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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctttttttaccaatgcatccaacatctttactttccaggcaatcctgtaaattttgtaactgcaatagtaaccctattttctggttcactgaagGATCTTCAAGGATGGGAAAACTATAGCAGCTGATAATGCACTGGACTATGCAGCAAACTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTCGAG

Basic information

species Oryza sativa
transcript LOC_Os11g33240.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 10
------------------------------gtagctttttttaccaatgcatccaacatctttactttcc--aggcaatcctgt----aaattttgtaactgcaatagtaaccctatttt-ctggttcactgaagGATCTTCAAGGATGGGAAAACTATAGCAGCTGATAATGCACTGGACTATGCAGCAAACTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTCGAG
                               |   |    ||||    |    || ||  |  | |||    ||  ||   |||    | |||||  || |  |  | |||   | |||   | |||   ||||| || ||||||||||||||| | |||| ||||||| || | ||||| ||||| ||||| || ||||| |||||||| ||||| || ||||  ||||| |||
gtagcttttgttcagatatatgcttcaatttttaatgcaattactggaggtcgcatcacttgaattttgtgaagttaaagttgtttacagattttagaatta-atgattaatattctttcatttgttgtttgaagAATTTTCAAGGATGGGAAATCAATAGAAGCTGATGATTCTCTGGATTATGCGGCAAATTTATCACATATGCTTGGTTTTGACGACCCCAGGATGCTGGAG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 11
-------------------------------------------------------gtagctttttttaccaatgcatcca--acatctttactttccaggcaatcctgt--aaattttgtaactgcaatagtaaccctattttctggttcactgaagGATCTTCAAGGATGGGAAAACTATAGCAGCTGATAATGCACTGGACTATGCAGCAAACTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTCGAG
                                                       ||   ||||||    ||    |     |||  | |  |||  |  ||      |  |||||||  || |     | ||      ||   | |||   ||||| || ||||||  ||||||| | |||| ||| |||||| |  |||||||||| ||||| || |||||||||||||| ||||| || || |||||||| |||
gtagcttttgtttagaaatgtttcatttttaatgcacttactggtggtgacatcagtcaattttttcctgaactagttgtgtacagatgtttttttgaaacagctgcattcaaattttagaattaatgaattatattgtttcatttgttttttgaagAATTTTCAAGAGTGGGAAATCAATAGAAGCCGATAATTCTTTGGACTATGCGGCAAATTTCTCACACATGCTTGGTTTTGACGACCCAAAAATGCTGGAG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 12
------------------------------------gtagctttttttaccaatg-catccaacatctttactttccaggcaatcctgtaaattttgtaactgcaatagtaaccctatttt-ctggttcactgaagGATCTTCAAGGATGGGAAAACTATAGCAGCTGATAATGCACTGGACTATGCAGCAAACTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTCGAG
                                    | |  |  |           ||  | |  | | ||   |  |     || |  |||||||  || |     | |||   |||||   | ||||  ||||| || ||||||| ||||||| | |||| | |||| ||| | ||||| ||||| ||||| || |||||||||||||| |||||||| || |||||||| |||
gtagcttttgttcagacatttgcttcaatttttaatgcaattactggaggtggcatcactcgaattttgtaaagttaaaattgtc-tacaaattttagaattattg-aataatattatttcatttgttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGCGGCAAATTTCTCACACATGCTTGGTTTTGATGACCCTAAAATGCTGGAG

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|3758954|gb|C96653.1|C96653
EST:     GTATGTTTACCGGAG                         GATCTTCAAGGATGGGAAAACTATAGCAGCTGATAATGCACTGGACTATGC
genomic: GTATGTTTACCGGAGgtagcttttt ... ttcactgaagGATCTTCAAGGATGGGAAAACTATAGCAGCTGATAATGCACTGGACTATGC
EST: gi|38470398|gb|CF954529.1|CF954529
EST:     TTAAATTTGATAGCTCGCCTTCCACCAGTGGCTTCGTATGTTTACCGGAG                         GATCTTCAAGGATGGGAAAACTATAGCAGCTGATAATGCACTGGACTATGC
genomic: TTAAATTTGATAGCTCGCCTTCCACCAGTGGCTTCGTATGTTTACCGGAGgtagcttttt ... ttcactgaagGATCTTCAAGGATGGGAAAACTATAGCAGCTGATAATGCACTGGACTATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatcctgtaaattttgtaactgcaatagtaaccctattttctggttcactgaagGATCTTCAAGGATGGGAAAACTATAGCAGCTGATAATGCACTGGACTATGCAGCAAACTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTCGAG
                          tagtaac  putative branch site (score: 1)
      tgtaaattttgtaa  TA-rich tract