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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgagctttgcatgtccctttcttcctttataatagtcatgcttcttaaatactctttacaatgtgaaataatgaaatccccttttcacgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG

Basic information

species Oryza sativa
transcript LOC_Os01g25189.4
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g25189.5 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G473533_T05 (Zea mays), 3'ss of exon 10
atttgagctttgcatgtccctttcttcctttataatag-tcatgcttcttaaatactctttacaatgtgaaataatgaaatccccttttcacgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG
  |   |||||  |||  || || | |||| |  | || | | || | || | |  ||||   ||||  |||  |  ||        | | |  | |||||||| || ||||||||||| |||||||| || ||  | |||||||| ||||| || ||||| |||||||||   ||
-ctcaggctttaaatgctcccttgtcccttaaagaaagatgaagcgtgttgagttgtcttgggaatgcaaaactacaaatattttaatcctccaattacagGGGCATCGCAAGGCACTGCAATTATCTCGGAGACCTGCTGCTAGCACTTTCGTTCAGCTTGCCCTGTGGAGTGAG

upper sequence: LOC_Os01g25189.5 (Oryza sativa), 3'ss of exon 14
lower sequence: AT3G52940.2 (Arabidopsis thaliana), 3'ss of exon 11
-------------------------atttgagctttgcatgtccctttcttccttta--taatagtcatgcttct--taaatactc------tttacaatgtgaaat--------aatgaaatcccctttt-cacgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG
                          | |  |||| |  |  || | |||   |||   |  |  |||||||     |||| | |       |   |||||  | ||        | | |  | |  ||||  |   |  |||||||||||||||||||||||||||| ||||| ||  |  |||| ||||| || || || || || |||||||  ||
gtatgttatatttatcttctcttgtttctttgcttggtttcgccatctctgtgtttgattgttcatcatgctgggaataaagagttgaaagttccgcaatgacacatttccgataacttaggtgctgttttgtatatatgacagGGGAATTGCAAGGCACTGTAATTACCTTGGCGACTTGATGCTTGCTCTGTCCTTCAGTTTGCCATGTGGAATAAG

upper sequence: LOC_Os01g25189.5 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv08s0007g03930.t01 (Vitis vinifera), 3'ss of exon 11
---atttgagctttgcatgtccctttcttcctttataatagtcatgcttcttaaatactctttacaatgtgaaataatgaaatccccttttcacgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG
   ||||  || ||         |  |  | | ||   |  ||||| ||  |    |     |  ||  |||  |    ||||   |  |   |    |  |||||||| ||||||||||||||||| ||||||||  |  || | || || || ||||| ||||| ||||| |  ||
atgatttatgccttttgctgatttggcaccttctactgttttcatgatttgt---catctcatttaaactgatgtccaaaaattttcaataatcttgttgaagGGGAATCGCAAGGCACTGTAATTACCTTGGGGACTTGTTGTTGGCACTGTCCTTTAGTTTACCTTGTGGGATAAG

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|88522833|gb|CI450626.1|CI450626
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88532936|gb|CI462268.1|CI462268
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88551911|gb|CI482008.1|CI482008
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88376078|gb|CI530582.1|CI530582
EST:     GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88527617|gb|CI455791.1|CI455791
EST:     GGT-AAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88555636|gb|CI485908.1|CI485908
EST:     GGT-AAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88478942|gb|CI416213.1|CI416213
EST:     GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88533815|gb|CI460483.1|CI460483
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|33689268|gb|CF317507.1|CF317507
EST:     GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88542985|gb|CI472349.1|CI472349
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88554518|gb|CI484704.1|CI484704
EST:     GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88532876|gb|CI461323.1|CI461323
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88537897|gb|CI466882.1|CI466882
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88552415|gb|CI482419.1|CI482419
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88549113|gb|CI478971.1|CI478971
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88840388|gb|CI079842.1|CI079842
EST:     GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88554216|gb|CI484383.1|CI484383
EST:     GGTAAAACTCGCAAACTTGTC-GGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88550467|gb|CI478444.1|CI478444
EST:     GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88546361|gb|CI475991.1|CI475991
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|87015902|gb|CI279654.1|CI279654
EST:     GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88536421|gb|CI466172.1|CI466172
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88227443|gb|CI226923.1|CI226923
EST:     GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88553441|gb|CI483555.1|CI483555
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
EST: gi|88527939|gb|CI456136.1|CI456136
EST:     GGTAAAACTCGCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTG                         GGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC
genomic: GGTAAAACTCCCAAACTTGTCGGGGGAAAGCTACTTGTATCTGGCTACTGgtaagatgga ... cgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttaaatactctttacaatgtgaaataatgaaatccccttttcacgcaatacagGGGAATTGCAAGGCACTGTAATTATCTTGGGGATATACTGCTAGCTCTTTCATTTAGCTTACCCTGTGGAACCAG
                                  tccccttttcacgc  CT-rich tract
                     tgaaataatgaaat  TA-rich tract