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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaatactagaactgatcctttctatgttagtagaatattccaatattagagatatacatgacctgtttactcagtgtttgaatattatgccgtgcagGGCAAGGATGATGGTTTGCGCATCGAGAAAAATGCTCTTCATGACAACTGGGATGATGCCGAGGGGTACTATA

Basic information

species Oryza sativa
transcript LOC_Os12g44330.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G151236_T03 (Zea mays), 3'ss of exon 4
-agaaaata-ctagaactgatcctttctatgttagtagaatattccaatattagagatatacatgacctgtttactcagtgtttgaatattatgccgtgcagGGCAAGGATGATGGTTTGCGCATCGAGAAAAATGCTCTTCATGACAACTGGGATGATGCCGAGGGGTACTATA
 |||   |  | |  |||     | || |     ||  | |  ||||||||||   | | |       | |||| | | |||   || || ||   || |||||||||| |||||||||||   | |||| |||||||||||||||||||||||||||||| || |||||||| |
aagagtctctccatgactcgaagtctcgaaccctgttta-ttctccaatattactaaaaaatcctttgt-tttatttattgtcacaaaatcattgtgtacagGGCAAGGGTGATGGTTTGCATGTTGAGAGAAATGCTCTTCATGACAACTGGGATGATGCAGATGGGTACTACA

upper sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G147811_T01 (Zea mays), 3'ss of exon 5
agaaaatactagaactgatcctttctatgttagtagaatattccaatattaga---gatatacatgacctgtttactcagtgtttgaat-attatgccgtgcagGGCAAGGATGATGGTTTGCGCATCGAGAAAAATGCTCTTCATGACAACTGGGATGATGCCGAGGGGTACTATA
   |  |   | |  ||    | ||||||   ||  | |  ||||||||||||    ||     || | |||||| |||||     | | ||| ||  || ||||| ||||||||||||||||  || |||| |||||||||||||||||||||||||||||| || |||||||| |
--tagttttcaaagatggaa-tatctatggctgttta-ttctccaatattagataaaattcctttgtcttgtttattcagtcacaaattcattgtgttgtacagGGAAAGGATGATGGTTTGCATATTGAGAGAAATGCTCTTCATGACAACTGGGATGATGCAGATGGGTACTACA

upper sequence: LOC_Os12g44330.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0011g03350.t01 (Vitis vinifera), 3'ss of exon 5
---------agaaaatactagaactgatcctt-tctatgttagtagaa-tattccaatattagagatatacatgacctgtttactcagtgtttgaatattatgccgtgcagGGCAAGGATGATGGTTTGCGCATCGAGAAAAATGCTCTTCATGACAACTGGGATGATGCCGAGGGGTACTATA
             ||| |    | ||| | || | | || |  | ||| || |    ||||  |   || | ||||||| ||     || |||        | |  | ||||| |  |  ||||| || |  || || |  | || |||||||||||| ||||||||||| ||||| |||||||
tgtcctatttattaatgccttgagtgacctttgtttgtgattttggaactaatatcttatttcaatcatgcttgacctgattg----gtatttt-------ttcttttcagGGAAGAGGAGATGGCTTACTAATTGAAAGGAGTGGTCTTCATGACAATTGGGATGATGCAGAGGGATACTATA

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|33690079|gb|CF318318.1|CF318318
EST:     TGTTTTGTGATGACATTTTTGGAGAATCACCTGCTGGCATCCGGAAATTG                         GGCAAGGATGATGGTTTGCGCATCGAGAAAAATGCTCTTCATGACAACTGG
genomic: TGTTTTGTGATGACATTTTTGGAGAATCACCTGCTGGCATCCGGAAATTGgtaggcttct ... tgccgtgcagGGCAAGGATGATGGTTTGCGCATCGAGAAAAATGCTCTTCATGACAACTGG
EST: gi|218495214|gb|FG943438.1|FG943438
EST:     TGTTTTGTGATGACATTTTTGGAGAATCACCTGCTGGCATCCGGAAATTG                         GGCAAGGATGATGGTTTGCGCATCGAGAAAAATGCTCTTCATGACAACTGG
genomic: TGTTTTGTGATGACATTTTTGGAGAATCACCTGCTGGCATCCGGAAATTGgtaggcttct ... tgccgtgcagGGCAAGGATGATGGTTTGCGCATCGAGAAAAATGCTCTTCATGACAACTGG
EST: gi|87016978|gb|CI286114.1|CI286114
EST:     TGTTTTGTGATGACATTTTTGGAGAATCACCTGCTGGCATCCGGAAATTG                         GGCAAGGATGATGGTTTGCGCATCGAGAAAAATGCTCTTCATGACAACTGG
genomic: TGTTTTGTGATGACATTTTTGGAGAATCACCTGCTGGCATCCGGAAATTGgtaggcttct ... tgccgtgcagGGCAAGGATGATGGTTTGCGCATCGAGAAAAATGCTCTTCATGACAACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattagagatatacatgacctgtttactcagtgtttgaatattatgccgtgcagGGCAAGGATGATGGTTTGCGCATCGAGAAAAATGCTCTTCATGACAACTGGGATGATGCCGAGGGGTACTATA
                                tgtttgaatattat  TA-rich tract