Maker produces duplicate mRNA sequence with different AED score, what is up with that?

Question

[Lesley Sitter]

Hopefully someone can help me find out what is happening.

I have used maker for a while now to annotate several genomes but this week I got something weird.

Maker made two mRNA predictions out of 1 gene (which normally means it's a splice variant or something like that) but this time the sequences are identical but it still puts it under two different names with two different AED scores.

Below are the two proteins this has happened to. Can someone shed some light on what has happened here? I would really appreciate it :D

With kind regards

>maker-SL2.40sc04057-exonerate_est2genome-gene-146.0-mRNA-1 protein AED:0.29 eAED:0.29 QI:167|1|1|1|0|0|4|279|99
MEMGSFFSVLIGEQFQEFGSLFSAKYNTNGNLLPPNFINVVGCLYGIGDMESLCEPGKRE
SLHCYKLGPKQWVAEVQFLGVVDHPNLDKLEYCDVGLFA
>maker-SL2.40sc04057-exonerate_est2genome-gene-146.0-mRNA-2 protein AED:0.31 eAED:0.31 QI:167|1|1|1|0|0|3|214|99
MEMGSFFSVLIGEQFQEFGSLFSAKYNTNGNLLPPNFINVVGCLYGIGDMESLCEPGKRE
SLHCYKLGPKQWVAEVQFLGVVDHPNLDKLEYCDVGLFA

>maker-SL2.40sc04135-exonerate_est2genome-gene-17.5-mRNA-1 protein AED:0.03 eAED:0.03 QI:141|1|1|1|0|0|3|232|168
MEIMLNNTVLTCASTLLPSTQDGVPLLAIETKVEGDQNTNDEQTKVVDADEEGGDGDDND
ENGNEGFEEGEEEYSDEGVHGNKSKGNAKKSNGEGEENGDAEDEEDVGEEGHDDDGDDDD
DGDDDNDDDEEAEEGEGEEEVVEDDDPEDDDEEDEEEEAIQPPKKRKK
>maker-SL2.40sc04135-exonerate_est2genome-gene-17.5-mRNA-2 protein AED:0.06 eAED:0.06 QI:92|1|1|1|0|0|2|232|168
MEIMLNNTVLTCASTLLPSTQDGVPLLAIETKVEGDQNTNDEQTKVVDADEEGGDGDDND
ENGNEGFEEGEEEYSDEGVHGNKSKGNAKKSNGEGEENGDAEDEEDVGEEGHDDDGDDDD
DGDDDNDDDEEAEEGEGEEEVVEDDDPEDDDEEDEEEEAIQPPKKRKK

Answer 1

[Lesley Sitter]

Figured it out :P

It seems that MAKER creates two gene models that are mostly identical except for the UTR, which isn't translated into the protein model off-course. Therefore you get two identical protein models but the gene models are slightly different (although not much).