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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcattgtgcatttcactagttgctgatctttaacagttgtttcttttgagGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG

Basic information

species Oryza sativa
transcript LOC_Os02g36740.5
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g36740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 5
gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcat---tgtgcatttcactagtt--gctgatctttaacagttgtttcttttgagGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG
                                                                                                    ||  ||| |||| |  |  |||   |    || |  ||  |   |||  | || |||   |  | || | ||| |||| | ||||||||||| || |||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||
----------------------------------------------------------------------------------------------------gttagtgattaatacattgtatatctcctgtgtttttttgtcgatgtaaagttaactgactctgttggtatttgacagCTATTTCTTTTGAGAGCGGCTGGATTTTTGCTGCCATGCTATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG

upper sequence: LOC_Os02g36740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G118957_T05 (Zea mays), 3'ss of exon 2
gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcattgtgcatttcactagtt--gctgatctttaacagttgtttcttttgagGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG
                                                                                                 |||| |   | |  |   |   | |  | |  ||  |    |  |||  | || | |   |  |||| |||||  ||| | ||||||||||| || |||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||
------------------------------------------------------------------------------------------------gttagcgatcgatacattgcatatctcctgtgttttttttggcgatgtaaagttaattgactctgctggtctttggcagCTATTTCTTTTGAGAGCCGCTGGATTTTTGCTGCCATGCTATATTATGGCTTGGGCTATTAGTATCATGCAGCGTCAAAGACAAAGACAG

upper sequence: LOC_Os02g36740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G02960.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggc-aagctatgactccttgcagttttagtgtgtggttaacatctgttattatttagttgctccttcattgtgcatttcactagttgctgatctttaac--agttgtttcttttgagGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG
                                                                  |||  |     |||||    |   ||    ||||  | | |  ||    || |||    || |||||   |  ||      |   ||  | |  |||||  |||    || |  | ||  |  | |||||||||||| | || ||||||||||||||||||||||| || |||||  | || || | |||||| ||||||
-----------------------------------------------------------------gtaagctcattgaagcttcttccttttttctttttcttttattttttgtctcagttgcatttaagttgtaacaccaa-----accacaaaattgtctgattcttattttagCTTGTCCTGCTCCGAGCTGCTGGATTTCTTCTTCCATGCTATATCATGGCTTGGGCCATCAGTATTCTACAGCGCCGAAGACAGAGACAG

upper sequence: LOC_Os02g36740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G62460.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttagatttttttttatgcagtcatgctctgctatcggttcatgttttaacttggccacacttaaatttggcaagctatgactccttgcagttttagtgtgtggttaacatctg-ttattatttagttgctccttcattgtgcatttcactagttgctgatctttaacagttgtttcttttgagGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG
                                                                          | | | ||   |||  |  | |   |||  ||     |  |||  || ||  ||  ||| |    |||| | | |||  ||  |  ||  | |     || | ||  |  |  | || ||||| ||| | || || || || |||||||||||||||||||||||  | ||||||| |||||||||||||
--------------------------------------------------------------------------gtacg-tacatctctct-tactcacagttcgttacagaattctcctttttgctttcttgttataacatttttcgtttt-cttttgtcttctttcggttagCTTTTCATGCTTCGAGCCGCTGGTTTTCTCCTCCCGTGTTACATCATGGCTTGGGCTATTAGTATATTACAACGTCGAAGACAAAGACAG

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|29663450|gb|CB659725.1|CB659725
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGTTGTTTCTTTTGAG            
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTA-TTT-TC------TC------Ggtaagttaga .
EST: gi|29677125|gb|CB673400.1|CB673400
EST:     TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGTTGTTTCTTTTGAG            
genomic: TAACCATTACTAGTAGTGATGATGAAGATGACGCATCTGCTA-TTT-TC------TC------Ggtaagttaga .
EST: gi|88240577|gb|CI239739.1|CI239739
EST:     GTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCG                         GGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTAT
genomic: GTAGTGATGATGAAGATGACGCATCTGCTATTTTCTCGgtaagttaga ... ttcttttgagGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccttcattgtgcatttcactagttgctgatctttaacagttgtttcttttgagGGCTGCTGGATTTTTGCTGCCATGCTATATCATGGCTTGGGCTATTAGTATCATGCAACGTCAAAGACAAAGACAG
                                ctttaac  putative branch site (score: 3)
                                         ttgtttctttt  putative PPT
                              atctttaa  TA-rich tract