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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagttttatccttcatatcatatgcatgcttagatagccaataatttgcaagattgtactatttaaatgtgcactgatcacagttggtttctttctttag

Basic information

species Oryza sativa
transcript LOC_Os01g21180.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g21180.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G180990_T01 (Zea mays), 5'ss of exon 3
TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagttttatccttcatatcatatgcatgcttagatagccaataatttgcaagattgtactatttaaatgtgcactgatcacagttggtttctttctttag
|||||  |||| |||||| | ||||||||||| || ||||| ||||| |||||||||||||||||||||| ||||||||| | |||  | |   |||  ||||   | |    ||  |||      |  || | ||    |   |    ||     |   ||| ||||| |  
TACCCCAGCCTTGAACCTTTGCTAGATGACTTGCTCCCAAAAAAGTCACCTATGATTGTTGTTAAATGgttagtagtttttttctt-gtttggcatgtttgctgccagacattatgtttttttttgtcataatgtt--gcttacctgaaattgttttgaatttttttctct--
















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|88361922|gb|CI682096.1|CI682096
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88664198|gb|CI673276.1|CI673276
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|163921070|gb|EG710133.1|EG710133
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88326211|gb|CI660024.1|CI660024
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88727487|gb|CI751142.1|CI751142
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|33688443|gb|CF316682.1|CF316682
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88692766|gb|CI736341.1|CI736341
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTNTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|29289887|gb|CB483501.1|CB483501
EST:     CTACTAGACGACTTACTTCC-AAGAAGTCGCCTATGATTGTTGTTAAATG                         CC-AAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88584551|gb|CI702113.1|CI702113
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|33812764|gb|CF332270.1|CF332270
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88732421|gb|CI755598.1|CI755598
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88581529|gb|CI698523.1|CI698523
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88582517|gb|CI699934.1|CI699934
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88573361|gb|CI664932.1|CI664932
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88329462|gb|CI648521.1|CI648521
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|218488231|gb|FG951457.1|FG951457
EST:     CTACTAGATGACTTACTTCCAAAGAAATCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88347712|gb|CI655065.1|CI655065
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88388325|gb|CI627864.1|CI627864
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACGTGTTTTTCA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCAC-TGTTTTTCA
EST: gi|88726864|gb|CI750519.1|CI750519
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88732153|gb|CI757001.1|CI757001
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|163928391|gb|EG714711.1|EG714711
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|55412623|gb|CV724999.1|CV724999
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88726544|gb|CI750199.1|CI750199
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTCTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88741938|gb|CI764443.1|CI764443
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88376867|gb|CI639192.1|CI639192
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|87012993|gb|CI297220.1|CI297220
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88405694|gb|CI609593.1|CI609593
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|25804409|gb|CA760370.1|CA760370
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATA
EST: gi|33665495|gb|CF296462.1|CF296462
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|58598583|gb|CK009111.1|CK009111
EST:     TACTAGATGACTTACTTCCAAAGAAAG-CGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: TACTAGATGACTTACTTCCAAAGAA-GTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88359324|gb|CI679851.1|CI679851
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88306080|gb|CI635086.1|CI635086
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88421818|gb|CI611697.1|CI611697
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|66917257|gb|CX104105.1|CX104105
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
EST: gi|88324957|gb|CI644968.1|CI644968
EST:     CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG                         CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA
genomic: CTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagtt ... ctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATGgtgagtagttttatccttcatatcatatgcatgcttagatagccaataatttgcaagattgtactatttaaatgtgcactgatcacagttggtttctttctttag

- - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - AGAAGT