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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatagatttgtgttcaacattttgttttcttcataaagtacatttttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA

Basic information

species Oryza sativa
transcript LOC_Os03g01850.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G008327_T01 (Zea mays), 3'ss of exon 4
------------------------------gtactatagatt--tgtgttcaacattttgttttcttcataaag--tacatttttttttcgtcataaagttcatttt--tcatttaccttttc----tatacactag-cacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                              | | | |  |||    ||||    |      | |  | |   |    | | || |   |   || ||  || |      | |  || | |||     ||||  |||| |||||||| ||||| |  || ||||||| ||||||||||||||| || || || ||||| ||||||||||| || || |||||| |  |||||||||| |||||||||||| ||||||| || || ||||||||||| ||||
gtacatttgttatgctctaacttgagaaagggagtctgaattgtcctgttagggaaaaaaatattgtgagggatgccaaagttatggattcccacaatttttacccgaataacgtaaccttttgctgtatattctagtcacattaattcacagtacatatctatgg-aagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATTCTGCTTGGAGCGCGGCAGTATTCCACACCAGTTGATGTGTGGTCTGTGGGCTGTATCTTTGCGGAAA

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143213_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------gtactatagatttgtgttcaacattttgttttcttcataaagtacatttttttt-tcgtcataaagttcatttttcatttaccttttctataca--ctag-cacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGT-TGGTTGTATCTTTGCAGAAA
                                              | | |||    ||  |   || || ||||          ||    ||   |     ||   | |    ||| |  |||   | |||  | |  |  |||| || || ||||||  ||  || ||||||| ||||||||||||||| || || || ||||| ||||||||||| |||||||||||| | || |||||||| |||||||||||  | ||||| || ||| ||||||||||| ||| 
gtaaatttgctatgctgcttattgcttaacttgagaaagggagtttgaattatcctattagggaaaaaatattgtgaggggtgccaaaattatggatcccaccgattttatacccatataacataaccttttgttgtctattctagtcatatcaactca--atacatatctatgg-aagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATCCTTCTTGGAGCGAGACAGTATTCCACACCAGTTGACGTATGGTCTGTGTGGCTGTATCTTTGCGGAA-

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143213_T02 (Zea mays), 3'ss of exon 4
----------------------------------------------gtactatagatttgtgttcaacattttgttttcttcataaagtacatttttttt-tcgtcataaagttcatttttcatttaccttttctataca--ctag-cacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                                              | | |||    ||  |   || || ||||          ||    ||   |     ||   | |    ||| |  |||   | |||  | |  |  |||| || || ||||||  ||  || ||||||| ||||||||||||||| || || || ||||| ||||||||||| |||||||||||| | || |||||||| |||||||||||  | ||||| ||                    
gtaaatttgctatgctgcttattgcttaacttgagaaagggagtttgaattatcctattagggaaaaaatattgtgaggggtgccaaaattatggatcccaccgattttatacccatataacataaccttttgttgtctattctagtcatatcaactca--atacatatctatgg-aagtatttttcagGTAGTGACATTATGGTACAGAGCTCCAGAAATCCTTCTTGGAGCGAGACAGTATTCCACACCAGTTGACGTATGGTCTGTG-------------------

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA05G25320.1 (Glycine max), 3'ss of exon 3
gtactatagatttgtgttcaacattttgttttcttcataaagtacatttttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                                  | | ||| || |  | ||||      ||||| |    |   |  |      |  | |||  |    ||    |    |   ||   | |||  | | ||| | |||| |||||  ||||||| |||||||| || ||  | ||||||||  | ||||||||||| ||||||||||| |||||||| || || || |||||||| |
---------------------------------cttaaaaaatataaatctttt-----gtaaaggtataatggtagatggacagtaaaaacatcaaattatctttttctgagttataaatttggcgattgtttgt-agGTGGTAACACTGTGGTACAGAGCTCCGGAAATTTTGCTTGGATCCCGTCAGTATTCTACCCCAGTTGATATTTGGTCAGTGGGATGCATATTTGCAGAGA

upper sequence: LOC_Os03g01850.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G14390.1 (Glycine max), 3'ss of exon 4
gtactatagatttgtgttcaacattttgttttcttcataaagtacatttttttttcgtcataaagttcatttttcatttaccttttctatacactagcacattaactcacaatggatgtctatgggaagtatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAGTATTCTACACCAGTTGATATGTGGTCAGTTGGTTGTATCTTTGCAGAAA
                                 ||  |  |  |  | || |  | | |     | | |||||| |  ||  |||  |||  | |  | ||||   ||    |  ||    || ||   |  |||  |||| || || || ||||| ||||||||||| ||  | ||||||||  | || |||||||| ||||||||| | |||||||| || ||||| |||||||| |
--------------------------------ttttgtggaa-aggtattgtggtaggctggttgatgatttttaacgtaa-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|29662032|gb|CB658307.1|CB658307
EST:     TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACATTTACTCATGAG                         GTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG
genomic: TTGGTTTAGCCAGGGCATTTGGAATTCCTGTCCGCACATTTACTCATGAGgtactataga ... tatttttcagGTTGTAACCTTGTGGTATAGAGCTCCAGAGATCCTTCTTGGATCAAGGCAG






















 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