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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattgatcatctgtattcaacttattagtttttttttttgtaatcataatttgttccaaaaattctaatggtatttatttttgacttatcaatacag

Basic information

species Oryza sativa
transcript LOC_Os09g07830.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G866758_T02 (Zea mays), 5'ss of exon 11
ATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatg-attgatcatctgt-attcaacttatt----agtttttttttttgtaatcataatttgttcca---aaaattctaatggtatttat----ttttgacttatcaatacag
 ||||| || |  || |||||||| ||||| |||||| | || |||||||| || ||||| || |||||||||| |||||| ||||||||||||||||| ||||| |||||   ||| | | |||  || ||    ||  |||| || || | | | | ||| ||  |   |  | | |  | ||| | ||    |||| |||| |||||| ||
TTTTACAACCACTCCAGCACTTGCAATACCAAAGGCTATCGCAAATGCTGGATTAGAGTCATCCCGTGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgcattgagtttcttttactcacattttttgtaagccttttgttatgcattgagagtttattttacttattactttttttgtaataatgtcttttttacttgtcaatatag

upper sequence: LOC_Os09g07830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G830250_T01 (Zea mays), 5'ss of exon 9
ATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatg-attgatcatctgtattca------acttattag--tttttttttttgtaatcataatttgttccaa--aaattctaatggtattta-------tttttgacttatcaa--tacag
 ||||| || |  || |||||||||||||| |||||| |  | |||||||| || ||||| || | |||||||| |||||| ||||||||||||||||| ||||| ||| |   | | ||| ||      | || |||   |||||| || || | | | | || |||  |    | | || ||  | |||         |||| |||||||||  |||||
TTTTACAACCACTCCAGCACTTGCCATACCAAAGGCTATCACAAATGCTGGATTAGAGTCATCCCATGTTGATTTCTATGAGATTAATGAAGCCTTTTCGgtatgtattcagtttttttatccactaaatattttttaagattttttgttatgcattgagagttagttttacttgattgcttatttttttttgaaatgtctttttacttatcaaaatacag

upper sequence: LOC_Os09g07830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT5G48230.1 (Arabidopsis thaliana), 5'ss of exon 10
ATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattgatcatctgtattcaacttattagtttttttttttgtaatcataatttgttccaaaaattctaatggtatttatttttgacttatcaatacag
 || || |||   || || ||||| ||||| || ||  ||||  ||||||| ||||| |||||||  |||||||||||||| || |||||||| ||| ||||| ||     ||||||| |||   |  |||  |  ||        ||  | ||  ||      |||| | |    | | | |||| ||            
TTTCACTACTGCTCCTGCTCTTGCTATACCAAAAGCCATTGCACATGCTGGTTTGGAATCTTCTCAAGTTGATTACTATGAGATCAATGAAGCATTTGCAgtaagaa----catctgtcttc--ttccttacataattgacaaaccattgtgatgcgt------aatttttactaaactgacttttcacag----------

upper sequence: LOC_Os09g07830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv00s0531g00050.t01 (Vitis vinifera), 5'ss of exon 10
ATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatga--ttgatcatctg--tattcaacttattagtttttttttttgtaatcataatttgttccaaaaattctaatggtatttatttttgacttatcaatacag
 ||||| |||| ||| || ||||| ||||| || ||| || ||||||||||| || || ||||||   |||||||||||||||| ||||| || ||  | ||| |   ||  || | ||  | ||  |||| |    | | |||| |  | | | | ||| | | ||   || | ||   |||| ||||   |            
GTTTACAACTACCCCAGCCCTTGCAATACCAAAAGCTATTTCTAATGCTGGCCTGAAGGCTTCTCAAATTGATTACTATGAAATAAATGAGGCTTTCGCCgtaaggatttattcttgtgcttgttatacttctaccatctcttttatcaagtaacagtttatgctaatt-ttatgatctcatttgttttctgcag----------

upper sequence: LOC_Os09g07830.2 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 11
ATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgatt--gatcatctgtattcaacttattagtttttttttttgtaatcataatttgttccaaaaattctaatggtatttatttttgacttatcaatacag
|||||| ||    || || ||||| || || || ||| || | ||||| ||||||||| ||||||   |||||||||||||||| |||||||||||| | ||| | ||     |||   | ||||||  | |       |  |||||  |||   | ||     | |||  || |  |  | |  || ||  |          
ATTTACTACAGCTCCAGCCCTTGCAATTCCAAAAGCTATTTCAAATGCAGGCTTGGAGGCTTCTCAAATTGATTACTATGAAATAAATGAAGCCTTTGCTgtaagtttttatgcattgatcttcaacacaatcacaaactcatttgt--tcaatctatgaattcacaatcttatt--ttgtcacattggatctgcag------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86536502|gb|CI176708.1|CI176708
EST:     TGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: TGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88256251|gb|CI358639.1|CI358639
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88267020|gb|CI378955.1|CI378955
EST:     AATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: AATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|86867692|gb|CI342669.1|CI342669
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88271010|gb|CI386865.1|CI386865
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88270745|gb|CI386003.1|CI386003
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|27410210|gb|CA923280.1|CA923280
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88243342|gb|CI244464.1|CI244464
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|86412530|gb|CI066935.1|CI066935
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88468574|gb|CI515056.1|CI515056
EST:     TTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGG-ATTCCTTCA
genomic: TTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88319137|gb|CI513201.1|CI513201
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88993566|gb|CI110387.1|CI110387
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88436026|gb|CI516562.1|CI516562
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         G
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacag-
EST: gi|88436026|gb|CI516562.1|CI516562
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         G
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacag-
EST: gi|29640958|gb|CB645965.1|CB645965
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|86498219|gb|CI140852.1|CI140852
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|87020189|gb|CI259259.1|CI259259
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88907680|gb|CI091078.1|CI091078
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88265504|gb|CI376406.1|CI376406
EST:     CTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: CTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88830971|gb|CI080395.1|CI080395
EST:     GCTGGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|33683367|gb|CF311606.1|CF311606
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88906443|gb|CI375515.1|CI375515
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88267537|gb|CI379472.1|CI379472
EST:     GAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88839196|gb|CI378120.1|CI378120
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         C
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacag-
EST: gi|88839196|gb|CI378120.1|CI378120
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         C
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacag-
EST: gi|5607308|gb|AU075980.1|AU075980
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|86431389|gb|CI085000.1|CI085000
EST:     GCTTGGAGTCTTCTCGTGTTGAGTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|88466571|gb|CI532378.1|CI532378
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|89182185|gb|CI113554.1|CI113554
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
EST: gi|86486603|gb|CI129236.1|CI129236
EST:     GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCA                         GCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA
genomic: GCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattga ... atcaatacagGCTGTTGCACTTGCAAATCAAAAGCTTCTTGGAATTCCTTCA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTACCACTAGCCCGGCACTTGCCATACCTAAGGCTCTTGCTAATGCTGGCTTGGAGTCTTCTCGTGTTGATTACTATGAAATTAATGAAGCCTTTTCAgtatgattgatcatctgtattcaacttattagtttttttttttgtaatcataatttgttccaaaaattctaatggtatttatttttgacttatcaatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC