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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttataagacaattttttttgactaactgtttatgagacaattagtagtgatacttccgtcttttaatgtacactgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA

Basic information

species Oryza sativa
transcript LOC_Os01g64660.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 8
gtttataagacaattttttttgactaactgtttatgagacaattagtagtgatacttccgtcttttaatgtacactgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA
           ||||  | | |||||      ||    | ||  |   || |||    || | |     |   |||  |||| |   |   || |||| ||     | |||| ||  |||||||||||| ||||||||||| || |||||||||||||||||||| ||||| ||||| |||||    ||||| || | 
-----------aattcatatagacta------tagagtataaacacacgt-atatccacgccatcagtgggttact--tgag-gtatatggtaatcatttg----atgtatgatt--ctctgtgcagATCCCAAAGAAAGGTAAAATTTATTCAGTGAATGAAGGAAATGCCAAAAACTGGGATCGTCCTACTGCTAC

upper sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ04554 (Selaginella moellendorffii), 3'ss of exon 7
gtttataagacaattttttttgactaactgtttatgagacaattagtagt-gatacttccgtcttttaatgtacactgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA
                                     |  | || |||   |||  |||| |   ||| |  | |  |||||  | |  | || | ||    ||      ||| ||   ||| |||||||||||||||| || || |||||||| |||||||| || ||||| || || ||||||||||| ||   |  
-------------------------------------gtaagttcgtaaaagatgattcctttcattattaca-atggatgattgtg--agatgcccaagattg------atgattttttctttgcagATACCAAAGAAGGGAAAAATTTATTCCGTGAATGAGGGCAATGCAAAGAACTGGGACGAGCCCACTAGATT

upper sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ36627 (Selaginella moellendorffii), 3'ss of exon 6
gtttataagacaattttttttgactaactgtttatgagacaattagta-gtgatacttccgtcttttaatgtacactgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA
                                     |  | || |||   |||  |||| |   ||| |  | |  |||||    |  | || | ||       | || ||| ||   ||| |||||||||||||||| || || |||||||| |||||||| || ||||| || || ||||||||||| ||   |  
-------------------------------------gtaagttcgtataagatgattcctttcattattaca-atggatgatt--gtgagatgcccaa------gatcgatgattgcttctttgcagATACCAAAGAAGGGAAAAATTTATTCCGTGAATGAGGGCAATGCAAAGAACTGGGACGAGCCCACTAGATT

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|29686739|gb|CB683014.1|CB683014
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|29621610|gb|CB626621.1|CB626621
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|38473796|gb|CF957928.1|CF957928
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|58588683|gb|CF986991.1|CF986991
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGAGATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|58590217|gb|CF988525.1|CF988525
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|29613014|gb|CB618027.1|CB618027
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|29617760|gb|CB622772.1|CB622772
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|33820806|gb|CF336207.1|CF336207
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|4714676|gb|AU055793.1|AU055793
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|27546650|gb|CA764792.2|CA764792
EST:     CACTCGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
EST: gi|29682614|gb|CB678889.1|CB678889
EST:     CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAG                         ATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT
genomic: CACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataaga ... ctctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcagATACCAAAGAAAGGGAAGATTTATTCAGTGAATGAAGGGAATGCGAAAAATTGGGACGAGCCTACCGCAAA
 cactgat  putative branch site (score: 3)
                                        cttcactct  putative PPT
               aaaatact  TA-rich tract