Secondary structure and small RNA-seq evidence for dme-mir-2498

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:16472199-16472340 - ATGT------------GATATTTTTTTCACATTTGCCA-----------TAATCTC---------CTTAAAATAGTA--AAGGCTGTTATGCTTATTTTTGT-GTTTTTTACAAAACTGGCATTCCCGTCT--T-AC-TTATTTTCAGAAAACTTACACCAA-AGTGCACAGATTGAAAAAA
droSim1 chr2R:15133840-15133990 - AAAAAGACAATAATGTGA--ATTTCATCAAA-TTGCCA-----------TAATCTC------------AAAATAGTAAAAAGTCTGTTATGCCTTTTTTTGT-GTGTTTTACAAAAC-CGTATAACCGACTTTT-AC-TTATTTTTAGAAAACTAACACCGA-CGTGTACAGAACGAAAAAA
droSec1 super_1:14027148-14027283 - AATT----------GTGA--ATTTCATCAAA-TTGGCA-----------TAATCTC------------AAAAT------AAGCCTGTTATGCTTTTTTTTGT-GTGTTTTACAAAATTTGCATATTCGACTTTT-AC-TTATTTTCAGAAAACTGACCACGA-TGTGCACAGATTGAAGAAA
droYak2 chr2R:12723862-12724011 + TTTG-------------ATTCTGCATTAGAAATCGCCACCCAACTTTGATT--TTT---------CTAGAAATATTT--AAGTCTGTTCTGCTTAGATTTGT-GAATTTGACAAAATCTGCACAGCCGGCT--T-AATGTATTTTTAGAAACTTAGCACCTTTTGTGTAAAGA---AAAAAC
droEre2 scaffold_4845:10617439-10617588 - TTTG-------------ATTCTGCTTCTTAAATCGCCACCCAACTTATAGT--ATT---------CCAAAAATATTT--AAGTCTGTTATGCATACTTTTGT-GAGTTTGACAAAATGTGCACAACCGGCT--T-ACTGTATTTTTAGAAAACAAACACCTTAGTTGTAAAGAA---TAAAC
droAna3 scaffold_13266:4132040-4132139 + AATA-------------AATAAACAA---AA-TT-------------------CTCAAATATTTAACGTAAAA-----------------ACTTAATTTTGTCGCGATATACAAATTTGGC------GCCA--AAAC-GTATTTTCATAAAATTTT--------------------AAGCTA
dp4 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 Unknown --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:16472199-16472340 - AT------------GTGATATTTTTTTCACATTTGCCA-----------TAATCTCCTTAAAATAGTA--AAGGCTGTTATGCTTATTTTTGTGTTTTTTACAAAACTGGCATTCCCGTCT--TACT-TATTTTCAGAAAACTTACACCAA-AGTGCACAGATTGAAAAAA
droSim1 chr2R:15133840-15133990 - AAAAAGACAATAATGTGA--ATTTCATCAAA-TTGCCA-----------TAATCTC---AAAATAGTAAAAAGTCTGTTATGCCTTTTTTTGTGTGTTTTACAAAAC-CGTATAACCGACTTTTACT-TATTTTTAGAAAACTAACACCGA-CGTGTACAGAACGAAAAAA
droSec1 super_1:14027148-14027283 - AAT----------TGTGA--ATTTCATCAAA-TTGGCA-----------TAATCTC---AAAAT------AAGCCTGTTATGCTTTTTTTTGTGTGTTTTACAAAATTTGCATATTCGACTTTTACT-TATTTTCAGAAAACTGACCACGA-TGTGCACAGATTGAAGAAA
droYak2 chr2R:12723862-12724011 + TTTG-------------ATTCTGCATTAGAAATCGCCACCCAACTTTGATT--TTTCTAGAAATATTT--AAGTCTGTTCTGCTTAGATTTGTGAATTTGACAAAATCTGCACAGCCGGCT--TAATGTATTTTTAGAAACTTAGCACCTTTTGTGTAAAGA---AAAAAC
droEre2 scaffold_4845:10617439-10617588 - TTTG-------------ATTCTGCTTCTTAAATCGCCACCCAACTTATAGT--ATTCCAAAAATATTT--AAGTCTGTTATGCATACTTTTGTGAGTTTGACAAAATGTGCACAACCGGCT--TACTGTATTTTTAGAAAACAAACACCTTAGTTGTAAAGAA---TAAAC

Small RNA-sequencing read pileup

Species Read pileup
droSim1
AAAAAGACAATAATGTGA--ATTTCATCAAA-TTGCCATAATCTC---AAAATAGTAAAAAGTCTGTTATGCCTTTTTTTGTGTGTTTTACAAAACCG-TATAACCGACTTTTACTTATTTTTAGAAAACTAACACCGACGTGTACAGAACGAAAAAASizeHit CountTotal NormTotalGSM343915
Embryo
.............................................................................................AACCG-TATAACCGACTTTTACT..........................................2211.0011
dp4
--------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

-18.8 -18.8 -18.8 -18.8 -18.8 -18.8

droSim1

-23.5 -23.5 -23.5 -23.5 -23.5 -23.5

droSec1

-17.5 -17.5 -17.3 -17.3 -16.7 -16.5

droYak2

-27.9 -27.9 -27.9 -27.9 -27.6 -27.6

droEre2

-27.3 -26.7

droAna3

-5.9 -5.8 -5.3 -5.2 -5.0 -4.9

dp4

No secondary structure predictions returned

droPer1

No secondary structure predictions returned

droWil1

No secondary structure predictions returned

droVir3

No secondary structure predictions returned

droMoj3

No secondary structure predictions returned

droGri2

No secondary structure predictions returned

Generated: 01/05/2013 at 05:10 PM