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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctgtgacgacaacaaatttgcatacgactctattcttacatttcagttctgctgtttagctatattgatattaactctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG

Basic information

species Oryza sativa
transcript LOC_Os01g21180.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g21180.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G180990_T02 (Zea mays), 3'ss of exon 2
gttctgtgacgacaac-aaatttgcatacgactctattc---ttacatttcagtt-------ctgctgtttagctatattgatattaactctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG
||| ||| |  ||||  |||| | | |     |||||||   || | ||||| ||       || |||  ||||| || | | |||||||| ||||||||||||  |||| |||||| | ||||||||||| || ||||| ||||| ||||||||||||||||||||
gttttgtcattacaaagaaatctacttggatttctattcattttccctttcaattacagaatcttctgcctagct-tactaaaattaactccattgcagTACCCCAGCCTTGAACCTTTGCTAGATGACTTGCTCCCAAAAAAGTCACCTATGATTGTTGTTAAATG
















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:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88664198|gb|CI673276.1|CI673276
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|163921070|gb|EG710133.1|EG710133
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88326211|gb|CI660024.1|CI660024
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88727487|gb|CI751142.1|CI751142
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|33688443|gb|CF316682.1|CF316682
EST:     AAGTTGAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88692766|gb|CI736341.1|CI736341
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88584551|gb|CI702113.1|CI702113
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|33812764|gb|CF332270.1|CF332270
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88732421|gb|CI755598.1|CI755598
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88581529|gb|CI698523.1|CI698523
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88582517|gb|CI699934.1|CI699934
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88573361|gb|CI664932.1|CI664932
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88329462|gb|CI648521.1|CI648521
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|218488231|gb|FG951457.1|FG951457
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAATCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88347712|gb|CI655065.1|CI655065
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88388325|gb|CI627864.1|CI627864
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88726864|gb|CI750519.1|CI750519
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88732153|gb|CI757001.1|CI757001
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|163928391|gb|EG714711.1|EG714711
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|55412623|gb|CV724999.1|CV724999
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88726544|gb|CI750199.1|CI750199
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88741938|gb|CI764443.1|CI764443
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88376867|gb|CI639192.1|CI639192
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|87012993|gb|CI297220.1|CI297220
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88405694|gb|CI609593.1|CI609593
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|25804409|gb|CA760370.1|CA760370
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|33665495|gb|CF296462.1|CF296462
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|58598583|gb|CK009111.1|CK009111
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAAG-CGCC
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAA-GTCGCC
EST: gi|88359324|gb|CI679851.1|CI679851
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88306080|gb|CI635086.1|CI635086
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88421818|gb|CI611697.1|CI611697
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|66917257|gb|CX104105.1|CX104105
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
EST: gi|88324957|gb|CI644968.1|CI644968
EST:     AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAG                         TACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT
genomic: AAGTTAAGGCCTCTGTGCAGCGGAAGATTCGGCAAAGTATTGCTGATGAGgttctgtgac ... tctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcttacatttcagttctgctgtttagctatattgatattaactctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG
                                      tattaac  putative branch site (score: 1)
                                            ctctatt  CT-rich tract
                              tatattgatattaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctgtgacgacaacaaatttgcatacgactctattcttacatttcagttctgctgtttagctatattgatattaactctattgcagTACCCTGGCCTCGAACCTCTACTAGATGACTTACTTCCAAAGAAGTCGCCTATGATTGTTGTTAAATG

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