PFLU_1226 missing
We’e removed PFLU_1226 from the annotation. This is an important gene (it is the basis of Sungbin’s PhD) that regulate’s itself using a transcriptional frameshift. So the CDS looks like it encodes a pseudogene, which is probably why the annotation was not transferred.
The complete CDS of PFLU_1226 is:
ATGGAAATCAACCCGATCCTTAACACCATCAAGGACCTGTCCGAGCGCTCCGAAACTATTCGGGGGTATCTTTGACTACGATCAAAAGCATGAGCGTCTGACCGAAGTCAATCGCGAGCTTGAAGATCCGGCTGTCTGGAACAAACCTGAATACGCCCAGGAGCTGGGCCGCGAGCGCGCTGCGCTGGCACAGATCGTCGACACCCTCGATGAGCTGAACACCGGCCTGGGTGATTGCCGTGACCTGCTGGACATGGCCGTCGAAGAAAACGACGAAGGCGCAGTGGGCGATGTCTTCGCCGAGCTGGCCCGTCTCGAGGAAAACCTCGCCAAGCTTGAATTCCGTCGCATGTTCAGCCATGAAATGGACCCGAACAACGCGTATCTGGACATCCAGGCCGGTTCCGGCGGCACCGAGGCCCAGGACTGGGCCAACATCCTGCTGCGCATGTACCTGCGCTGGGCCGACAAGCGCGGTTTCGACGCGACCATCATGGAGCTGTCGGCCGGTGAAGTCGCGGGTATCAAAGGCGCGACGGTGCATATCAAGGGTGAGTACGCCTTTGGTTGGCTGCGGACCGAGATCGGCGTTCACCGTCTGGTGCGCAAGAGCCCGTTCGACTCCGGCAACCGTCGCCATACCTCGTTCTCCGCCGTGTTCGTCTCGCCAGAGATCGACGATAAGGTGGAAATCGAGATCAACCCGGCCGACTTGCGTATCGACACCTACCGCTCCTCTGGTGCCGGTGGTCAGCACGTAAACACCACTGACTCGGCCGTACGGATTACCCACGTACCGACCAACACCGTGGTCAGCTGCCAGAACGAACGTTCCCAGCACGCCAACAAGGACACCGCCATGAAAATGCTGCGGGCCAAGTTGTACGAGCAGGAAATGCAGAAGCGCAACGCCGCTTCCCAGGCGCTGGAGGACACCAAGTCGGATATCGGCTGGGGTCACCAGATCCGTTCTTATGTGCTCGATGCGTCGCGGATCAAGGATCTGCGCACTAACATCGAACGCAGCGACTGTGACAAGGTGCTCGACGGCGATATCGACGAATACCTGGAAGCCAGCCTGAAATCGGGCCTGTAA
I’m not sure we can find a way to include the frameshift (maybe annotate the whole thing as a single gene with two different CDS annotations?). The most important thing would be to restore the CDS.
It encodes a protein a protein that starts
MEINPILNTIKDLSERSETIRGYL
and then shifts reading frame to continue as
DYDQKHERLTEVNRELEDPAVWNKPEYAQELGRERAALAQIVDTLDELNTGLGDCRDLLD MAVEENDEGAVGDVFAELARLEENLAKLEFRRMFSHEMDPNNAYLDIQAGSGGTEAQDWA NILLRMYLRWADKRGFDATIMELSAGEVAGIKGATVHIKGEYAFGWLRTEIGVHRLVRKS PFDSGNRRHTSFSAVFVSPEIDDKVEIEINPADLRIDTYRSSGAGGQHVNTTDSAVRITH VPTNTVVSCQNERSQHANKDTAMKMLRAKLYEQEMQKRNAASQALEDTKSDIGWGHQIRS YVLDASRIKDLRTNIERSDCDKVLDGDIDEYLEASLKSGL