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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtacctttggctttgccttttttattttctaacattcttcttgttcacaagtgcttgagtttgactagctctgaatgtgatgatcagCTGGAACCCAGATGCAATTGTATTCAATTCCTGGCAACAGTATGGCACTCCTAGTTATTGGATGCAAACATATTTCCGTGAATCAAGTGGTTCTGTGATT

Basic information

species Oryza sativa
transcript LOC_Os11g03780.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03780.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 15
---------gttagtacctttggctttgccttttttattttctaacattcttcttgttcacaagtgcttgagtttgactagctctgaatgtgatgatcagCTGGAACCCAGATGCAATTGTATTCAATTCCTGGCAACAGTATGGCACTCCTAGTTATTGGATGCAAACATATTTCCGTGAATCAAGTGGTTCTGTGATT
         |||   |  |      ||    |  ||  |   | |  | |   |  | | |  |    | |  |    | |     | |    |  | || |||||||| ||||||||||||||||| ||||  || |  ||||| |||||||| |||||| |||||  || ||||   || ||||||||  |     ||
aagtaaagtgttttcatttcaaatgttatggtggttggtaaatcatgtacagttgttcctcttgatggtaaactaagattgtgtcaatttctgtcgttagGTGGAACCCGGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAACTATTTTTCTCAGAGTCAAGTGGAGCAACACTT

upper sequence: LOC_Os11g03780.2 (Oryza sativa), 3'ss of exon 15
lower sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 14
-gttag-tacctttggctttgccttttttat--tttctaacattcttc---ttgttca--caagtgcttgagtttgactagctctgaatgtgatgatcagCTGGAACCCAGATGCAATTGTATTCAATTCCTGGCAACAGTATGGCACTCCTAGTTATTGGATGCAAACATATTTCCGTGAATCAAGTGGTTCTGTGATT
 || |  |   ||    | |    ||    |  || |||| ||   |    ||||||   |   ||  | |  |    | |     | |    | || || |||||||||||||||||||||||||| ||||  || |  ||||| |||||||| |||||| |||||  || ||||   || || |||||  |     ||
agtaaaatgttttcaattctaatgttaaggtggttactaaaatatgtagaattgttcctcctgatggctaaactaatattgtgtcaatttctgtcattagGTGGAACCCAGATGCAATTGTATTCAACTCCTTTCAGCTCTATGGAACTCCTAGCTATTGGGTGCAAGTATTTTTCTCAGAGTCGAGTGGAGCAACACTT

upper sequence: LOC_Os11g03780.2 (Oryza sativa), 3'ss of exon 15
lower sequence: PP1S106_48V6.2 (Physcomitrella patens), 3'ss of exon 17
-----gttagtacctttggctttgccttttttattttctaacattcttcttgttcacaagtgcttga--gtttgactagctctgaatgtgatgat--cagCTGGAACCCAGATGCAATTGTATTCAATTCCTGGCAACAGTATGGCACTCCTAGTTATTGGATGCAAACATATTTCCGTGAATCAAGTGGTTCTGTGATT
        || |   |   ||||  | |   ||   |  |  |   |   | |  ||   | ||     |   |   |  | ||  |||| |     ||| |||||||||||||||||||| ||||| || |||||||| || || || || || || ||| | ||    |  ||     | || |  ||| | |   ||
catcacacagaatagtccactttttcctccctaaaataaagaacagtaaatttctacgcatactgagtggaagggacatttatgtgtgtgttcgcaacagATGGAACCCAGATGCAATTGTTTTCAACTCTTGGCAACAATACGGGACACCCAGCTACTGGGTTCAGCATTTCTTTAAAAACTCCAACGGTGCCGACCTT

upper sequence: LOC_Os11g03780.2 (Oryza sativa), 3'ss of exon 15
lower sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 14
--------gttagtacctttggctttgccttttttattttctaacattcttcttgttcacaagtgc---ttgagtttgactagctc-tgaatgtgatgatcagCTGGAACCCAGATGCAATTGTATTCAATTCCTGGCAACAGTATGGCACTCCTAGTTATTGGATGCAAACATATTTCCGTGAATCAAGTGGTTCTGTGATT
        || |    | |    | | |||  |  |     ||  | |     ||   |  | ||     ||||    |||||||  |   |||| ||| ||| |||||||| ||||||||||| ||||| ||||||||||||||||| || || || || ||| | |||  || ||||    |||| |  ||  |     | 
tacagaaggtgaaggtcatca--tatccctcgtggaacacgtatgaattgaaatgaagaggaatgtaagctgagaa-aactagctggtctgtgtggtgaccagATGGAACCCCGATGCAATTGTCTTCAACTCCTGGCAACAGTATGGGACACCCAGCTACTGGGTTCAACAATTTTTCAAGAAATCCAACGGCGCCTACCTC

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|27548162|gb|CA766165.2|CA766165
EST:     TTCAGATGGCAAGCTATGCACCGCTCTTCGTAAATGACAATGACCCGCAC                         CTGGAACCCAGATGCAATTGTTTTCAATTCCTGGCAACAATATGGCACTC
genomic: TTCAGATGGCAAGCTATGCACCGCTCTTCGTAAATGACAATGACC-GCACgttagtacct ... tgatgatcagCTGGAACCCAGATGCAATTGTATTCAATTCCTGGCAACAGTATGGCACTC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcttcttgttcacaagtgcttgagtttgactagctctgaatgtgatgatcagCTGGAACCCAGATGCAATTGTATTCAATTCCTGGCAACAGTATGGCACTCCTAGTTATTGGATGCAAACATATTTCCGTGAATCAAGTGGTTCTGTGATT
                          gtttgac  putative branch site (score: 4)