dme-mir-2535b

dme-mir-2535b

This mirtron resides on the same gene as dme-mir-1007, namely CG1718.
mir-2535b should reside one intron upstream of the mir-1007. In the ananassae gene ortholog however (GF21827), the next intron upstream does not align well with the other species' orthologs:

Species	Coordinate	Alignment
dm3	chrX:21169287-21169387 -	ACGTACATCACTAAGGTAAGTGACTATGCCG-----GGATTGTGGTTAT---TGAACTTAGCG----TCTCCACT--CACGGC-ATTT--CAT------------TCACTTGCAGTACATCACCGCCGAG
droSim1	chrX:12918307-12918407 +	ACGTACATCACCAAGGTAAGTGACTATGCCG-----GGATTGTGGTTAT---TATACTTAGCG----TCTCCACT--CACGGC-ATTT--CAT------------TCACTTGCAGTACATCACCGCCGAG
droSec1	super_8:3476294-3476394 -	ACGTACATCACCAAGGTAAGTGACTATGCCG-----GGATTGTGGTTAT---TATACTTAGAG----TCTCCACT--CACGGC-ATTT--CAT------------TCACTTGCAGTACATCACCGCCGAG
droYak2	chrX:20345010-20345110 -	ACGTACATCACCAAGGTAAGTGACAATGCCG-----GGATTGTGGTTAT---TGAAAATACCT----TCTCCACT--CACGGC-ATTA--TAT------------TCACTTGCAGTACATCACCGCCGAG
droEre2	scaffold_4690:17698644-17698744 -	ACGTACATCACCAAGGTAAGTGACAGTGCCG-----GGATTGTGGTTAT---TAAAAATACCT----TCTCCACT--CACGGC-ATTT--CAT------------TCACTTGCAGTACATCACCGCCGAG
droAna3	scaffold_13334:1053972-1054064 +	TCTGGCTACCGATTGGTGAGTTATCG----A-----CATTATCGATTTCTATCGATTT----------------------------CTATCGAGTTAAAAAAATCCCCTTTCCAGATCTGTGTCAAACGC
dp4	chrXL_group1a:9058690-9058790 +	ACGTACATCACAAAGGTAAGTGGCTATGCCGCGACGGGATTG------------AACCTCTCATCTCTCACCTCT--CACGGC-ATAT--CAA------------TCACTTGCAGTACATCACCGCCGAG
droPer1	super_15:1452144-1452244 +	ACGTACATCACAAAGGTAAGTGGCTATGCCGCGACGGGATTG------------AACCTCTCATCTCTCACCTCT--CACGGC-ATAT--CAA------------TCACTTGCAGTACATCACCGCCGAG
droWil1	Unknown	ACTTACATTACCAAGGTGAGT----------------------------------------------------------------TTT--GTT------------TTTCTTACAGTACATTACATCGGAG
droVir3	Unknown	ACGTGCATTACCAAGGTAAGC-----------------------------------------------CTCTTCT--CACGAC-ATCCCTTAA------------TCCCTTGCAGTACGTTGCCAACGAA
droMoj3	Unknown	ACATGCATAACCAGGGTAAGTGCTCA-GCTG-----CTtTTtTttTttT---tgttTTTTttT-------------------T-tTTT--CGT------------CGCCTTACAGTACATCTCCAAGGAG
droGri2	scaffold_15203:11132616-11132716 +	ACCTACATTACTAAGGTATGT------TCGA-----TGATTTTGGTTTTTTTTGGCTTTACTT----TCACCGTTTACACGACAATTT--CAT------------CCTTTTGCAGTACGTGACCAGTGAG

The true orthologous intron in ananassae actually span over 400nt. The sequence shown in the alignment below is only the two flanking ends of that intron (hence the unknown coordinate):

No changes

dme-mir-2535b

Species	Coordinate	Alignment
dm3	chrX:21169287-21169387 -	ACGTACATCACTAAGGTAAGTGACTATGCCG-----GGATTGTGGTTATTGAA---CTTAGCG----TCTCCACT--CACGGCATTT--CATTCACTTGCAGTACATCACCGCCGAG
droSim1	chrX:12918307-12918407 +	ACGTACATCACCAAGGTAAGTGACTATGCCG-----GGATTGTGGTTATTATA---CTTAGCG----TCTCCACT--CACGGCATTT--CATTCACTTGCAGTACATCACCGCCGAG
droSec1	super_8:3476294-3476394 -	ACGTACATCACCAAGGTAAGTGACTATGCCG-----GGATTGTGGTTATTATA---CTTAGAG----TCTCCACT--CACGGCATTT--CATTCACTTGCAGTACATCACCGCCGAG
droYak2	chrX:20345010-20345110 -	ACGTACATCACCAAGGTAAGTGACAATGCCG-----GGATTGTGGTTATTGAA---AATACCT----TCTCCACT--CACGGCATTA--TATTCACTTGCAGTACATCACCGCCGAG
droEre2	scaffold_4690:17698644-17698744 -	ACGTACATCACCAAGGTAAGTGACAGTGCCG-----GGATTGTGGTTATTAAA---AATACCT----TCTCCACT--CACGGCATTT--CATTCACTTGCAGTACATCACCGCCGAG
droAna3	Unknown	ACTTATATTACAAAGGTAAGTAT---------------------------------------------------C--CAAGTTATTTC-CTTCAATTTTCAGTTCATAACCGCCGAA
dp4	chrXL_group1a:9058690-9058790 +	ACGTACATCACAAAGGTAAGTGGCTATGCCGCGACGGGAT---------TGAA---CCTCTCATCTCTCACCTCT--CACGGCATAT--CAATCACTTGCAGTACATCACCGCCGAG
droPer1	super_15:1452144-1452244 +	ACGTACATCACAAAGGTAAGTGGCTATGCCGCGACGGGAT---------TGAA---CCTCTCATCTCTCACCTCT--CACGGCATAT--CAATCACTTGCAGTACATCACCGCCGAG
droWil1	Unknown	ACTTACATTACCAAGGTGAGT---------------------------------------------------------------TTT--GTTTTTCTTACAGTACATTACATCGGAG
droVir3	Unknown	ACGTGCATTACCAAGGTAAGC-----------------------------------------------CTCTTCT--CACGACATCCCTTAATCCCTTGCAGTACGTTGCCAACGAA
droMoj3	Unknown	ACATGCATAACCAGGGTAAGTGCTCA-GCTG-----CTtTTtTttTttTtgtt---TTTTttT-------------------TtTTT--CGTCGCCTTACAGTACATCTCCAAGGAG
droGri2	scaffold_15203:11132616-11132716 +	ACCTACATTACTAAGGTATGT------TCGA-----TGATTTTGGTTTTTTTTGGCTTTACTT----TCACCGTTTACACGACAATTT-CATCCTTTTGCAGTACGTGACCAGTGAG