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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatagatttgtgttcaacattttgttttcttcataaagtacattttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA

Basic information

species Oryza sativa
transcript LOC_Os03g02680.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 4
-----------------gtactatagatttgtgttcaacattttgttttcttcataaagtacattttttttcgtcataaagtt-----------catttttcattt----------accttttc---tatacactag-cacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                   |||  |||   |   ||   ||| |  | |      |||  | ||| |      |   ||||||           || |||| |             |||||||    ||||  |||| |||||||| ||||| |  || ||||||| ||||||||||||||| || || || ||||| ||||||||||| || || |||||| |  |||||||||| |||||||||||| ||||||| || || ||||||||||| ||||
gtacatttgttatgctctaacttgagaaagggagtctgaattgtcctgttagggaaaaaaatattgtgagggatgccaaagttatggattcccacaatttttacccgaataacgtaaccttttgctgtatattctagtcacattaattcacagtacatatctatgg-aagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATTCTGCTTGGAGCGCGGCAGTATTCCACACCAGTTGATGTGTGGTCTGTGGGCTGTATCTTTGCGGAAA

upper sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G143213_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------gtactatagatttgtgttcaacattttgttttc--ttcataaagtacattttttttcgtcataaagttcatttttcatttaccttttctataca--ctag-cacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGT-TGGTTGTATCTTTGCAGAAA
                                              | | |||    ||  |   || || ||||      | |  ||| ||    |     ||   | |    ||| |  |||   | |||  | |  |  |||| || || |||||  |||  || ||||||| ||||||||||||||| || || || ||||| ||||||||||| |||||||||||| | || |||||||| |||||||||||  | ||||| || ||| ||||||||||| ||| 
gtaaatttgctatgctgcttattgcttaacttgagaaagggagtttgaattatcctattagggaaaaaatattgtgaggggtgccaaaattatggatcccaccgattttatacccatataacataaccttttgttgtctattctagtcatatcaactc--aatacatatctatgg-aagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATCCTTCTTGGAGCGAGACAGTATTCCACACCAGTTGACGTATGGTCTGTGTGGCTGTATCTTTGCGGAA-

upper sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 4
----------------------------------------------gtactatagatttgtgttcaacattttgttttc--ttcataaagtacattttttttcgtcataaagttcatttttcatttaccttttctataca--ctag-cacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                                              | | |||    ||  |   || || ||||      | |  ||| ||    |     ||   | |    ||| |  |||   | |||  | |  |  |||| || || |||||  |||  || ||||||| ||||||||||||||| || || || ||||| ||||||||||| |||||||||||| | || |||||||| |||||||||||  | ||||| ||                    
gtaaatttgctatgctgcttattgcttaacttgagaaagggagtttgaattatcctattagggaaaaaatattgtgaggggtgccaaaattatggatcccaccgattttatacccatataacataaccttttgttgtctattctagtcatatcaactc--aatacatatctatgg-aagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATCCTTCTTGGAGCGAGACAGTATTCCACACCAGTTGACGTATGGTCTGTG-------------------

upper sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA05G25320.1 (Glycine max), 3'ss of exon 3
gtactatagatttgtgttcaacattttgttttcttcataaagtacattttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                                  | | ||| || |  | ||||     ||||| |    |   |  |      |  | |||  |    ||    |    |   ||   | |||  | | ||| | |||| |||||  ||||||| |||||||| || ||  | ||||||||  | ||||||||||| ||||||||||| |||||||| || || || |||||||| |
---------------------------------cttaaaaaatataaatctttt----gtaaaggtataatggtagatggacagtaaaaacatcaaattatctttttctgagttataaatttggcgattgtttgt-agGTGGTAACACTGTGGTACAGAGCTCCGGAAATTTTGCTTGGATCCCGTCAGTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA

upper sequence: LOC_Os03g02680.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 4
gtactatagatttgtgttcaacattttgttttcttcataaagtacattttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                             |||  |   || |||   || |  | | |     | | |||||| |  ||  |||  |||  | |  | ||||   ||    |  ||    || ||   |  |||  |||| || || || ||||| ||||||||||| ||  | ||||||||  | || |||||||| ||||||||| | |||||||| || ||||| |||||||| |
-----------------------------ttttgtggaaaggta---ttgtggtaggctggttgatgatttttaacgtaa-tttaatatttatt--cccatt---tctgtgtttataataattggtgattgtttgtagGTGGTGACATTATGGTACAGAGCTCCAGAAATATTGCTTGGATCTCGTCATTATTCTACGCCAGTTGATGTTTGGTCAGTGGGATGTATATTTGCAGAGA

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|29658305|gb|CB654580.1|CB654580
EST:     TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAG                         GTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
genomic: TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAGgtactataga ... tatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
EST: gi|86499530|gb|CI142163.1|CI142163
EST:     TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAG                         GTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
genomic: TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAGgtactataga ... tatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
EST: gi|58682943|gb|CK071630.1|CK071630
EST:     TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAG                         GTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
genomic: TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAGgtactataga ... tatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
EST: gi|218491447|gb|FG947046.1|FG947046
EST:     TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAG                         GTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
genomic: TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAGgtactataga ... tatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
EST: gi|29688121|gb|CB684396.1|CB684396
EST:     TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAG                         GTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
genomic: TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAGgtactataga ... tatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
EST: gi|87021528|gb|CI274135.1|CI274135
EST:     TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACATTTACTCACGAG                         GTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
genomic: TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAGgtactataga ... tatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
EST: gi|163918232|gb|EG715284.1|EG715284
EST:     TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAG                         GTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
genomic: TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAGgtactataga ... tatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
EST: gi|157650675|gb|EX450309.1|EX450309
EST:     TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAG                         GTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
genomic: TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAGgtactataga ... tatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
EST: gi|8860073|gb|AU097391.1|AU097391
EST:     TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAG                         GTTGTAACCTTGTGGTATAGAGCTCCCAGAGATCCTTCTTGGATCAAGGCA
genomic: TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACGTTTACTCACGAGgtactataga ... tatttttcagGTTGTAACCTTGTGGTATAGAGCT-CCAGAGATCCTTCTTGGATCAAGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                   aactcac  putative branch site (score: 2)
                                             tatttttc  putative PPT
                                          aagtattttt  TA-rich tract