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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGATCTACACTTTTTTGTAACTGGAGGTGATGAAGAGAATGAGCTCATTTTAGCATCTGTTCTTCAGGGCTTCTCTGAAGCTATTGATTACCTTCTCAGgtgtggacatttcctgtgccgtacactcctatcttttttaacatccattataaatgcttgtcagtactgtatactattttaacaactctctttcttgttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g62150.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62150.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G20370.1 (Glycine max), 5'ss of exon 3
AAGATCTACACTTTTTTGTAACTGGAGGTGATGAAGAGAATGAGCTCATTTTAGCATCTGTTCTTCAGGGCTTCTCTGAAGCTATTGATTACCTTCTCAGgtgtggacatttcctgtgccgtacactcctatcttttttaacat-ccattataaatgcttgtcagtactgtatactat-tttaacaactctctttcttgttttcag
|||| || || || ||||| ||||| ||||| || || |||||||||||| ||||||| |||||||| || |||| ||| ||  |       ||  | ||||      ||||   ||    ||   |  | |      | |  | || |||   ||  |  || ||  ||| || |   ||| | |                    
AAGACCTGCATTTCTTTGTCACTGGTGGTGAAGATGAAAATGAGCTCATTCTAGCATCAGTTCTTCAAGGTTTCTTTGATGCAGTCACCCTTCTGTTGAGgt------atttttggttgtatatcttgatttaaaacctgatgtgcctttactgatcatgctctgtg-tgtttattgccttttatag-------------------

upper sequence: LOC_Os01g62150.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G09800.1 (Arabidopsis thaliana), 5'ss of exon 4
AAGATCTACACTTTTTTGTAACTGGAGGTGATGAAGAGAATGAGCTCATTTTAGCATCTGTTCTTCAGGGCTTCTCTGAAGCTATTGATTACCTTCTCAGgtgtggacatttcctgtgccgtacactcctatcttttttaacatccattataaatgcttgtcagtactgtatactattttaacaactctctttcttgttttcag
| || || ||||| ||||| |||||||||||  | || || |||||||| ||||| ||||||||||| ||||| | ||| ||| |||     ||||| |||| |     |||    || |         |  |||| ||   ||  || |   ||       | ||  ||||  |       || | || ||| || ||  |||
AGGACCTTCACTTCTTTGTTACTGGAGGTGAAAATGAAAACGAGCTCATCTTAGCTTCTGTTCTTCAAGGCTTTTTTGATGCTGTTGCACTTCTTCTGAGgtatt--tgtttgacttgacaactgaatatgcctttatt--tattgatcaaccatctccacaactaaagtatgatg------catccctttttttttttaccag

upper sequence: LOC_Os01g62150.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv09s0002g01710.t01 (Vitis vinifera), 5'ss of exon 3
AAGATCTACACTTTTTTGTAACTGGAGGTGATGAAGAGAATGAGCTCATTTTAGCATCTGTTCTTCAGGGCTTCTCTGAAGCTATTGATTACCTTCTCAGgtgtggacatttcctgtgccgtacactcctatcttttttaacatccattataaatgcttgtcagtactgtatactattttaacaactctctttcttgttttcag
| ||||| ||||| ||||| |||||||||||||| || || || ||||| |||||  | ||||||||||||||||| || ||  |||     || ||||||| | |  ||        |  ||  || |  |  ||  |  ||||  | || |    |  |   | ||   |       ||| |  ||     | | || | ||
AGGATCTGCACTTCTTTGTGACTGGAGGTGATGATGAAAACGAACTCATCTTAGCCACAGTTCTTCAGGGCTTCTCCGATGCAGTTGCCCTTCTCCTCAGgtattgtaatcata---actctagccttcatttcttgatttcatctctgatgatctgtaattgatgcttctttgccacctaaaacatcatacccattttgttag

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|33656563|gb|CF279177.1|CF279177
EST:     TTAGCATCTGTTCTTCAGGGCTTCTCTGAAGCTATTGATTACCTTCTCAG                         AAACAAAGTGCACAGAAGGGCTGCGCTTGAAAACTTGGATCTTATCTTCTT
genomic: TTAGCATCTGTTCTTCAGGGCTTCTCTGAAGCTATTGATTACCTTCTCAGgtgtggacat ... ttgttttcagAAACAAAGTGCACAGAAGGGCTGCGCTTGAAAACTTGGATCTTATCTTCTT
EST: gi|33688268|gb|CF316507.1|CF316507
EST:     TTAGCATCTGTTCTTCAGGGCTTCTCTGAGGCTATTGATTACCTTCTCAG                         AAACAAAGTGCACAGAAGGGCTGCGCTTGAAAACTTGGATCTTATCTTCTT
genomic: TTAGCATCTGTTCTTCAGGGCTTCTCTGAAGCTATTGATTACCTTCTCAGgtgtggacat ... ttgttttcagAAACAAAGTGCACAGAAGGGCTGCGCTTGAAAACTTGGATCTTATCTTCTT
EST: gi|58686756|gb|CK075443.1|CK075443
EST:     TAGCATCTGTTCTTCAGAGGCTTCTCTGAAGCTATTGATTACCTTCTCAG                         AAACAAAGTGCACAGAAGGGCTGCGCTTGAAAACTTGGATCTTATCTTCTT
genomic: TAGCATCTGTTCTTCAG-GGCTTCTCTGAAGCTATTGATTACCTTCTCAGgtgtggacat ... ttgttttcagAAACAAAGTGCACAGAAGGGCTGCGCTTGAAAACTTGGATCTTATCTTCTT
EST: gi|33657559|gb|CF280173.1|CF280173
EST:     TTAGCATCTGTTCTTCAGGGCTTCTCTGAAGCTATTGATTACCTTCTCAG                         AAACAAAGTGCACAGAAGGGCTGCGCTTGAAAACTTGGATCTTATCTTCTT
genomic: TTAGCATCTGTTCTTCAGGGCTTCTCTGAAGCTATTGATTACCTTCTCAGgtgtggacat ... ttgttttcagAAACAAAGTGCACAGAAGGGCTGCGCTTGAAAACTTGGATCTTATCTTCTT
EST: gi|88386053|gb|CI570688.1|CI570688
EST:     TTAGCATCTGTTCTTCAGGGCTTCTCTGAAGCTATTGATTACCTTCTCAG                         AAACAAAGTGCACAGAAGGGGTGGGCTTGAAAACTTG
genomic: TTAGCATCTGTTCTTCAGGGCTTCTCTGAAGCTATTGATTACCTTCTCAGgtgtggacat ... ttgttttcagAAACAAAGTGCACAGAAGGGCTGCGCTTGAAAACTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGATCTACACTTTTTTGTAACTGGAGGTGATGAAGAGAATGAGCTCATTTTAGCATCTGTTCTTCAGGGCTTCTCTGAAGCTATTGATTACCTTCTCAGgtgtggacatttcctgtgccgtacactcctatcttttttaacatccattataaatgcttgtcagtactgtatactattttaacaactctctttcttgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC