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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATTATTCCTGGTCTACCTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaatttcctttttcagatactcataaatcatcttatgaatttcataaggagctctttacttgaaaacgaaagatccataagcagccatgaaatt...

Basic information

species Oryza sativa
transcript LOC_Os05g41930.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g41930.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G033117_T01 (Zea mays), 5'ss of exon 3
GTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATTATTCCTGGTCTACCTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgt---taatttcct--ttttcagatactcataaatcatcttatgaatttcataaggagctctttacttgaaa-acgaaagatccataagcagccatgaaatt
 ||||||||||||||||||||||||||||||||||| | ||||||  | ||||||||||||||||||||||| ||||| |||||||||||||||||||||||||||   |  ||  ||  ||| | ||| |    ||| | | |  | || ||  |||  |  | ||   |||  | || |||||| | |  | ||| |  |    
TTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATCACTCCTGGCTTGCCTCTTTTCCTCTATAACTACACAACCCACCAGCTTCATGGGGTATTTGAGgtgtgtgattggttatctgatttcctgattcctgcaaagcctatc-tcaagttgttaaacacttgttcgtttgtcatacaaaagatacttttg-agctaaaa----

upper sequence: LOC_Os05g41930.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G011923_T01 (Zea mays), 5'ss of exon 3
GTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATTATTCCTGGTCTACCTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaatttcct-ttttcagatactcataaatcatcttatgaatttcataaggagctctttacttgaaa-acgaaagatccataagcagccatgaaatt--
 ||||||||| ||||||||||||||||||| ||||||| |||||| || ||||||||||||||||||||||| || || ||||||||||||||||||||||||||| | | ||   ||| |  || |     || | |||  |||| ||  |||  || | |||  | |  | | | |||||  |     ||| |  |||||  
ATTGCCAGCACGATATCGTGATTCAGTCCGGGCAATTACTCCTGGCCTGCCTCTTTTCCTCTATAACTACACCACTCACCAGCTTCATGGGGTATTTGAGgtgtgtgattatctgatttcctcattcctgcgaagcctctc-tgaaattgttaaacagttgtttgttcgtcatatgtaagat--aggctgagcta-aaaattgt
















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|25800238|gb|CA756199.1|CA756199
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29676071|gb|CB672346.1|CB672346
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|218501446|gb|FG958594.1|FG958594
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|58668957|gb|CK057643.1|CK057643
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|38470564|gb|CF954695.1|CF954695
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTATAGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29687868|gb|CB684143.1|CB684143
EST:     ACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: ACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29676451|gb|CB672726.1|CB672726
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|58679924|gb|CK068611.1|CK068611
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATGGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|109974438|gb|DT806909.1|DT806909
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAAGATCTAATATTGATCCCACTGCATGGGAA
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAA
EST: gi|87006984|gb|CI275292.1|CI275292
EST:     AGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: AGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|22307916|gb|BQ909138.1|BQ909138
EST:     ACACGACCCATCAGCTTCATGGGGTTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAA
genomic: ACACGACCCATCAGCTTCATGGGG-TATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAA
EST: gi|163928377|gb|EG712621.1|EG712621
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29669163|gb|CB665438.1|CB665438
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29667743|gb|CB664018.1|CB664018
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29676329|gb|CB672604.1|CB672604
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|86823854|gb|CI258846.1|CI258846
EST:     ACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: ACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|41882529|gb|BX927965.1|BX927965
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATACTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29675861|gb|CB672136.1|CB672136
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|218502990|gb|FG954156.1|FG954156
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29642637|gb|CB647644.1|CB647644
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|7134957|gb|AU082757.1|AU082757
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|218500689|gb|FG944959.1|FG944959
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29617826|gb|CB622838.1|CB622838
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29642202|gb|CB647209.1|CB647209
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|163928338|gb|EG714682.1|EG714682
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|218481318|gb|FG953310.1|FG953310
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29657474|gb|CB653749.1|CB653749
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|86500670|gb|CI143303.1|CI143303
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|84117273|gb|CD151040.1|CD151040
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29618262|gb|CB623274.1|CB623274
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|86831539|gb|CI299597.1|CI299597
EST:     ACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: ACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|218479007|gb|FG957145.1|FG957145
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATAGATCCCACTGCATGGGAAGATATG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29675022|gb|CB671297.1|CB671297
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATGGGAAGATAAG
EST: gi|29673873|gb|CB670148.1|CB670148
EST:     CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAG                         GCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATG
genomic: CTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaat ... ctcatatcagGCTTCTAGTTTTGGAGGATCTAATATTGATCCCACTGCATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCCAGCAAGATATCGTGATTCAGTCCGAGCAATTATTCCTGGTCTACCTCTTTTCCTCTATAACTACACGACCCATCAGCTTCATGGGGTATTTGAGgtgtgttaatttcctttttcagatactcataaatcatcttatgaatttcataaggagctctttacttgaaaacgaaagatccataagcagccatgaaatt

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