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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgcgaaaataatatccattttttacaataattaaattttaactgtaatgtgaaataaggcctgcttctttttttgcagGCAACTGCGACAAATAAAGTGCAAATTGATTTGATAGAGATGCTTCATATCCCTAGATGTGTCAAGTTTGTCAGCACAATTAACAGGCCCAACCTTTTCT

Basic information

species Oryza sativa
transcript LOC_Os11g48090.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G451856_T02 (Zea mays), 3'ss of exon 6
gtgagttgcgaaaataatatc------cattttttacaataattaaattttaactgtaatgtga-aataaggcctgcttctttttttgcagGCAACTGCGACAAATAAAGTGCAAATTGATTTGATAGAGATGCTTCATATCCCTAGATGTGTCAAGTTTGTCAGCACAATTAACAGGCCCAACCTTTTCT
|| |||   | ||| ||  ||      ||||   |   | || |||||| |   || | |     | |   ||||   |  | |||||||||||||||| |||| ||| || ||||| ||||| || |||||||| || ||||| |||||  ||||||||||||||||| ||||||||||||||||||| |
gtaagtaaagtaaaaaagttcaaataacattcaattttagaagtaaattgtgcgtgaactccagcagttgagccta--taatattttgcagGCAACTGCAACAAGTAAGGTCCAAATGGATTTAATGGAGATGCTCCACATCCCGAGATGCATCAAGTTTGTCAGCACAGTTAACAGGCCCAACCTTTTTT

upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 5
--------------------------gtgagttgcgaaaataatatccattttttacaataattaaat-tttaactgtaatgtgaaataaggcctgcttctttttttgcagGCAACTGCGACAAATAAAGTGCAAATTGATTTGATAGAGATGCTTCATATCCCTAGATGTGTCAAGTTTGTCAGCACAATTAACAGGCCCAACCTTTTCT
                            |  |||| || | |||    |  ||| | |    ||  ||  |||| | | || |  | |||    ||    || |||| ||||||||||| ||  | |  || |||| |||| ||||||||||| | ||||| |||||||||||||| || ||||||||  | || ||||| ||| | || |
gtacgtctttatctcaagtttctgttaagtattgcaaataaaattattagatttgatatgcttttcatacttaattttgatttctattaa----tgacatttatttttcagGCAACTGCTACTCAGAGGGTCCAAAATGATCTGATAGAGATGTTGCATATTCCTAGATGTGTCAAATTCGTCAGCACTGTCAATAGGCCAAACTTGTTTT

upper sequence: LOC_Os11g48090.3 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G31360.1 (Arabidopsis thaliana), 3'ss of exon 5
---------gtgagttgcgaaaata-atatccattttttacaataatt----aaattttaactgt---aatgtgaaataaggcctgcttctttttttgcagGCAACTGCGACAAATAAAGTGCAAATTGATTTGATAGAGATGCTTCATATCCCTAGATGTGTCAAGTTTGTCAGCACAATTAACAGGCCCAACCTTTTCT
         |     ||  ||| |  ||| | || ||||| |||| ||     ||  || | | |   | | |    |||  | |  |   | | |||||||||||||| ||| | ||||| |||| |||| ||||||||||||| ||||| |||| ||| ||||| ||||| ||||   |||||||||| || || || |
tcagtgggtgcagaatgtcaaattctataacaatctttta-aatattttgtggaaggttgaatatttcattttttcctaattctttatgtctctattgcagGCAACTGCTACACAGAAAGTTCAAAATGATCTGATAGAGATGCTGCATATTCCTAAATGCGTCAAATTTGTGAGCAGTGTTAACAGGCCAAATCTCTTTT

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|29682976|gb|CB679251.1|CB679251
EST:     TTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTTTAACT                         GCAACTGCGACAAATAAAGTGCAAATTGATTTGATAGAGATGCTTCATATC
genomic: TTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTTTAACTgtgagttgcg ... ttttttgcagGCAACTGCGACAAATAAAGTGCAAATTGATTTGATAGAGATGCTTCATATC
EST: gi|58661067|gb|CK049747.1|CK049747
EST:     TTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTTTAACT                         GCAACTGCGACAAGTAAAGTGCAAATTGATTTGATAGAG
genomic: TTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTTTAACTgtgagttgcg ... ttttttgcagGCAACTGCGACAAATAAAGTGCAAATTGATTTGATAGAG
EST: gi|58690628|gb|CK079315.1|CK079315
EST:     TTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTTTAACT                         GCAACTGCGACAAGTAAAGTGCAAAT-GATTTGATAGAGATGCTTCATATC
genomic: TTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTTTAACTgtgagttgcg ... ttttttgcagGCAACTGCGACAAATAAAGTGCAAATTGATTTGATAGAGATGCTTCATATC
EST: gi|29673292|gb|CB669567.1|CB669567
EST:     TTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTTTAACT                         GCAACTGCGACAAATAAAGTGCAAATTGATTTGATAGAGATGCTTCATATC
genomic: TTGGCATTTTAAAGGTCCAGTTTCCCAGTGTTCCTATGATAGCTTTAACTgtgagttgcg ... ttttttgcagGCAACTGCGACAAATAAAGTGCAAATTGATTTGATAGAGATGCTTCATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaataattaaattttaactgtaatgtgaaataaggcctgcttctttttttgcagGCAACTGCGACAAATAAAGTGCAAATTGATTTGATAGAGATGCTTCATATCCCTAGATGTGTCAAGTTTGTCAGCACAATTAACAGGCCCAACCTTTTCT
            ttttaac  putative branch site (score: 2)
                                    cctgcttctttttttg  putative PPT
     aattaaattttaactg  TA-rich tract