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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgactattctgagaagtcaatacttgatttaccaagtgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA

Basic information

species Oryza sativa
transcript LOC_Os12g01580.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G150557_T01 (Zea mays), 3'ss of exon 6
gtaatgac-tattc------tgagaagtcaatacttgatttaccaagtgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA
||||  || |  |       |||||| |  | |||| ||||   |||  || | ||  | ||| ||  | |     || |||||||||||||||||||||| ||||||| ||  | |||||| |||| ||||||                                                      
gtaagaacgtgcttgaaaaatgagaattttacacttaatttctgaagacatgtacagagattt-atgttcac-aattgttggatttttgcagTTTGTCACTATTTCTCAGCCGGTGAATGCTATTGCATTTGTGG-----------------------------------------------------

upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G890665_T02 (Zea mays), 3'ss of exon 9
gtaatgac-tattc------tgagaagtcaatacttgatttaccaagtgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA
||||  || |  ||      ||||||||    | || ||||   |||  || | ||  | ||| || ||     | || |||| ||||||||||||||||  ||||||| ||  | |||||| |||| || |||   |||||||||||||||||||||||||||||||| |  |  ||||| || || 
gtaagaacatgctccagaaatgagaagtttgcagttaatttctgaagaaatgtacagagattt-at-gttcccagttgttggacttttgcagTTTGTCACCATTTCTCAGCCGGTGAATGCTATTGCATTCGTGGCTGATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACG

upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G150557_T01 (Zea mays), 3'ss of exon 7
gtaatgactattctgagaagtcaatacttgatttaccaagtgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATG--GATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA
                   |     | |     ||  ||| | | | |  |  |||  ||        |  ||  |    ||    |||   | | | |    | | ||   |   ||| ||| ||  ||  |||||||||||||||||||||||||||||||| |  |  ||||| || || 
-------------------gcttgcaat--gcatattaagcgttgtccgctaatttctta-----caacgcataaaaccatgtg--ttgctgcggatgcgttgcta-taggggtgtttgtgtt-gtagtgCTGATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACG

upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G38330.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaatgactattctgagaagtcaatacttgatttaccaag-tgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA
||||   ||  |||   ||  ||  |   | || |  | | |  | |   |   | |   | ||||     | ||| |   ||||||||||  |||  ||||||||  | |||||| | ||||||||  ||||||||||||| |||||||| |||||||| |  || |  || || ||||  
gtaagatcttatcttttaatccagaaagagtttgaaaagggtagtctcagacaatatctaaataat-----gttggctggatgcagTTTGTGGCTGGATCTCAACCGGTGAATGCTCTAGCGTTTGTTTTGGATGGGCTCTATTATGGTGTCTCTGACTTCGGATTTGCCGCTTATTCTATG

upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv08s0058g00510.t01 (Vitis vinifera), 3'ss of exon 10
--------gtaatgactattctgagaagtcaata------cttgatttaccaagtg-atatgcaatggttttatagtaattggc-tgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA
        ||    | | |  ||   |||  |||      |||   | |    ||| ||  || |||   ||  || ||||    | ||  | |||||||||||||  |||  ||||||||||| |||||| |||| ||||| || ||||| ||||||||||| ||||| |||||||  |  |  || ||||| |  
gtttccatgtggc-attctattggtgagtgcataaactggcttacctcatttggtgcatgggctatgtcatttaagaaatttatgttataaaattttgcagTTTGTTGCTGGATCTCAACCAATGAATGCTATTGCATTTGTTATTGATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATG

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|29639601|gb|CB644610.1|CB644610
EST:     TGTTTACAGATGATGCAGCAGTTTTAGACGTTGCCCAAACTGGAGTCTGG                         TTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGG
genomic: TGTTTACAGATGATGCAGCAGTTTTAGACGTTGCCCAAACTGGAGTCTGGgtaatgacta ... atttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGG
EST: gi|25806216|gb|CA762177.1|CA762177
EST:     GACGTTGCCCAAACTGGAGTTTGG                         TTNGTCCCTGTTTCTCAACCCATAAATGCTGTTGCGTTTGTGAAGGATGGG
genomic: GACGTTGCCCAAACTGGAGTCTGGgtaatgacta ... atttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaccaagtgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA
                                    ggctgat  putative branch site (score: 4)
                                              tttttgc  putative PPT
                       ttttatagtaatt  TA-rich tract