Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagatagtttaaatatcatatgctactttcattttgatatatttattttattgggctcatatagtcatatatttgtgttgtgaccttgtttcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT

Basic information

species Oryza sativa
transcript LOC_Os09g32526.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32526.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G115757_T03 (Zea mays), 3'ss of exon 1
tagatagtttaaatatcatatgctactttcattttgatatatttattttattgggctcatatagtcatatatttgtgttgtgaccttgtttcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT
   | | ||   ||  ||| |||| |  ||||||  |   |||  |||     || || |||| | ||     | ||    |   |  ||| |  ||||| ||||||| ||||| ||||||||||||||||||||||| ||||  ||||||||||||||||||
---aaatttaggatcgcatgtgctgccatcatttgcaccaattattttaggcaggttcttatattgatgc---tatgcctgggtat--tttaaaatgcagtacaagccGGAATCATGCAGCATTCAAGCTCACAAAGGTGACAAGGTTAAAGTTCACTACCGT

upper sequence: LOC_Os09g32526.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G115757_T02 (Zea mays), 3'ss of exon 2
-----tagatagtttaaatatcatatgctactttcattttgatatatttattttattgggctcatatagtcatatatttgtgttgtgaccttgtttcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT
      | | | ||   ||  ||| |||| |  ||||||  |   |||  |||     || || |||| | ||     | ||    |   |  ||| |  ||||| ||||||| ||||| ||||||||||||||||||||||| ||||                    
gagtgcaaaaatttaggatcgcatgtgctgccatcatttgcaccaattattttaggcaggttcttatattgatgc---tatgcctgggtat--tttaaaatgcagTACAAGCCGGAATCATGCAGCATTCAAGCTCACAAAGGTGACAAG------------------

upper sequence: LOC_Os09g32526.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G115757_T01 (Zea mays), 3'ss of exon 2
-----tagatagtttaaatatcatatgctactttcattttgatatatttattttattgggctcatatagtcatatatttgtgttgtgaccttgtttcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT
      | | | ||   ||  ||| |||| |  ||||||  |   |||  |||     || || |||| | ||     | ||    |   |  ||| |  ||||| ||||||| ||||| ||||||||||||||||||||||| ||||  ||||||||||||||||||
gagtgcaaaaatttaggatcgcatgtgctgccatcatttgcaccaattattttaggcaggttcttatattgatgc---tatgcctgggtat--tttaaaatgcagTACAAGCCGGAATCATGCAGCATTCAAGCTCACAAAGGTGACAAGGTTAAAGTTCACTACCGT

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|88694794|gb|CI738832.1|CI738832
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|88376918|gb|CI639243.1|CI639243
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|88733695|gb|CI756872.1|CI756872
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|163925746|gb|EG714582.1|EG714582
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|55432912|gb|CV729479.1|CV729479
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|88827078|gb|CI777643.1|CI777643
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|5004128|gb|AU069277.1|AU069277
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|33687579|gb|CF315818.1|CF315818
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|66928292|gb|CX115140.1|CX115140
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGTGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|218484090|gb|FG956007.1|FG956007
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGTGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|163927898|gb|EG713510.1|EG713510
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|58678099|gb|CK066786.1|CK066786
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGTGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|88375448|gb|CI681220.1|CI681220
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|88739216|gb|CI762724.1|CI762724
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|58676104|gb|CK064791.1|CK064791
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGTGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|86903638|gb|CI300492.1|CI300492
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|33686364|gb|CF314603.1|CF314603
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|88347332|gb|CI632617.1|CI632617
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|88574137|gb|CI665906.1|CI665906
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|218491364|gb|FG953091.1|FG953091
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGTGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|163920086|gb|EG709856.1|EG709856
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|88576196|gb|CI670341.1|CI670341
EST:     CCTCCGCCAAGAAATCCGGAGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|88332240|gb|CI643657.1|CI643657
EST:     CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
EST: gi|10794952|gb|AU108918.1|AU108918
EST:     -CTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAG                         CACAAGCCAG-ATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA
genomic: CCTCCGCCAAGAAATCCGGCGACGTGACGGAGCTCCAGATCGGCGTCAAGgtaacccgct ... tcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttattgggctcatatagtcatatatttgtgttgtgaccttgtttcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT
                                      ccttgtttc  CT-rich tract
             atatagtcatatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagatagtttaaatatcatatgctactttcattttgatatatttattttattgggctcatatagtcatatatttgtgttgtgaccttgtttcacttgcagCACAAGCCAGAATCCTGCAGCATTCAAGCTCACAAAGGCGACAGAGTTAAAGTTCACTACCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA