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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaattcaaaacgcttgccactgtttaagataatatgaagagtaaatattaacttgaccacagtcattgagtcacataaactgtgctgtttgttgtccagACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGTTCAGGAACTGCAAATACTGCTGGCCCTTCTCCAAGTTCTGCACCATCAA

Basic information

species Oryza sativa
transcript LOC_Os01g42260.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42260.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G022383_T02 (Zea mays), 3'ss of exon 7
ggaattcaaaacgcttgccactgtttaagataatatgaagagtaaatattaacttgaccacagtcattgagtcaca---taaact-gtgctgtttgttgtccagACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGTTCAGGAACTGCAAATACTGCTGGCCCTTCTCCAAGTTCTGCACCATCAA
        | || ||  |   |    |   | || | |  | | |  | ||  |   |||| |   | || |  ||   | |||| || | |||| |  | |||||  | || ||||| ||||| || || ||||||||||||||||||||||||||||| || || ||||||||||| || ||||||||||||||||| || |
-atccctcagaccctcactgttaca-acattcatcttagaacttagaactacttc--ccactggtttagattggcaaagtgaacttgtaccgtttctgattcagACAGCGAAAAAGAGAAAGAAGCCAGGCTCATCCTCTGGTAGAGCCAATAGTTCAGGCACAGCCAATACTGCTGGTCCCTCTCCAAGTTCTGCACCCTCGA

upper sequence: LOC_Os01g42260.4 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G425377_T01 (Zea mays), 3'ss of exon 2
-ggaattcaaaacgcttgccactgtttaagataatatgaagagtaaatattaacttgaccacagtcattgagtcacataaac-tgtgctgtttgttgtccagACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGTTCAGGAACTGCAAATACTGCTGGCCCTTCTCCAAGTTCTGCACCATCAA
 |   ||     | ||  |   |     |       | |  | | |  | || |   ||  |  |   |  |  |  | ||| ||| |||||| | || |||||  |||||||||| ||||| || || ||||||||||||||||| ||||||||||| || || ||||||||||| || |||||||||||||||||||| |
tgtcttttgtctccctcactgttacaacattcgtccttagaacttagaactaccc--actgctttagattggcaaagtgaacctgtactgtttctggttcagACAGCAAAGAAGAGAAAGAAGCCAGGCTCATCCTCTGGTAGAGCTAATAGTTCAGGCACAGCCAATACTGCTGGTCCCTCTCCAAGTTCTGCACCATCGA
















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|58664118|gb|CK052804.1|CK052804
EST:     CTATGCCTGTTGATGGGGGCATGCCAAACTCTTTCGGTGGAGTTGATCAA                         ACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGT
genomic: CTATGCCTGTTGATGGGGGCATGCCAAACTCTTTCGGTGGAGTTGATCAAgtataattct ... tgttgtccagACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGT
EST: gi|58608601|gb|CK036634.1|CK036634
EST:     CTATGCCTGTTGATGGGGGCATGCCAAACTCTTTCGGTGGAGTTGATCAA                         ACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGT
genomic: CTATGCCTGTTGATGGGGGCATGCCAAACTCTTTCGGTGGAGTTGATCAAgtataattct ... tgttgtccagACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGT
EST: gi|58671957|gb|CK060643.1|CK060643
EST:     CTATGCCTGTTGATGGGGGCATGCCAAACTCTTTCGGTGGAGTTGATCAA                         ACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGT
genomic: CTATGCCTGTTGATGGGGGCATGCCAAACTCTTTCGGTGGAGTTGATCAAgtataattct ... tgttgtccagACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGT
EST: gi|58655398|gb|CK044078.1|CK044078
EST:     CTATGCCTGTTGATGGGGGCATGCCAAACTCTTTCGGTGGAGTTGATCAA                         ACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGT
genomic: CTATGCCTGTTGATGGGGGCATGCCAAACTCTTTCGGTGGAGTTGATCAAgtataattct ... tgttgtccagACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGT
EST: gi|33797972|gb|CF324846.1|CF324846
EST:     CTATGCCTGTTGATGGGGGCATGCCAAACTCTTTCGGTGGAGTTGATCAA                         ACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGT
genomic: CTATGCCTGTTGATGGGGGCATGCCAAACTCTTTCGGTGGAGTTGATCAAgtataattct ... tgttgtccagACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGT
EST: gi|58591655|gb|CF989963.1|CF989963
EST:     CTATGCCTGTTGATGGGGGCATGCCAAACTCTTTCGGTGGAGTTGATCAA                         ACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGT
genomic: CTATGCCTGTTGATGGGGGCATGCCAAACTCTTTCGGTGGAGTTGATCAAgtataattct ... tgttgtccagACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattaacttgaccacagtcattgagtcacataaactgtgctgtttgttgtccagACTACAAAGAAGAGGAAGAAACCTGGTTCATCCTCTGGTAGAGCCAATAGTTCAGGAACTGCAAATACTGCTGGCCCTTCTCCAAGTTCTGCACCATCAA
                            acataaa  TA-rich tract