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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatcatgtctagcactttttatcatgttgatgtaatgagaatgatgtttccatgaaaatggattatttcatgggggaatttcataagaaataatgaacagtcctttggatagggtttagcaccagtagtattatgactgtctcacacttatgatttggcaatgaaatttttgctcaatacag

Basic information

species Oryza sativa
transcript LOC_Os03g58040.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g58040.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G178415_T02 (Zea mays), 5'ss of exon 5
ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatc-atgtctagcac-tttttatcatgttgatgtaatgagaatgatgtttccatgaaaatggattatttcatgggggaatttcataagaaataatgaacagtcctttggatagggtttagcaccagtagtattatgactgtctcacacttatgatttggcaatgaaatttttgctcaatacag
|||||||| |||||||||||||||||||||||||| |||||||| ||||||||||| ||||| ||||| ||||| ||||| | | || | ||   | |||| | |||||   |||| ||| || |||||||  |    || |   ||         | |  || |||| |  |                                                                                           
ACAATGGCATGGATACTTGACGAATACTCAAAGTTCCATGGTTACTCACCTGCTGTTGTGACAGGAAAGCCTGTGgtaagcaactatctatactgcattttcaacatgtatgtgtactgaaaacgatgttttgagatcaaagttgtaaaatgctctgaagatttataaaaggtgg-----------------------------------------------------------------------------------------

upper sequence: LOC_Os03g58040.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 5'ss of exon 4
ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatcatgtctagcactttttatcatgttgatgtaatgagaatgatgtttccatgaaaatggattatttcatgggggaatttcataagaaataatgaacagtcctttggatagggtttagcaccagtagtattatgactgtctcacacttatgatttggcaatgaaatttttgctcaatacag
|||||||| ||||| ||||| ||||||||||| || |||||  |||| |||||||| || |||||||||||  ||||||||  |   ||||   |    | | | |||| |    |     | |||| | ||    |||  |  | |  ||| |   |||| ||     |  ||||    |  ||||   ||                                                                      
ACAATGGCTTGGATTCTTGATGAATACTCAAAATTCCATGGACATTCTCCTGCTGTTGTCACTGGAAAACCCATTgtaagtgaccgttctaat-cgcggttttaggttggttcggt-----ttatgtgttca-actaatctaaaactgaatgag---atttgatttttgaggatga----tgttttgagcag----------------------------------------------------------------------

upper sequence: LOC_Os03g58040.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT5G18170.1 (Arabidopsis thaliana), 5'ss of exon 4
ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatcatgtctagcactttttatcatgttgatgtaatgagaatgatgtttccatgaaaatggattatttcatgggggaatttcataagaaataatgaacagtcctttggatagggtttagcaccagtagtattatgactgtctcacacttatgatttggcaatgaaatttttgctcaatacag
|||||||| ||||| ||||| |||||||| ||||||||||| || || ||||| || ||||||||||||||  |||||||||        |  | |    ||| ||||    ||||||   || | |  |||    ||||  | ||    |    |||                                                                                                        
ACAATGGCTTGGATTCTTGATGAATACTCTAAGTTTCATGGATACTCGCCTGCAGTTGTGACTGGAAAACCCATTgtaagtaaag-----aataatcacaatcttgttttgctaatga--ctggtttaaccacctgaatgtttaatgatgtttatgaaccag----------------------------------------------------------------------------------------------------

upper sequence: LOC_Os03g58040.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv08s0007g07400.t01 (Vitis vinifera), 5'ss of exon 6
ACAATGGCGTGGATACTTGACGAATACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatcatgtctagcactttttatcatgttgatgtaatgagaatgatgtttccatgaaaatggattatttcatgggggaatttcataagaaataatgaacagtcctttggatagggtttagcaccagtagtattatgactgtctcacacttatgatttggcaatgaaatttttgctcaatacag
|| ||||| |||||||| || || ||||| || |||||||| || ||||||||||||||||||||||| ||| |||| |||||      ||||||| ||    ||| ||   | |  || |    ||||  |  | ||| |    ||| ||       |    ||      |||      |  ||    ||                                                                       
ACCATGGCATGGATACTAGATGAGTACTCGAAATTTCATGGCTACTCACCTGCTGTGGTGACTGGAAAGCCTATTgtgagtata-----tagcactctt----atgatgggttgaaaagtacag-gtttataccataattgtaggtttgatt------tcctgtagatgtaaatttctgctgattcaagta-----------------------------------------------------------------------

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|29674431|gb|CB670706.1|CB670706
EST:     ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT                         GACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatca ... ctcaatacagGACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTG
EST: gi|58680379|gb|CK069066.1|CK069066
EST:     ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT                         GACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatca ... ctcaatacagGACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTG
EST: gi|88428743|gb|CI599459.1|CI599459
EST:     ACTCAAAGTTT-ATGGTTATTCAC-TGCTGTGGTGACTGGAAAAC-TGTT                         GACCTTGGAGGATAACTTGGAAAAAATG-AGCTACTGGAAGGGGAGT-CTG
genomic: ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatca ... ctcaatacagGACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTG
EST: gi|29673988|gb|CB670263.1|CB670263
EST:     ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT                         GACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatca ... ctcaatacagGACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTG
EST: gi|163928511|gb|EG711396.1|EG711396
EST:     ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT                         GACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatca ... ctcaatacagGACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTG
EST: gi|29679310|gb|CB675585.1|CB675585
EST:     ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT                         GACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatca ... ctcaatacagGACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTG
EST: gi|88314120|gb|CI602452.1|CI602452
EST:     ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTT                         GACCTTGGAGGATCAATTGGAAGGGATGCAGCTACTGGAAGGGGAGTTCTG
genomic: ACTCAAAGTTTCATGGTTATTCACCTGCTGTGGTGACTGGAAAACCTGTTgtaagtatca ... ctcaatacagGACCTTGGAGGATCACTTGGAAGAGATGCAGCTACTGGAAGGGGAGTTCTG