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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcaccatgctgtatacttttgatttatcatatgtttaaaatttttaatgtggaggagggataatgcatggacctttgacttttttataatatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATATCAAGACTCTGTTTGTTGATCATTCTTGTGGACAACCAAATGGTGCTCGT

Basic information

species Oryza sativa
transcript LOC_Os03g14980.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G030422_T03 (Zea mays), 3'ss of exon 6
-agcaccatgctgtatacttttgatttatcatatgtttaaaatttttaatgtggaggagggataatgcatggacctttgacttttttataatatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATATCAAGACTCTGTTTGTTGATCATTCTTGTGGACAACCAAATGGTGCTCGT
 |  | |  | | |  |  | ||| |      |    |  ||||     | |  |       |  |     |          ||||  | || | |  |||||||||||||||||||||||||||||| || ||||||||||| ||||| |||||||| || |||||||||||||| ||||||||||| |||||||| |||
taaaaacg-gatttgcagctctgagtaggggcaaccatgcaattccccctttccatttcattttgtatggtgggtaaccttattttgttcatgtttgacagCTTAAACTGGCAGCACCAGCTTTGCAAGAACCCTAGACCTAATCCTGACATCAAGACCCTTTTTGTTGATCATTCATGTGGACAACCGAATGGTGCACGT

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 4
agcaccatgctgtatacttttgatttatcatatgtttaaa-atttttaatgtggaggagggataatgcatggacctttgacttttttataatatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATATCAAGACTCTGTTTGTTGATCATTCTTGTGGACAACCAAATGGTGCTCGT
    | | | |  ||   ||   || |  ||   ||| |   |  ||||||  ||      ||||    ||     |||   || || |  ||   |||||  | ||||||||||||||||||||||| || || || || || ||||| |||||||| |||||| |||||||  |||||||||  || |||||||| |||
ttttcaacgtttcatgtgttgttttaaatattcttttcattgtacttaatg-agaatttaaataagaattgctttcttgtgcttattttgttaccctgcagTCTCAACTGGCAGCACCAGCTTTGCAAGAACCCAAGGCCGAATCCTGACATCAAGACACTGTTTATTGATCACACTTGTGGACCTCCTAATGGTGCCCGT

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ36405 (Selaginella moellendorffii), 3'ss of exon 8
agcaccatgctgtatacttttgatttatcatatgtttaaaatttttaatgtggaggagggataatgcatggacctttgacttttttataatatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATATCAAGACTCTGTTTGTTGATCATTCTTGTGGACAACCAAATGGTGCTCGT
                              |  ||      ||||  |  |      | | | ||  | | |         ||||| |  | | |  |||| | || ||||| || ||||||||||| |||||||| || ||||| |||||||| ||||||||||| |||||| | ||| |    || ||||| || || 
-----------------------------gtgcgtccctgcttttccagctacttctgtgctgatagaagaaatacatttctttttttcttttttcccagCCTCAATTGGCAACATCAGCTTTGCAAGAATCCTAGGCCCAACCCAGATATCAAAACTCTGTTTGTAGATCATACCTGTAGCGCGCCGAATGGAGCCCGC

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 4
agcaccatgctgtatacttttgatttatcatatgtttaaaatttttaatgtggaggagggataatgcatggacctttgacttttttataatatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATATCAAGACTCTGTTTGTTGATCATTCTTGTGGACAACCAAATGGTGCTCGT
           ||       || |||  ||  |  ||           ||  ||     || |||||||     |||  |||||||      |||  |||| | || ||||| || ||||||||||| |||||||| || ||||| |||||||| ||||||||||| |||||| | |||||    || ||||| || || 
-----------gtgcgtacctgcttttccagctactt--------ctgtgctgatagaaga-aatgcatttctttttttctttttt------tgtc-cagCCTCAATTGGCAACATCAGCTTTGCAAGAATCCTAGGCCCAACCCAGATATCAAAACTCTGTTTGTAGATCATACCTGTGGCGCGCCGAATGGAGCCCGC

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ37833 (Selaginella moellendorffii), 3'ss of exon 4
agcaccatgctgtatacttttgatttatcatatgtttaaaatttttaatgtggaggagggataatgcatggacctttgacttttttataatatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATATCAAGACTCTGTTTGTTGATCATTCTTGTGGACAACCAAATGGTGCTCGT
                              |  ||      ||||  |  |      | | | ||  | | |         ||| | || | | || |||| | || ||||| || ||||||||||| |||||||| || ||||| |||||||| ||||||||||| |||||| | |||||    || ||||| || || 
-----------------------------gtgcgtacctgcttttccagctacttctgtgctgatagaagaaatgcatttctttgtttatttttttccagCCTCAATTGGCAACATCAGCTTTGCAAGAATCCTAGGCCCAACCCAGATATCAAAACTCTGTTTGTAGATCATACCTGTGGCGCGCCGAATGGAGCCCGC

upper sequence: LOC_Os03g14980.2 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ35798 (Selaginella moellendorffii), 3'ss of exon 4
agcaccatgctgtatacttttgatttatcatatgtttaaaatttttaatgtggaggagggataatgcatggacctttgacttttttataatatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATATCAAGACTCTGTTTGTTGATCATTCTTGTGGACAACCAAATGGTGCTCGT
                     |      | |   |||  |  |  |  ||||  |   | | ||       || |||   |||||| |  | | |  |||| | || ||||| || ||||||||||| |||||||| || ||||| |||||||| ||||||||||| |||||| | |||||    || ||||| || || 
---------------------gtgcgtccctgcttttccagctacttctgtgctgatagaagaa-----atacatttcgtttttttct--tttttcccagCCTCAATTGGCAACATCAGCTTTGCAAGAATCCTAGGCCCAACCCAGATATCAAAACTCTGTTTGTAGATCATACCTGTGGCGCGCCGAATGGAGCCCGC

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|58653134|gb|CK041814.1|CK041814
EST:     CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAG                         CTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATAT
genomic: CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAGgtagcacatg ... tatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATAT
EST: gi|29656775|gb|CB653050.1|CB653050
EST:     CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAG                         CTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATAT
genomic: CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAGgtagcacatg ... tatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATAT
EST: gi|29629469|gb|CB634478.1|CB634478
EST:     CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAG                         CTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATAT
genomic: CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAGgtagcacatg ... tatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATAT
EST: gi|27334445|gb|CA882896.1|CA882896
EST:     CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAG                         CTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCCAACCCTGATAT
genomic: CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAGgtagcacatg ... tatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATAT
EST: gi|163918634|gb|EG710316.1|EG710316
EST:     CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAG                         CTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATAT
genomic: CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAGgtagcacatg ... tatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATAT
EST: gi|88426720|gb|CI584083.1|CI584083
EST:     CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAG                         CTTAAACTGGCAGCACCAG
genomic: CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAGgtagcacatg ... tatgttgcagCTTAAACTGGCAGCACCAG
EST: gi|29656774|gb|CB653049.1|CB653049
EST:     CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAG                         CTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATAT
genomic: CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAGgtagcacatg ... tatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATAT
EST: gi|88717854|gb|CI739366.1|CI739366
EST:     CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAG                         CTTAAACTGGCAGCACCAG
genomic: CAGTTTCCAAATCTGAAGAGCTCCAGATTGCGGACACTTATAAACCAGAGgtagcacatg ... tatgttgcagCTTAAACTGGCAGCACCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgtggaggagggataatgcatggacctttgacttttttataatatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATATCAAGACTCTGTTTGTTGATCATTCTTGTGGACAACCAAATGGTGCTCGT
                             tttgacttttttataa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcaccatgctgtatacttttgatttatcatatgtttaaaatttttaatgtggaggagggataatgcatggacctttgacttttttataatatgttgcagCTTAAACTGGCAGCACCAGCTTTGCAAAAATCCTAGACCTAACCCTGATATCAAGACTCTGTTTGTTGATCATTCTTGTGGACAACCAAATGGTGCTCGT

- - -catgctg
- - - - - - - - - - - - - - catatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgg