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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggactctgggagttcgtgatgctttgcttaatttatttgattggcatgtctcatacaattgattgagtcatcaacattgttcacactttctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g57220.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g57220.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 9
gggactctgggagttcgtgatgctttgcttaatttatttgattggcatgtctcatacaattgattgagtcatcaacattgtt----cacactttctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG
     |    || |   |   | | | ||| | | | |  |||  ||| | || |   |     | | ||||  ||| | |     |||| |||  || | ||||||||||||||||||||||||||| ||||||||||||||||||| |||||| | |||||||| |||
----ttgatcgaatatattgggttattcttgaataagtgaattcacatatttcctggtaactgctcactcatttacactatctttccacatttttgtttgccagATATTTTACTTCATTGGATTTGGAATGTTCTGCCTTGAATCACTGCTCAGCATCGTTGTCATTCAG

upper sequence: LOC_Os01g57220.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 10
gggactctgggagttcgtgatgctttgcttaattta-tttgattggcatgtctcatacaattgattgagtcatcaacattgttcacactttctttcg-acagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG
    |        || |  |     | |  |||  |   | |     ||    | |   | |||||||    | |  ||  ||  | |  | |  |    |||| || |||||||||||||||||| |||||||| ||||| |  |  ||||| ||   || || |||
-atgcctcatccttttgcaa-atactacagaatgcaacctaagcaatattctgcttctgaatgattgatcttttattatgattttctccatttgccttgtagATCTTCTACTTCATTGGATTTGGATTGTTCTGCGTTGAAACTTTGATCAGCATTTGGGTTATTCAG

upper sequence: LOC_Os01g57220.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 10
gggactctgggagttcgtgat---gctttgcttaatttatttgattggcatgtctcatacaattgattgagtcatcaacattgttcacactttcttt-cgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG
    |  ||  |  |  | ||   | ||      | |   ||  ||    | |         |||   ||   ||    ||  || |||||| || |    |||||||| ||| | |||||||||||| ||||||||||||||||||| |||||  |    ||  | |||
----ccttgacaaattattatcaggattcatggtagtggctttttttttttcttcttcttttttgtaagaaggattgggatcatttacacttcctatattgcagATATTCTACCTTATTGGATTTGGATTGTTCTGCCTTGAATCACTGCTCAGTATCTGGGTTGTTCAG

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|25803449|gb|CA759418.1|CA759418
EST:     TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTAAGC
genomic: TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGGgtaagtctca ... ctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
EST: gi|11370676|gb|AU164981.1|AU164981
EST:     TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG                         G
genomic: TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGGgtaagtctca ... ctttcgacag-
EST: gi|11370676|gb|AU164981.1|AU164981
EST:     TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG                         G
genomic: TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGGgtaagtctca ... ctttcgacag-
EST: gi|86258735|gb|CI065088.1|CI065088
EST:     TGATGTCATAGGAAACAATGCTATTGTGGGG                         ATATTCTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
genomic: TGATGTCATAGGAAACAATGCTATTGTGGGGgtaagtctca ... ctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
EST: gi|87035348|gb|CI189970.1|CI189970
EST:     TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
genomic: TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGGgtaagtctca ... ctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
EST: gi|89180045|gb|CI044324.1|CI044324
EST:     TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
genomic: TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGGgtaagtctca ... ctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
EST: gi|55412661|gb|CV725037.1|CV725037
EST:     TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGACTGTTTTGCCTTGAATCACTACTCAGC
genomic: TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGGgtaagtctca ... ctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
EST: gi|86889655|gb|CI299853.1|CI299853
EST:     TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
genomic: TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGGgtaagtctca ... ctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
EST: gi|3760903|gb|C98157.1|C98157
EST:     TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
genomic: TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGGgtaagtctca ... ctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
EST: gi|33683758|gb|CF311997.1|CF311997
EST:     TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
genomic: TGGGATTTTGCCGGCTATTGATGTCATAGGAAACAATGCTATTGTGGGGgtaagtctca ... ctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
EST: gi|88988413|gb|CI037656.1|CI037656
EST:     TATTGATGTCATAGGAAACAATGCTATTGTGGGG                         ATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC
genomic: TATTGATGTCATAGGAAACAATGCTATTGTGGGGgtaagtctca ... ctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtctcatacaattgattgagtcatcaacattgttcacactttctttcgacagATATTTTACTTCATTGGATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG
            aattgat  putative branch site (score: 4)
                                   ttcacactttctttc  putative PPT
        atacaatt  TA-rich tract