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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaagctaattgcaggcactaacctaaagcgttgttctttggacttctgttcatgccattgcgataataattttttttctaatttaaccttctctgtgtcacagATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTG

Basic information

species Oryza sativa
transcript LOC_Os02g31874.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G144254_T03 (Zea mays), 3'ss of exon 6
gtaattaagctaattgcaggcactaacctaaagcgttgttctttggacttctgttcatgccattgcgataataattttttttctaatttaaccttctctgtgtcacagATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTG
               | | |  ||||||||| ||||||||| |  | || ||       |   |||  | ||  | | |  |  || |  |  | | || ||| ||||||||  ||||||||||||||  ||||  | |||||||||||||||||||||||||||||||| |||||||||||||| || ||||| || ||||||||||
---------------gtatg-gctaacctaatgcgttgttcatgaggctact-------ctgctgctcttatt-tgtctaattcaactccatatgccctatgtgacagATGGGAAGATTGAATGAAGGGTTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATCTGTACAGGATTTG

upper sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G477146_T02 (Zea mays), 3'ss of exon 9
gtaattaagctaattgcaggcactaacctaaagcgttgttctttggacttctgttcatgccattgcgataataattttttttctaatttaaccttc------tctgtgtcacagATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTG
               | | |  ||||||||| | ||||||| |  | || ||   | |||   ||   |  ||  |  || ||||||| ||  | |        | ||| ||||||||| ||| ||||||| || |||||  | |||||||||||||||||||||||||||||||| |||||||||||||| || |||||||| ||||||||||
---------------gtatg-gctaacctaatgtgttgttcctgaggctactccgc-tgctgctgttttcctacgtcgttgtctaattcaagttccgtatgccttatgtgacagATGGCAAGACTGAATGAGGGGCTGTCATTATTTGATGCAATACTGATTGTTCCAATGTTTCAAATTGCTTGGACCTTCTTCTCTATTTGTACAGGATTTG

upper sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA02G07510.2 (Glycine max), 3'ss of exon 10
-----------------gtaattaagctaattgcagg----cactaacctaaagcgttgttctttggactt---ctgttcatgccattgcgataataattttttttctaatttaaccttctctgtgt-cacagATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTG
                 ||||  |   |  |||  ||     |  ||  |       |||| |   ||  |    | || | |  | |     |  ||| |   | ||||   | |||| ||    |   |||||| | || ||||||||||| |||||  | ||||||||||| || |||||||| ||||||||||| || ||||| || || || || || ||||||||| 
gtaaggctttttcttgggtaa--agattctttgttgggctttatcaatttgtgctaatgttttgatgaggtaactttttgaagttaatttttgacaaatgtgaatgctaacgaagccttttccaattgtgcagATGACCAGGTTGAATGAAGGACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAGCATGGACTTTGTTCTCAATATGTACAGGATTTA

upper sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA16G26550.1 (Glycine max), 3'ss of exon 10
--------------gtaattaag-ctaattgcagg----cactaacctaaagcgttgttct--ttggacttctgttc-atgccattgcgataataattttttttctaatttaaccttctctgtgt-cacagATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTG
               |  | |||  |  |||  ||     |  ||  |     | |||| |  | ||    || ||  | |  | |     |  ||| |   | ||||      ||| ||    |   |||||| | || ||||||||||| |||||  | ||||||||||| || |||||||| |||||||||||  | ||||| || || || || || ||||||||| 
gtaaggctttttctttggtaaagattctttgttgggctttatcaatttgtgctgatgttttgatggggtaactttttgaagttaatttatgacaaatgtgaatgctaacccggtcttttccaattgtgcagATGACCAGGTTGAATGAAGGACTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAGATAACATGGACTTTCTTCTCAATCTGTACAGGATTTA

upper sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT3G26670.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaattaagctaattgcaggc-actaacctaaagcgttgttctttggacttctgttcatgccattgcgataataattttttttctaatttaaccttctctgtgtcacagATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTG
||||  ||   ||   || || ||| |  ||     | || |||||   | | ||| |  | ||   | || | |  |     |   ||| |  | || | |||  |||||| | ||||||||||||||  ||||||| | ||||||||| || || |||||||||||||||||||||||||| || || || || || |||||||   
gtaa--aaaaaaacctcaagctactgaaata--ttttggtgctttgttgtgccgttgagactatatagttactgaagtaaaaacgtctttcatgtgct-tctgttgcagATGACAAGATTGAATGAAGGATTGTCTCTATATGATGCAATTCTCATAGTTCCAATGTTTCAGATTGCTTGGACTTTCTTCTCCATCTGTACAGGATGCA

upper sequence: LOC_Os02g31874.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv14s0068g00780.t01 (Vitis vinifera), 3'ss of exon 9
gtaattaagctaattgcaggcactaacctaaagcgttgttctttggacttctgttcatgccattgcgataataattttttttctaatttaaccttctctgtgtcacagATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTG
  |   ||    |    ||  || ||   ||| |  || |        ||       |   |||  |  || || |  | |    || | | || ||        |||||||| || ||||| |||||  ||||  | ||||||||||| || |||||||| |||||||| ||||||||||| || || |||||||| ||||||||||
agagagaaaaagaaaaaagaaacaaaaaaaaatcaatgctgcaattggttggacatgttaaattttgcaaacaactgatat----atattatctccttc----tgcagATGGCAAGGTTGAACGAAGGGTTGTCATTGTTTGATGCAATTCTTATTGTTCCCATGTTTCAAATTGCTTGGACTTTCTTCTCTATTTGTACAGGATTTG

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|58688305|gb|CK076992.1|CK076992
EST:     GGTTCACATACTCAATGCTTCTGTTGTTCCTCTTTACAGCTGGCTTTTGG                         ATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTT
genomic: GGTTCACATACTCAATGCTTCTGTTGTTCCTCTTTACAGCTGGCTTTTGGgtaattaagc ... tgtgtcacagATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgccattgcgataataattttttttctaatttaaccttctctgtgtcacagATGGCGAGATTGAATGAAGGCCTGTCTCTTTTTGATGCAATACTGATTGTTCCAATGTTTCAGATTGCTTGGACCTTTTTTTCTATTTGCACAGGATTTG
                                      ccttctctgt  CT-rich tract
        attgcgataataattt  TA-rich tract