Secondary structure and small RNA-seq evidence for dme-mir-4919

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2R:11833377-11833466 +	TGGACATACTAAATGGTGAGTCTC-----T--------------------AGGGGATTAGCAAGCTATAATT---------------------------------TCTCACTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droSim1	chr2R:10571957-10572046 +	TGGACATACTAAATGGTGAGTCTC-----T--------------------AGGGGATTAGCAAGCTATAATT---------------------------------CCTCAATTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droSec1	super_1:9333409-9333498 +	TGGACATACTAAATGGTGAGTCTT-----T--------------------AGGGGATTAGCAAGCCATAATT---------------------------------CCTCACTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droYak2	chr2R:17148711-17148800 -	TGGACATACTGAATGGTGAGTCTC-----T--------------------AGGGGATTAGCAAGCCATGATT---------------------------------CCTCCCTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droEre2	scaffold_4845:14024563-14024652 -	TGGACATACTAAATGGTGAGTCTC-----T--------------------AGGGGATTAGCAAGCCATATTT---------------------------------CCACACTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGAG
droAna3	scaffold_13266:11891001-11891093 -	TGGACATACTGAATGGTGAGTTTACAAGTCG-------------------------GCACTAAT--------TTTTGAAGCGGGAATGTGAATATGA----------------------GCCGTAAATTGCAGAAGCGGTGCTGGGCG
dp4	chr3:18992460-18992549 -	TGGACATCTTAAATGGTGAGTCTTCCATTCCAGTTCCTTTGCGTTTTGTC----------------------------------------------------------CACTGATTCACTCAAACTTATACAGAGGCCGTTTTGGGTG
droPer1	super_242:24174-24263 -	TGGACATCTTAAATGGTGAGTCTTCCATTCCAGTTCCTTTGCGTTTTGTC----------------------------------------------------------CACTGATTCACTCAAACTTATACAGAGGCCGTTTTGGGTG
droWil1	scaffold_181150:1332685-1332769 -	TGGACATAATAGCGGGTGAGTGAA---------------------------AGAGAT-ACGAGATTACAATT---------------------------------TG-GATTACATTTT-TGGTTGGTCGCAGAAACGTCAATGGGTA
droVir3	scaffold_12875:17265801-17265883 +	TCGATGTGCTGAATGGTGAGCTTT--GCCTG-------------------AGTGGGTC--------------CACACC-----------AAATCCTAATC-----C--------------CATTTATTTGCAGAGGCTGTGCTGGGCG
droMoj3	scaffold_6496:10745157-10745258 -	TCGATGTGCTAAATGGTAAGTCCC--ACTTC--------------------AGGCACTTCTAATCT-----------------------GAATATTAATACTCTTTCTTTCTCTCTCTC-TCCTGTCTTGCAGAGGCTGTACTTGGCG
droGri2	scaffold_15245:16779329-16779419 +	TCGATGTTTTAAATGGTGCGTGCTTAACTTG-------------------------AAAGAGAT--------CTCACAAAT------------------------CCAATCTTAATTAAGTGATTCATTGCAGAGGCTGTTCTGGGTG

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2R:11833377-11833466 +	TGGACATACTAAATGGTGAGTCTCTAGGGGATTAGCAAGCTATAATTTCTCACTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droSim1	chr2R:10571957-10572046 +	TGGACATACTAAATGGTGAGTCTCTAGGGGATTAGCAAGCTATAATTCCTCAATTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droSec1	super_1:9333409-9333498 +	TGGACATACTAAATGGTGAGTCTTTAGGGGATTAGCAAGCCATAATTCCTCACTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droYak2	chr2R:17148711-17148800 -	TGGACATACTGAATGGTGAGTCTCTAGGGGATTAGCAAGCCATGATTCCTCCCTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG
droEre2	scaffold_4845:14024563-14024652 -	TGGACATACTAAATGGTGAGTCTCTAGGGGATTAGCAAGCCATATTTCCACACTTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGAG

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

TGGACATACTAAATGGTGAGTCTC-------------TAGGGGATTAGCAAGCTATAATTCCTCAATTAATCCCTGAACGACTTGCAGAGGCCGTTTTGGGTG	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
...................................................................TAATCCCTGAACGACTTGCAG...............	21	1	8.00	8	8
...............GTGAGTCTC-------------TAGGGGATTAGC......................................................	21	1	7.00	7	7
...............GTGAGTCTC-------------TAGGGGATT.........................................................	18	1	1.00	1	1

dp4

TGGACATCTTAAATGGTGAGTCTTCCATTCCAGTTCCTTTGCGTTTTG-------------TCCACTGATTCACTCAAACTTATACAGAGGCCGTTTTGGGTG	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-17.4	-17.0	-16.8	-16.5

droSim1

-17.3	-17.0	-16.7

droSec1

-17.4	-17.3	-17.2	-17.1	-17.1	-17.1

droYak2

-17.4	-17.0	-17.0	-16.7

droEre2

-17.4	-17.0

droAna3

-8.3	-7.7	-7.6	-7.6

dp4

-6.7	-6.1	-6.04	-5.9

droPer1

-6.7	-6.1	-6.04	-5.9

droWil1

-6.4	-5.6

droVir3

-10.3	-10.2

droMoj3

-4.8	-4.1	-4.0	-3.8

droGri2

-10.8	-10.8	-9.9

Generated: 01/05/2013 at 05:20 PM