Secondary structure and small RNA-seq evidence for dme-mir-4914

Legend:

mature

star

mismatch

12 Drosophila species corrected alignment

Species	Coordinate	Alignment
dm3	chr2L:2737553-2737676 +	AGACGAGCCCACAACGTGAGTGA-GAGCGAGT------TCCAAT-----------------------GTGGTCC----------------------TCGAAACCAGTTGTGCTTCGATCAGATTCCAAAATTGACACATT--CCG---------------------------------ACCTTGAATCA-CCCACAGCGGATTGGACAGCTC
droSim1	chr2L:2697912-2698035 +	AGACGAGCCCACAACGTGAGTGA-GAGCGAGT------TTCATT-----------------------GTGGTCC----------------------TCGAAACCAGTTGCGCTCCGATCAGATTCCAAAATTGACACATT--CCG---------------------------------ACCTTGAATCA-CCCACAGCGGCTTGGACAGCTC
droSec1	super_5:903635-903758 +	AGACGAGCCCACAACGTGAGTGA-GAGCGAGT------TCCATT-----------------------GTGGTCC----------------------TCGAAACCAGTTGCGCTCCGATCAGATTCCAAAATTGACACATT--CCG---------------------------------ACCTTGAATCA-CCCACAGCGGCTTGGACAGCTC
droYak2	chr2L:2732711-2732833 +	AGACGAGCCCACAACGTGAGTGA-GA----------GGTCCATT-----G-----------T-----GTGATCC----------------------CCAAAACCAGTTCTACTCAGATCTGATTCC-AAATTGACACATTCTCTG---------------------------------ACCTTGAATCA-CCCACAGCGGATTGGATAGCTC
droEre2	scaffold_4929:2790150-2790269 +	AGACGAGCCCACAACGTGAGTGA-GA----------GGTCCATT-----------------------GTGGTCC----------------------TTGAAACCAGTTCCGCTCGGTTCATGATGCCAGATTGACACATT--CCG---------------------------------ACCTTTAATCA-CCCACAGCGGATTGGACAGCTC
droAna3	scaffold_12916:13439490-13439581 +	GGACGAGCCAACAACGTAAGT--------------------------------------------------TCT----------------------CTGAAACCATTC----------CAATTTTCAAACTTATCAAGTT--G-----------------------------------TTAATGTCTTT-CACACAGGGGCTTGGATAGTTC
dp4	chr4_group4:2073904-2074060 +	AGACGAGCCCACAACGTAAGTATCGAACGAGTGAGAGGACCA-GACCAG--AGGCAGCATCTGCGATGCGGTCGAAAAGAGAAGAGAAACCAGAGAGCTAAACCAGTTGCTGACT-----------------GACATTCC--ACA---------------------------------ACCTTGAACCATCCCACAGAGGCCTGGATAGTTC
droPer1	super_10:1078988-1079144 +	AGACGAGCCCACAACGTAAGTATCGAACGAGTGAGAGGACCA-GACCAG--AGGCAGCATCTGCGATGCGGTCGAAAAGAGAAGAGAAACCAGAGAGCTAAACCAGTTGCTGACT-----------------GACATTCC--ACA---------------------------------ACCTTGAACCATCCCACAGAGGCCTGGATAGTTC
droWil1	scaffold_180772:1508923-1509021 +	AGACGAGCCCACAACGTAAGTAA-TAACAAA------------------------------------------------------------------AAAGACCGGTTATTTCCT-----------------G---------TTAGCCTTGAACTTAACCAACATCTC-------------------AA-CCAACAGAGGCCTGGACAGCTC
droVir3	scaffold_12963:11356884-11356997 +	AGACGAGCCCACAACGTAAGCAA-GAATAGAG------A------ATGCAATCAAT-----------G----------------------------CGGAAACCAGTTGCTGACT-----------------AACATGTG--CTTACCTTGAAATTG-----T---------------------AACCA-TTCGCAGGGGCCTGGATAGTTC
droMoj3	scaffold_6308:1548466-1548588 -	CGACGAGCCCACGTCGGGCCTGG-------A-----C-TCCTTTACCGC--CCACAGC---------------------------------------GTC---------------GTCCAGGTGCTGAAGAAGCTA----------TCGCAAAAGGG-----CAAGACCGTCATACTGACCATACATCA-GCCATCG----TCGGAGCTCTT
droGri2	scaffold_15252:5474360-5474483 +	GGACGAGCCCACAACGTAAGTGA-AA----------CA-CCGAAACACCA-----------C-----ACAATC------------------------GAGAACCAGTTACTGACT----AA------GCATTATTATTTT--TTAACCTTGAAATTG-----CATCGC------------------ATC-CATACAGGGGCCTGGACAGTTC

Reduced alignment with Hairpin orthologs

Species	Coordinate	Alignment
dm3	chr2L:2737553-2737676 +	AGACGAGCCCACAACGTGAGTGA-GAGCGAGT------TCCAAT-----------------------GTGGTCC----------------------TCGAAACCAGTTGTGCTTCGATCAGATTCCAAAATTGACACATT--CCG---------------------------------ACCTTGAATCA-CCCACAGCGGATTGGACAGCTC

Small RNA-sequencing read pileup

Species

Read pileup

droSim1

AGACGAGCCCACAACGTGAGTGA-GAGCGAGT--------------------------TTCATTGTGGTCC----------------------TCGAAACCAGTTGCGCTCCGATCAGATTCCAAAATTGACACATTCCGACCTTGAATCA-CCCACAGCGGCTTGGACAGCTC	Size	Hit Count	Total Norm	Total	GSM343915 Embryo
No Reads

dp4

AGACGAGCCCACAACGTAAGTATCGAACGAGTGAGAGGACCAGACCAGAGGCAGCATCTGCGATGCGGTCGAAAAGAGAAGAGAAACCAGAGAGCTAAACCAGTTGCTG-----------------ACTGACATTCCACAACCTTGAACCATCCCACAGAGGCCTGGATAGTTC	Size	Hit Count	Total Norm	Total	GSM343916 Embryo	GSM444067 Head
No Reads

Secondary Structure

dm3

-19.0	-18.3

droSim1

-15.0	-15.0	-14.9	-14.9	-14.9	-14.8

droSec1

-15.7	-15.7	-15.3	-15.3	-15.2	-14.9

droYak2

-22.7	-22.2	-22.1	-22.1

droEre2

-22.9	-22.9	-22.9	-22.8	-22.8	-22.8

droAna3

-4.6	-3.9	-3.8	-3.7	-3.6	-3.6

dp4

-20.5	-20.1	-20.0	-19.6	-19.5	-19.5

droPer1

-20.5	-20.1	-20.0	-19.6	-19.5	-19.5

droWil1

-3.9	-3.8	-3.5	-3.5	-3.3	-3.3

droVir3

-11.0	-10.8	-10.6	-10.4	-10.3	-10.2

droMoj3

-23.1	-22.7

droGri2

-4.3	-4.2	-3.7	-3.5	-3.4	-3.4

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