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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAGgtaacatgacaaattaatatgctcagttgatgagttgaacaaaacaaagtgcaccatcaagcacagaaagctttttttgcttcttataacttggtagttt...

Basic information

species Oryza sativa
transcript LOC_Os12g29990.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g29990.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G420055_T01 (Zea mays), 5'ss of exon 9
GTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAGgtaacatgacaaattaatatgctcagttgatgagttgaacaaaacaaagtg--caccatcaagcacagaaagctttttttgcttcttataacttggtagttt-----
|||||||||||||||||||||| |||||||||||  |||| || || ||||| || || ||||||| ||||||| |||||||||||||||||      ||  ||    |||    || ||   ||| | ||      |||  |||  | |||   |   |   |    | | |  | ||||    ||   |     
GTGTCATGATTGCTTGGACTGGGATTGAGCATTTTGTTGCCGGGAGGTTTGAGGACCCACCTGCTGCTGATGAGTCTGATGATATGCAGgtat----gcagtttggcttgc---atttattttttgtaaaagtttctgtgttcacttttaagtttaactattatgcacttcgttctctaaccatttatgctggctg

upper sequence: LOC_Os12g29990.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA03G03250.1 (Glycine max), 5'ss of exon 12
GTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAGgtaacatgacaaattaatatgctcagttgatgagttgaacaaaacaaagtgcaccatcaagcacagaaagctttttttgcttctt---ataacttggtagttt--
|||| |||||||||||||||||||||||||| |||      || |||| |||   ||||||| |||  || || ||||| ||  |   |||    |  |   | || |   |      ||   | || |||| ||   |  | || |       |    |   || || ||||    ||   || | |   |  
GTGTAATGATTGCTTGGACTGGTATTGAGCACTTCCGCATGGGAAGATATGACCCTCCTCCTCCTGCAGAAGAACCTGAAGACTTTGTGgtgtgttttcc--tgaaca---ttgacaaatatatagatcaaagcattttttatcagctgaatttgctttcccattatgattctctagatggatttgaaaaataa
















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|86890175|gb|CI321352.1|CI321352
EST:     CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG                         TATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
genomic: CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAGgtaacatgac ... cttaacacagTATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
EST: gi|89198378|gb|CI007438.1|CI007438
EST:     CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG                         TATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
genomic: CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAGgtaacatgac ... cttaacacagTATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
EST: gi|29684472|gb|CB680747.1|CB680747
EST:     CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG                         TATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
genomic: CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAGgtaacatgac ... cttaacacagTATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
EST: gi|29616288|gb|CB621300.1|CB621300
EST:     CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG                         TATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
genomic: CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAGgtaacatgac ... cttaacacagTATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
EST: gi|29637789|gb|CB642798.1|CB642798
EST:     CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG                         TATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
genomic: CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAGgtaacatgac ... cttaacacagTATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
EST: gi|87009957|gb|CI277458.1|CI277458
EST:     CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG                         TATGACCTGCGTCCAAGGTGGCCTCTTGGTGAAGAATATTCAGAAGGAAGA
genomic: CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAGgtaacatgac ... cttaacacagTATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
EST: gi|29641596|gb|CB646603.1|CB646603
EST:     CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG                         TATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
genomic: CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAGgtaacatgac ... cttaacacagTATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
EST: gi|29664761|gb|CB661036.1|CB661036
EST:     CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAG                         TATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA
genomic: CAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAGgtaacatgac ... cttaacacagTATGACCTGCGTCCAAGGTGGCCTCTTGGTGAGGAATATTCAGAAGGAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTCATGATTGCTTGGACTGGTATTGAGCATTTCATTGCAGGCAGATTTGATGATCCTCCTGCTGTTGATGAGCCTGATGATATGCAGgtaacatgacaaattaatatgctcagttgatgagttgaacaaaacaaagtgcaccatcaagcacagaaagctttttttgcttcttataacttggtagttt

- - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT