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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttctgcacatcttgccaccggttgccagctgtcttgcacattactcaggtatcttttttttcttctgttgactcaagtcatacttgatgtgatccacagGTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG

Basic information

species Oryza sativa
transcript LOC_Os05g01240.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G156956_T02 (Zea mays), 3'ss of exon 12
gtaggttctgcacatcttgccaccggttg---ccagctgtcttgcacattactcaggtatcttttttttcttctgttgactcaagtcatacttgatgtgatccacagGTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG
||| || || | | |  ||||| |  |||   |||     |  |   |||  |   |  |    ||||| ||   |||  |  | | ||| ||||||  ||| ||||||||| | ||||||||||||||||||||||||||||||| ||||| ||||| || ||||||||||| || |||||||||||||||
gtacgt-ctacgccttatgccaacttttgattccatacacccaggctattgtttcaggctggcgtttttttttctttg--tagacttatagttgatgccatcaacagGTACACCAGTAAGCTGCTTTTGGCTGTCATTGATGAGAATCACCGAGGAACTTATGATTTCATCTACCTTCCAATTGATTTTAAG

upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ29695 (Selaginella moellendorffii), 3'ss of exon 6
gtaggttctgcacatcttgccaccggttgccagctgtcttgcacattactcaggtatcttttttttcttctgttgactcaagtcatacttgatgtgatccacagGTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG
                                       |   |||| |  |   | |       ||||  | |||    | | |   ||  |  |      |||||||  |  ||||||||| || |    ||||| ||| |||||||||| |||||||||||||||||| | |||||||| ||||||
--------------------------------------gtaagcattccgaacagagca-----gtcttgcggtgat---atttacgttt--ttcggcttttagGTACACATCAAAGCTGCTTCTGTCGACAATTGACGAGCACCACCGTGGTACCTACGATTTCATCTATTTACCAATTGACTTTAAG

upper sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ28200 (Selaginella moellendorffii), 3'ss of exon 8
gtaggttctgcacatcttgccaccggttgccagctgtcttgcacattactcaggtatcttttttttcttctgttgactcaagtcatacttgatgtgatccacagGTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG
                                                    |  | | ||    ||||  | | |    | | |   ||  |  |      |||||||  |  ||||||||| || |    ||||| ||| |||||||||| |||||||||||||||||| | |||||||| ||||||
----------------------------------------------------gtaagcattccagtcttgcggtcat---atttacgttt--ttcggcttttagGTACACATCAAAGCTGCTTCTGTCGACAATTGACGAGCACCACCGTGGTACCTACGATTTCATCTATTTACCAATTGACTTTAAG

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|58602954|gb|CK013482.1|CK013482
EST:     AAGGGTGAAGATTCACGCACCACCCTGATGATCAAGAACATACCAAACAA                         GTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAAC
genomic: AAGGGTGAAGATTCACGCACCACCCTGATGATCAAGAACATACCAAACAAgtaggttctg ... tgatccacagGTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAAC
EST: gi|33381398|gb|CF196741.1|CF196741
EST:     AAGGGTGAAGATTCACGCACCACCCTGATGATCAAGAACATACCAAACAA                         GTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAAC
genomic: AAGGGTGAAGATTCACGCACCACCCTGATGATCAAGAACATACCAAACAAgtaggttctg ... tgatccacagGTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAAC
EST: gi|29674666|gb|CB670941.1|CB670941
EST:     AAGGGTGAAGATTCACGCACCACCCTGATGATCAAGAACATACCAAACAA                         GTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAAC
genomic: AAGGGTGAAGATTCACGCACCACCCTGATGATCAAGAACATACCAAACAAgtaggttctg ... tgatccacagGTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAAC
EST: gi|218489237|gb|FG949713.1|FG949713
EST:     AAGGGTGAAGATTCACGCACCACCCTGATGATCAAGAACATACCAAACAA                         GTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAAC
genomic: AAGGGTGAAGATTCACGCACCACCCTGATGATCAAGAACATACCAAACAAgtaggttctg ... tgatccacagGTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaggtatcttttttttcttctgttgactcaagtcatacttgatgtgatccacagGTACAACTGTAAGCTGCTTTTGGCTGTCATTGATGAGAACCACCGTGGAACCTACGATTTCATCTATCTCCCAATTGATTTTAAG
     tatcttttttttctt  TA-rich tract