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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAATGGCTCTTCTACTCTTAAGGCATACACTAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcattgtgcatttcactagttgctgatctttaacag

Basic information

species Oryza sativa
transcript LOC_Os02g36740.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g36740.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G156734_T01 (Zea mays), 5'ss of exon 5
CTAATGGCTCTTCTACTCTTAAGGCATACACTAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttag-atttttttttatgcagtc-atgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcattgtgcatttcactagttgctgatctttaacag
 | ||||| ||| | ||| | ||||||||||| ||||||||||  || |||||||||||||| |||||||||||||||||||| ||| |  | |   || |||     |  || | |  | ||| |  |   || |   || |     |   ||||| ||                                                                                                
TTGATGGCCCTTTTGCTCCTGAGGCATACACTGACCATTACTAACAGCGATGATGAAGATGATGCATCTGCTATTTTCTCGgttagtgattaatacattgtatatctcctgtgtttttttgtcgatgtaaagttaa--ctgactctgttggtatttgacag-----------------------------------------------------------------------------------------------

upper sequence: LOC_Os02g36740.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G118957_T05 (Zea mays), 5'ss of exon 2
CTAATGGCTCTTCTACTCTTAAGGCATACACTAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttag-atttttttttatgcagtcatgctctgctatcggtt-catgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcattgtgcatttcactagttgctgatctttaacag
 | ||||| ||||| ||| | ||||||||| | ||||||||||  ||||||||||||||||| |||||||||||||||||||| ||  |    |   ||  ||    || ||   |  | | ||     |    | | ||| |    ||    |||||||                                                                                                
TTGATGGCCCTTCTGCTCCTGAGGCATACATTGACCATTACTAACAGTGATGATGAAGATGATGCATCTGCTATTTTCTCGgttagcgatcgatacattgcatatc-tcctgtgttttttttggcgatgtaaagttaattgactctgctggtctttggcag-----------------------------------------------------------------------------------------------
















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|218486849|gb|FG957899.1|FG957899
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGC-
EST: gi|29663450|gb|CB659725.1|CB659725
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|58602522|gb|CK013050.1|CK013050
EST:     TAACCATTACTAGTAGTGATGATGAAGATAACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|29677125|gb|CB673400.1|CB673400
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|33793334|gb|CF322548.1|CF322548
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|86869793|gb|CI316521.1|CI316521
EST:     AACCACTACTACTACTGATGATGAAGATGACGCATC-GCCTATTTTCTCC                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: AACCATTACTAGTAGTGATGATGAAGATGACGCATCTG-CTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|5803574|gb|AI978544.1|AI978544
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|29686718|gb|CB682993.1|CB682993
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|27576199|gb|CA998893.1|CA998893
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|88841916|gb|CI081172.1|CI081172
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|27578072|gb|CB000767.1|CB000767
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|29686717|gb|CB682992.1|CB682992
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|27554462|gb|CA998362.1|CA998362
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|86887217|gb|CI326032.1|CI326032
EST:     GCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: GCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|88243846|gb|CI242968.1|CI242968
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTTGAGGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCT
EST: gi|58695300|gb|CK083987.1|CK083987
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         TTGTTTCTTTTTGAGGGCTGCTGGATTTTTTGCTGCCATGCTATATCATGG
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... tctttaacagTTGTTTCTTTT-GAGGGCTGCTGGATTTTT-GCTGCCATGCTATATCATGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAATGGCTCTTCTACTCTTAAGGCATACACTAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcattgtgcatttcactagttgctgatctttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG