dme-mir-280
Changes
The reported simulans ortholog reported in the 12-way alignment is wrong as shown below:
The correct ortholog was found in all the 7 strains trace reads using LASTZ and the melanogaster sequence as the query. This ortholog should lie in a gap region of the simulans reference assembly (chr2R:2844465-2844618).
>dme-mir-280-dm3
CTGACGTGTGTATGCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATATGCAAGTCGAGGTCCTCCACACTGCACTCGCCGCCTCGA
>zee54c10.b1:599-724
CTGACGTGTGTGTGCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATATGCAAGTCGAGGTCCTGCACACTGCACTCGCCGCCTCGA
Corrected alignment:
| Species | Coordinate | Alignment |
|---|---|---|
| dm3 | chr2R:4185596-4185720 + | CTGACGTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAT---GCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAAGTC--------------------------------GAG----------------------------GTCCTC-----------CA---C---------AC----------TGCACTC-GCCGCCTCGA-------------- |
| droSim1 | zee54c10.b1:599-724 + | CTGACGTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGT---GCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAAGTC--------------------------------GAG----------------------------GTCCTG-----------CA---C---------AC----------TGCACTC-GCCGCCTCGA-------------- |
| droSec1 | super_1:1832273-1832397 + | CTGACGTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGT---GCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAAGTC--------------------------------GAG----------------------------GTCCTG-----------CA---C---------AC----------TGCACTC-GCCGCCTCGA-------------- |
| droYak2 | chr2L:16840791-16840915 + | CTGACGTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGT---GCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAACTT--------------------------------GAG----------------------------GTCCTG-----------CA---C---------AC----------TGCACTC-TCCCGCTCGA-------------- |
| droEre2 | scaffold_4929:18446687-18446817 - | CTGACGTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGT---GCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAAGTC--------------------------------GAG----------------------------GTCCAG-----------CA---CACTGCAC--AC----------TGCACTT-GCC-CCTCGA-------------- |
| droAna3 | scaffold_13266:1806990-1807233 - | TTGAAATGTG-----------------------TGTATGTGGGTGGGTGGGTG---------------------------------------------------------TGTGT---------------------------GCACTTTCTGCCATCCAGACTGCCAGCCAGCCATCTAGCCAGCCTGCCTGACTGCTTTCCTTGCCACTTGTG-----TGTATGTGTGTGTGTG-------------------TATGA---GCTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATA--TGCAAG----------------------------------------------------------------C---CTGAACAACTTTGGAA---C---------AC----------TGCAATC-GCCTTCTGGA-------------- |
| dp4 | chr3:2170016-2170201 + | TTGATGCCtg-----------------------tgtgtgtgtgt-----------------------------------------------------gt--------gtgtgtgtCCAGTCGGTGTCATGAGGCGTATGCCG----------------------------------------------------------------------------T-----GTGTGTGTGTG-------------------TGTGA---GACGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATG--TGCAGCTG--------------------------------AAG----------------------------AGCCTG-----------TC---CATTGCAC-------------------AAT-CC-CCACCC-------------- |
| droPer1 | super_2:2339680-2339867 + | TTGATGCCTG-----------------------TGTGTGTGTGTG---------------------------------------------------------------TGTGCGTCCAGTCGGTGTCATGAGGCGTATGCCg----------------------------------------------------------------------------t-gtgtgtgtgtgtgtg-------------------tgtgA---GACGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATG--TGCAGCTG--------------------------------AAG----------------------------AGCCTG-----------TC---CATTGCAC-------------------AAT-CC-CCTCCC-------------- |
| droWil1 | scaffold_180701:589914-590141 + | TTGATG----CCCCAACACACACCCACCTCCTATCTATCTAT---------------------------CTATCTCTGTCTCACCATAACTGA------g----------------------------------------------------------------------------------------------------------------------t-gtgtgtgtgtgtgtg-------------------tgtat---gtTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATG--TGCAA---C----CGAAGCAGCAGAAGCCAGGCCCAAGTAG--AAGCAA--------------------AAGGCCTG-----------AA---C---------AT----------TGCACT------------T--GGGCCATACGC |
| droVir3 | scaffold_12875:9206154-9206327 + | TTGATGT---C-------------------------------------------GTCTTTGTGTGCCAT----------------------GTGTGTGT--------GTGTGTGTCCA-----------------------------------------------------------------------------------------------------------------------------------TTTTGTGTGT---GTTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATACA--------TGCCA-----------------G-------------------AGCAGTGCATGCAACTGCC---------------------CAC-AATGCACAT-------------------T----------TCT-----ATCCGC |
| droMoj3 | scaffold_6496:17934933-17935113 - | TTGATGT---C-------------------------------------------GTCGTTGTGTACCAT----GCATTCG----------TGT------GTGCCTGTG----------------------------------------------------------------------------------------------------------TGTG---------TGC----G-------------------TGTGT---GTTAGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATACA--------TGCCA-----------------GGCC---------------GGCCAGTGCATGCAACTTCT---------------------CTC-AATGCATAT-------------------T----------CCA-----ATCCAC |
| droGri2 | scaffold_15245:2520625-2520797 + | TTGATGT---T-------------------------------------------GTCGTTGAGT-----CTAtgtctgtg----------tgt------gtgtgtgtgtg-------------------------------------------------------------------------------------------------------------tgtgt------------gtgcgagtgtCCAGTTCGTGTGT---GTTGGCTTTTATGTATTTACGTTGCATATGAAATGATATTTATAGTAAACAGATTATTTTATATGCAGGTATACATGCAAC-----------------------------------------------------------TCCTT--------------------CTC----------AATGGATCCCCA-------------------------------C |