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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataggccgaatatatatttgattcgatagtatttttcctttgacaatttggatgcaatgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT

Basic information

species Oryza sativa
transcript LOC_Os06g01630.6
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 17
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 16
gtataggccgaatatatatttgattcgatagtatttttcctttgacaatttggatgcaatgtc----ttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT
   |  |   | |   ||| | | ||  || |  | |   |  |  ||  ||     ||| ||    |  ||||| || || || ||||| || ||||||||||| |||||||| || ||||||||||||||  |||| ||||| || ||| | || ||| | ||  |||| |
--gtgagagaattcattatcttactcactaatcatatctttcagtaaacatgctaataatctcgttttctcagGGAGGAACATTTACTGTCTCTAACTTGGGAGGACCTTTTGGCATCAAGCAATTCTGTGCAGTCGTTAATCCACCTCAAGCCGCCATTCTAGCAGTTGGAT

upper sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
-----------gtataggccgaatatatatttgat------tcgatagtatttttcctttgacaatttggatgcaatgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT
           || |       ||   |  |||        ||| |||  |||  | | ||| || | |  |       ||||||||| || || || |||||||| ||  ||||||| || ||||| || |||||||||||||||||| | |||||||| || ||||  ||| | || ||||| |
gtaaaaattatgtttcaatgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctccttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT

upper sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 16
-----------------gtataggccg--aatatatatttgattcgatagtatttttcctttgacaatttggatgcaatgtct-tgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT
                   || ||||   |||  ||  ||||||  ||  |  | ||        | ||      ||   | | ||||||| ||||| || ||||| || ||||||||||| || |||||| | || ||||| ||||||||  | |||||||| ||||| |  ||  | ||  |||| |
gtaactgcattaccttctaattggccatcaatggatggttgattgtatcatggtcttttaaatgaacttcatgatcatcatatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT

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|25803971|gb|CA759932.1|CA759932
EST:     AACTGGCTTAGAGAGCAAGGGACACCAGCCTTAAGCCAGAGGATTATGTG                         GGTGGCACTTTCCCTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
genomic: AACTGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
EST: gi|38477221|gb|CF961354.1|CF961354
EST:     AACTGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAG                         GGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
genomic: AACTGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
EST: gi|58585940|gb|CF984248.1|CF984248
EST:     AACTGGCTCAGAGAGCAAGGGACAACAGACTTAAGCCAGAGGATTATGAG                         GGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
genomic: AACTGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
EST: gi|24468761|gb|CA305710.1|CA305710
EST:     ACTTGGCTCAGAGAGCAAGGGACAACAGACTTAAGCCAGAGGATTATGAG                         GGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
genomic: AC-TGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
EST: gi|86871900|gb|CI332072.1|CI332072
EST:     AGCCTTAAGCCAGAGGATTATGAG                         GGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
genomic: AGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
EST: gi|89198662|gb|CI016747.1|CI016747
EST:     AACTGGCTCAGAGAGCAAGGGACNACAGCCTTAAGCCAGAGGATTATGAG                         GGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA
genomic: AACTGGCTCAGAGAGCAAGGGACAACAGCCTTAAGCCAGAGGATTATGAGgtataggccg ... tgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatttgattcgatagtatttttcctttgacaatttggatgcaatgtcttgcagGGTGGCACTTTCACTGTGTCAAACTTGGGAGGCCCTTTTGGAATTAAGCAATTCTGTGCCATCGTAAATCCTCCACAATCAGCAATTTTGGCTATTGGCT
                         ctttgac  putative branch site (score: 4)
             atagtattttt  TA-rich tract