Example 4: Alternative Transcript Termination

perl xGAEVAL.pl --clean_db --GFF examples/example4.gff3

Description:

This example illustrates the ability of GAEVAL to determine the presence of alternative cleavage/polyadenylation site usage based on the clustering of end defining evidence such as three-prime EST alignments. In this example, An Arabidopsis gene locus ( At3g20080 ) shows evidence of alternative transcriptional termination in connection with alternative splicing.

GAEVAL Results:

Incongruency Analysis (At3g20080.1)

1:  Alternative Cleavage / PolyA site detected:
2:   7013701
3:    Supporting Evidence: 2
4:    Documented by 'LOCAL' annotations:
5:     At3g20080.2
    

Incongruency Analysis (At3g20080.2)

  Alternative Cleavage / PolyA site detected:
   7010654
    Supporting Evidence: 3
    Documented by 'LOCAL' annotations:
     At3g20080.1
    

Incongruency Analysis (At3g20080.3)

  Alternative Cleavage / PolyA site detected:
   7013701
    Supporting Evidence: 2
    Documented by 'LOCAL' annotations:
     At3g20080.2
   7010654
    Supporting Evidence: 3
    Documented by 'LOCAL' annotations:
     At3g20080.1
    

For an explanation of the analysis used to cluster end-defining evidence refer to the folowing document on 'Three-Prime Evidence Groups'.

• line 1: GAEVAL has found a putative alternative cleavage/polyA site
• line 2: The average genomic location of the TPEG
• line 3: Count of end-defining evidence involved in this TPEG
• line 4: This cleavage/polyA site is used by annotation isoform
• line 5: The annotation isoforms using this cleavage/polyA site

Discussion:

This region shows evidence suggesting that both cleavage/polyA sites as defined by the At3g20080.1 and At3g20080.2 annotations are valid sites of transcriptional termination. The terminal boundary of At3g20080.3 however is not supported by an end-defining evidence group.