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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagttttatccttcatatcatatgcatgcttagatagccaataatttgcaagattgtactatttaaatgtgcactgatcacagttggtttctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g21180.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G180990_T01 (Zea mays), 3'ss of exon 3
gtgagtagttttatccttcatatcatatgcatgcttagatagccaataatttgcaagattgtactatttaaatgtgcactgatcacagttggtttctttcttt----agCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT
    ||| || ||   ||    | | ||  ||  ||| | ||   | ||  | |  |  ||| ||||    | || ||||||| ||||||  || |||||||     |||||||||||||| |||||||| |||||||||||||| || || ||||||||||| |||||||||||||||||||||||| |||| |||||||||||||
---cgtatttgtactgttttggtgaaata-ata-ttaaacagatta-aacatacttgtgtgttctat---gaagttcactgataacagtttattcctttcttcctgcagCCAAAATCATCTTAATCTTGTAGTGGTGAATAATGTTCCTCTATTTTTCAATATACGTGATGGTCCTTACATGCCAACCCTGCGTCTTCTTCATCAGT

upper sequence: LOC_Os01g21180.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G41130.2 (Glycine max), 3'ss of exon 3
gtgagtagttttatccttcatatcatatgcatgcttagatagccaataatttgcaagattgtactatttaaatgtgc--actgatcacagttggt--ttctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT
  |  |  || |    ||  | |  | |   |  ||   | ||    | |||||    |  ||   ||||    | |  |||| |     ||  |  || ||  | ||| || || ||||| ||||| ||  | ||||| || || ||||||||||||| | |||||||||| || |||||||| |||||||| ||||| ||||  |
--gtttgattgtggttttttttttgtttttttcttt---ttgcgtgcattttgctgtgtcataacttttatggtttctaactggttctttttcctccttgttcttgtagTCAGAACCATCTCAATCTGGTTCTTGTGAACAACGTGCCACTGTTTTTCAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTAT

upper sequence: LOC_Os01g21180.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0060g01920.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------gtgagtagttttatccttcatatcatatgcatgct-tagatagccaataatttgcaa-gattgtactatttaa----------atgtgcactgatcacagttggtttctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT
                       ||   |   |||    ||| | | |  |   |||| | ||       |  ||    |  |||   ||||  ||          || ||  ||||  |    |  ||||||   |||| ||||| ||||||||||| ||| |||| || ||||| ||||||||||||||| | || ||||| ||||||||||| || || || |||||||| || |
gttctcactgtcttattagttttgttgtttcctttgatgttcttgttagtttgttgctgttgagttttggttcttcatgataattactctatccaacatataagagatttgttctgacaaacccttttttcttctattagTCAAAACCATCTGAATCTGGTGTTGGTCAACAATGTGCCACTGTTTTTCAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAAT

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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaagattgtactatttaaatgtgcactgatcacagttggtttctttctttagCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT
                          cactgat  putative branch site (score: 3)
                                      ttggtttctttcttt  putative PPT
       attgtactatttaaat  TA-rich tract