Local Annotation Isoforms: 2
17:       LOCAL:At3g20080.3
18:       LOCAL:At3g20080.2
19:   7011158..7012037
20:     Additional Intron
21:      Supporting evidence: 2
22:      Documented by Local Annotation Isoforms: 1
23:       LOCAL:At3g20080.2
24:   7012875..7012977
25:     Additional Intron
26:      Supporting evidence: 2
27:      Documented by Local Annotation Isoforms: 1
28:       LOCAL:At3g20080.2

For an explanation of the introns categories used in this section see the folowing document on incongruent introns.

line 3: GAEVAL has found an 'Alternative Intron'
line 5: This incongruent intron has been documented (used as part of the annotated structure) for 1 isoform of the current annotation
line 6: The transcript using this intron is 'At3g20080.3'
line 11: GAEVAL found an 'Alternatively Annotated Intron'
line 20: GAEVAL found an 'Additional Intron'

Incongruency Analysis (At3g20080.2)

 1:  Incongruent Introns Detected:
 2:   7008467..7008910
 3:     Alternative Intron
 4:      Supporting evidence: 1
 5:      Documented by Local Annotation Isoforms: 1
 6:       LOCAL:At3g20080.3
 7:   7009426..7009445
 8:     Alternative Intron
 9:      Supporting evidence: 1
10:   7009740..7009818
11:     Alternatively Annotated Intron
12:      Supporting evidence: 1
13:   7010477..7010978
14:     Alternatively Annotated Intron
15:      Supporting evidence: 1
16:     Conflicting Intron
17:      Conflicting evidence: 1
18:      Supporting evidence: 1
19:   7011158..7012037
20:     Alternatively Annotated Intron
21:      Supporting evidence: 1
22:   7012875..7012977
23:     Alternatively Annotated Intron
24:      Supporting evidence: 1

For an explanation of the introns categories used in this section see the folowing document on incongruent introns.

line 16: GAEVAL has found a 'Conflicting Intron'

Discussion:

Five alternative intron structures were determined to exists for this locus. When documented by alternative transcript isoforms these introns are noted as such in the GAEVAL output. Interestingly the 7010477..7010978 intron appears to be involved in the selection of an alternative transcriptional termination site.