Eaat2_in6

chr2L:738436-738507 -

Candidate
[View on UCSC Genome Browser {Cornell Mirror}]

mirtron

Legend:

   mature strand at position 738487-738507
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species Coordinate Alignment
dm3 chr2L:738421-738522 - CGTGGACTGGTTTGTGTGAGTATGG---------AT----------------------C-TAATTTGTA-----ATGGCAGTTCCACTGCGAAAAAGCTTTATCGAAGATCCATCTCCTTGCAGGGATCGGATTCGCAC
droSim1 chr2L:739962-740062 - CGTGGACTGGTTTGTGTGAGTATGG---------AT----------------------C-TGATTTGGA-----ATGGCAGTTCCACTGCGCCAAAGCTTTATCGAAGATTCTTCT-CTTGCAGGGATCGGATTCGCAC
droSec1 super_14:710120-710220 - CGTGGACTGGTTTGTGTGAGTATGG---------AT----------------------C-TGATTTGGA-----ATGGCAGTTCCACTGCACAAAAGCTTTATCGAAGATTCTTCT-CTTGCAGGGATCGGATTCGCAC
droYak2 chr2L:721660-721764 - CGTGGACTGGTTTGTGTGAGTATGG---------AT----------------------C-TGATTAGGATTCCAAT-GTAATTCTACTGCGAAACAGCTTCATCGAAGGTTCTTCT-CTTGCAGGGATCGGATTCGCAC
droEre2 scaffold_4929:793076-793176 - CGTGGACTGGTTTGTGTGAGTATGG---------AT----------------------C-CGATTCAGA-----ATGCTGATTCCACTGCGAAGAAGCTTCATCGAAGGGGCTTCT-CTTGCAGGGATCGGATTCGCAC
droAna3 scaffold_12916:1707814-1707900 - CGTGGACTGGTTTGTGTGAGTATGA---------GA----------------------T-GGATGGAGGGCTCAG-------T---CCGTGTAGTAACCACAT---------CCCC-TTTCCAGAGACCGCATCCGCAC
dp4 chr4_group3:8989807-8989896 + CGTCGACTGGTTTGTGTAAGTCCTG---------ATCCC-GACTCTCCTCCTTAGAGCTTCGCTTCATT--------------------------------------GTGTCCTTT-GCTGCAGCGACCGCATTCGGAC
droPer1 super_8:173764-173853 + CGTCGACTGGTTTGTGTAAGTCCTG---------ATCCC-GACTCTCCTCCTTAGAGCTTCGCTTCATT--------------------------------------GTGTCCTTT-GCTGCAGCGACCGCATCCGGAC
droWil1 scaffold_180772:2492802-2492889 + CGTCGATTGGTTTGTGTAAGTACA-------------TT-GGCCTTTTTACACAGAGAT-TGATTCATA-----------------------------------ATACTTTA-TTTATTGCCAGTGATCGTATTCGCAC
droVir3 Unknown CGTGGATTGGTTTGTGTAAGTA------------------------------------------------------------------------------------------------TTGCAGAGATCGCATTCGCAC
droMoj3 Unknown CGTGGATTGGTTTGTGTAAGTAGAG---------C------------------------------------------------------------------------------TAT-ATTGCAGTGATCGCATACGCAC
droGri2 Unknown TGTCGATTGGTTTGTGTAAGTACTGGGGGAGGGGATTATGGATTATCCCAAATATAGTTTTGAATT----------------------------------T--------ATAAATT-CTTAAAGTGATCGCATTCGCAC

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species Coordinate Lastz Id Alignment
dm3 chr2L:738421-738522 - NA CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTAATTTG-----------TAATGGCAGT-----TC-CACT-GCGAA--AAAGCTTTATCGAA-G--------------ATCCAT---CTCCTTGCAGGGATCGGATTCGCAC
droSim1 chr2L:739962-740062 - 2 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAATGGCAGT-----TC-CACT-GCGCC--AAAGCTTTATCGAA----------------GATTCT---TCTCTTGCAGGGATCGGATTCGCAC
droSec1 super_14:710120-710220 - 2 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAATGGCAGT-----TC-CACT-GCACA--AAAGCTTTATCGAA----------------GATTCT---TCTCTTGCAGGGATCGGATTCGCAC
droYak2 chr2L:721660-721764 - 2 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTAG-----------GATTCC-AATGTAATTC-TACT-GCGAA--ACAGCTTCATCGAA----------------GGTTCT---TCTCTTGCAGGGATCGGATTCGCAC
droEre2 scaffold_4929:793076-793176 - 2 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CCGATTCA-----------GAATGCTGAT-----TC-CACT-GCGAA--GAAGCTTCATCGAA----------------GGGGCT---TCTCTTGCAGGGATCGGATTCGCAC
droEug1 scf7180000409554:1463548-1463649 - 4 CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GACTAATTAC-----TC-CCCC-GAAGA--AGTCGCTTAACAAA-G--------------GACTCT---GTTCTTGCAGGGATCGCATTCGCAC
droBia1 scf7180000302261:3089215-3089316 + 1 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTTC-----------GAGTGGTTAT-----CG-CACG-GGGAA--AGCCACTAATGCAA-G--------------GGATCT---TGTGTTGCAGGGATCGGATTCGGAC
droTak1 scf7180000415856:360180-360285 - 5 CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAGTGGCTAT-----CCTCATT-AGGTA--GATGACTAACCCAA-G--------------GAATCTTGTCTTGTCGCAGGGATCGGATTCGCAC
droEle1 scf7180000491026:48627-48723 + 1 CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GTTTGTTTTT-----CT-CAAC-CGAAT--G----GTAACCTAC----------------AATTTA---ACATTTCTAGGGATCGGATTCGCAC
droRho1 scf7180000767553:111843-111943 + 1 CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAACATCTTT-----CT-GGGG-GCAAT--CATAATTTATACAA----------------TATTTG---GGATTTCCAGGGACCGGATTCGCAC
droFic1 scf7180000453904:1013475-1013577 - 2 CGTGGACTGGTTTGTGTGAGTACGG-----AT------CTGGCTTT-----------GGTTGC-GGT-T---AA-CCCT-GGGGAGTAGTGAGTAATGTGG----------------GCCTTC---CACTTTTCAGGGACAGGATTCGGAC
droKik1 scf7180000301725:290060-290161 + 1 CGTGGACTGGTTTGTGTGAGTATGA-----AGGGGGT---TTTCTG-------------------GT-----AT-CCTTGAGGGG--GATATTTGACCTAA-AGGGAT----------TATGT---TTTCCTAAAGGGATCGAATTCGCAC
droAna3 scaffold_12916:1707814-1707900 - 1 CGTGGACTGGTTTGTGTGAGTATGA-----GA------TGGATGGAGGGCTCAGTCCGTGTAG-------------------------TAACC-------------------------ACATC---CCCTTTCCAGAGACCGCATCCGCAC
droBip1 scf7180000396728:369103-369188 - 2 CGTCGACTGGTTTGTGTGAGTATGG-----GA------CCCAGTCC-----------GTGTGT--------------------------------------AAACCACTGTT--ATAATCCAC---TTCCCTCCAGAGATCGCATCCGCAC
dp4 chr4_group3:8989807-8989896 + 3 CGTCGACTGGTTTGTGTAAGTCCTG-----A-----------TCCC-----------GACTC-----------------------TC----CTCC----TTAGAGCTTCGCTTCATTGTGTCC---TTTGCTGCAGCGACCGCATTCGGAC
droPer1 super_8:173764-173853 + 3 CGTCGACTGGTTTGTGTAAGTCCTG-----A-----------TCCC-----------GACTC-----------------------TC----CTCC----TTAGAGCTTCGCTTCATTGTGTCC---TTTGCTGCAGCGACCGCATCCGGAC
droWil1 scaffold_180708:429041-429131 + 1 CGTGGATTGGTTGCTGTAAGCAATATAT--AT------CTCTTTTG-----------CATAAT-TGT---------ATA-ATGCC---------AACTGCT------------------AATT---TATTTTCCAGGGATCGGTTCCGCAC
droVir3 scaffold_12723:5465392-5465486 - 1 TGTCGACTGGCTGCTGTATGTAAAT-----GC------TAGAACTT-----------TATGT-----------------------TT----GGTC----CTGGATATACATTTTCTGTTCGAT---TAATTTTTAGTGATCGTTTCCGCAC
droMoj3 scaffold_6500:11048776-11048863 - 5 TGTCGATTGGCTACTGTATGTAGATGTC--AA---AATTTGTACTT-----------GACTGT-----------------------T----ATTTATTGAA-----------------ATTTG---ATTGTCTTAGGGATCGTTTCCGTAC
droGri2 scaffold_15252:7120755-7120854 - 4 TGTCGATTGGTTTGTGTAAGTACTGGG-GGAGGGGAT-----TATG-----------GATTA-----------------------TC----CCAA----ATATAGTTTTGAATTTATAAATTC---TGATTTAAAGTGATCGCATTCGCAC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species Alignment
dm3
CGTGGACTGGTTTGTGTGAGTATGG---------AT----------------------C-TAATTTGTA-----ATGGCAGTTCCACTGCGAAAAAGCTTTATCGAAGATCCATCTCCTTGCAGGGATCGGATTCGCACSizeHit CountTotal Norm
droSim1
CGTGGACTGGTTTGTGTGAGTATGG---------AT----------------------C-TGATTTGGA-----ATGGCAGTTCCACTGCGCCAAAGCTTTATCGAAGATTCTTCT-CTTGCAGGGATCGGATTCGCACSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
..............................................................ATTTGGA-----CTGGCACTTCC......................................................1812.000.000.000.002.00
.........GTTTGTGTGTGTATGG---------GT----------------------.................................................................................1811.001.000.000.000.00
............................................................................................CAAAACTTTATCGAAGGT.............................1811.000.000.001.000.00
droSec1
CGTGGACTGGTTTGTGTGAGTATGG---------AT----------------------C-TGATTTGGA-----ATGGCAGTTCCACTGCACAAAAGCTTTATCGAAGATTCTTCT-CTTGCAGGGATCGGATTCGCACSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
droYak2
CGTGGACTGGTTTGTGTGAGTATGG---------AT----------------------C-TGATTAGGATTCCAAT-GTAATTCTACTGCGAAACAGCTTCATCGAAGGTTCTTCT-CTTGCAGGGATCGGATTCGCACSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
droEre2
CGTGGACTGGTTTGTGTGAGTATGG---------AT----------------------C-CGATTCAGA-----ATGCTGATTCCACTGCGAAGAAGCTTCATCGAAGGGGCTTCT-CTTGCAGGGATCGGATTCGCACSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
droAna3
CGTGGACTGGTTTGTGTGAGTATGA---------GA----------------------T-GGATGGAGGGCTCAG-------T---CCGTGTAGTAACCACAT---------CCCC-TTTCCAGAGACCGCATCCGCACSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
.......................GA---------GA----------------------x-GGATGGAGGGGT...................................................................1612.000.000.002.000.00
...............GTGAGTATGA---------GA----------------------T-GGATGG.........................................................................1911.000.001.000.000.00
....................GATGA---------GA----------------------x-GGATGGAGGGC....................................................................1811.000.001.000.000.00
............................................................CGATGGTGGGCTCAG-------T---CCG..................................................1911.000.001.000.000.00
dp4
CGTCGACTGGTTTGTGTAAGTCCTG---------ATCCC-GACTCTCCTCCTTAGAGCTTCGCTTCATT--------------------------------------GTGTCCTTT-GCTGCAGCGACCGCATTCGGACSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
CGTCGACTGGTTTGTGTAAGTCCTG---------ATCCC-GACTCTCCTCCTTAGAGCTTCGCTTCATT--------------------------------------GTGTCCTTT-GCTGCAGCGACCGCATCCGGACSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
droWil1
CGTCGATTGGTTTGTGTAAGTACA-------------TT-GGCCTTTTTACACAGAGAT-TGATTCATA-----------------------------------ATACTTTA-TTTATTGCCAGTGATCGTATTCGCACSizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
..................................................................................................................TTATTGCCAGTGGTTGTAT......1911.000.001.000.000.00
...................................................................................................................TATTGCCAGTGGTTGTAT......1811.000.001.000.000.00
CGTCGATTGGTTTGTTGA.........................................................................................................................1811.000.000.000.001.00
droVir3
CGTGGATTGGTTTGTGTAAGTA------------------------------------------------------------------------------------------------TTGCAGAGATCGCATTCGCACSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
droMoj3
CGTGGATTGGTTTGTGTAAGTAGAG---------C------------------------------------------------------------------------------TAT-ATTGCAGTGATCGCATACGCACSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
TGTCGATTGGTTTGTGTAAGTACTGGGGGAGGGGATTATGGATTATCCCAAATATAGTTTTGAATT----------------------------------T--------ATAAATT-CTTAAAGTGATCGCATTCGCACSizeHit CountTotal NormV109
Male body

12-way Secondary Structure

dm3 droSim1 droSec1 droYak2 droEre2 droAna3 dp4 droPer1 droWil1 droVir3 droMoj3 droGri2
RNAfold Image
UNAFold Image

20-way Secondary Structure

dm3 droSim1 droSec1 droYak2 droEre2 droEug1 droBia1 droTak1 droEle1 droRho1 droFic1 droKik1 droAna3 droBip1 dp4 droPer1 droWil1 droVir3 droMoj3 droGri2
RNAfold Image
UNAFold Image

Generated: 04/20/2012 at 05:26:19 EDT