dme-mir-1014

The D. willistoni ortholog reported in the MAF does not fold into a hairpin and is not expressed.
- Found a better ortholog by using LASTZ to search the D. willistoni genome.
  - This ortholog folds into a hairpin and is expressed.
  - It has an adjusted percent similarity of 64% to the D. melanogaster sequence.
  - The MAF did not report this ortholog in a chains.
  - LASTZ also found the ortholog reported in the MAF. It had an adjusted similarity of 57% to the D. melanogaster sequence.
- Note that this mirtron is located on the D. melanogaster gene salty. Flybase did not report a D. willistoni ortholog for this gene.

The miRNA appears confidently lost in D. virilis through D. grimshawi.

Corrected Alignment:

dme-mir-1014

Species	Coordinate	Alignment
dm3	chr3R:27579231-27579328 -	TGGCCTTTTCTCAAGGTATAATGGAAATAGATTTTAAT------CGCAG----GC---------GCGTC----AGTGG-----TTG--AATTAA------------AATTCATTTTCATTTGCAGTTACTGGATACAACA
droSim1	chr3R:27196220-27196317 -	TGGCCTTCTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCTG----GC---------GCGTC----AGTGG-----TTG--AATTAA------------AATTCATTTTCATTTGCAGTTACCGGATACAACA
droSec1	super_31:233822-233919 -	TGGCCTTCTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCTG----GC---------GCGTC----AGTGG-----TTG--AATTAA------------AATTCATTTTCATTTGCAGTTACCGGATACAACA
droYak2	chr3R:28513868-28513965 -	TGGCCTTTTCCCAAGGTATAATGGAAATAGATTTTAAT------CGCAG----GC---------GCGTC----AGTGG-----TTG--AATTAA------------AATTCATTTTCATTTGCAGTCACCGGATACAACA
droEre2	scaffold_4820:396401-396498 +	TGGCCTTTTCGCAAGGTATAATGGAAATAGATTTTAAT------CGCAG----GC---------GCGTC----AGTGG-----TTG--AATTAA------------AATTCATTTTCATTTGCAGTCACCGGATACAACA
droAna3	scaffold_12911:3510618-3510715 +	TGGCATTCTCCCAAGGTATAATGAAAATTGATTTTAAT------CACAC----GG---------ATCGG----AGTGG-----CAA--AATTAA------------AATTCATTTTCATTTGCAGTCACGGGATACAATG
dp4	chr2:14711225-14711322 +	TGGCCTTCTCCCAAGGTACAATGGAAATAGATTTTAAT------CGGGT----TT---------CGTTT----GGCGG-----TGA--AATTAA------------AATTCATTTTCATTTACAGTGACCGGCATCAACA
droPer1	super_0:5703122-5703219 -	TGGCCTTCTCCCAAGGTACAATGGAAATAGATTTTAAT------CGTGT----TT---------CGTTT----GGCGG-----TGA--AATTAA------------AATTCATTTTCATTTACAGTGACCGGCATCAACA
droWil1	scaffold_181130:8196915-8197021 +	TGGCATTTTCTCAAGGTGAAATGAAAATAAATTTTAATTCGGATAGAAA----GC---------TAATCTAATTGT-A-----TTG--CATTAA------------AATTCGTTTTCATTTGCAGTATCTGGTCTAAATA
droVir3	Unknown	TGGCATTCTCTCAAGGTATG---TACATATTTTTAAAT----------------------------------------------TT--AACCAG------------TATTTACTTTTGTTCACAGTGACCGGCATAAATA
droMoj3	scaffold_6540:30646887-30646982 +	TTGCCTTCTCTCAAGGTAAG--------T-GCTTTGACT-----T---------A---------GCAAA----AGTTA-----TTT---ACTAGAAGTGTTTCTCTGCTTTCGTTTCATCCACAGTGACCGGTGTAAATA
droGri2	scaffold_14624:997050-997159 -	TGGCCTTTTCACAGGGTATGCAGAGCT-TGATTA------------TTTGATTGCTCATTTTACACATT----A-TAAATAAATTATATATATA------------TATACATATGTTATTGCAGTGACTGGCGTAAATA