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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatctaaaaattaatttaccagaaacgctcctgaattgtttcaatgacatttatctatcctacatctcgattcacagttgttttttcttttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCACCGTTTTTCCTCGGTTCAGCCGTCTTGTTTGCCATAAAGGATGCGATAT

Basic information

species Oryza sativa
transcript LOC_Os03g31550.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g31550.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 9
tcatctaaaaattaatttaccagaaacgctcctgaattgtttcaatgacatttatctatcctacatctcgattcacagttgtttt----ttcttttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCACCGTTTTTCCTCGGTTCAGCCGTCTTGTTTGCCATAAAGGATGCGATAT
   |  |    || |  ||  |  || | |  ||  ||| |  |   | |||  | ||||  |  | |  | | |   || |  |    |   ||||||| ||||| |||   ||||||||||  ||||| || ||||| || || ||||||||||| |||||||| ||||| |||||||| ||||| |||||||||||||| |
-tttacagcccttgaaatat-actaatgtttttgccttggtgta-caaaattattttatctcatgttttcagttatt-ttatcctaaaatgactttcgttgcagGGTGTTCCAAATCCAAAGGCTATTCATTCTTCCAAAGCCGTGGGAGAGCCACCATTTTTCCTAGGTTCCGCCGTCTTATTTGCGATAAAGGATGCGATCT
















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|66922960|gb|CX109808.1|CX109808
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTCGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|38468990|gb|CF953121.1|CF953121
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         T
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacag-
EST: gi|38468990|gb|CF953121.1|CF953121
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         T
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacag-
EST: gi|86892453|gb|CI332353.1|CI332353
EST:     TGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|88840157|gb|CI079611.1|CI079611
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAACCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|88842795|gb|CI371695.1|CI371695
EST:     TCAAGGTCTCACTTTTGAA-                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTTTAGGAGAGCCA
genomic: TCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|8856279|gb|AU093597.1|AU093597
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|86522508|gb|CI162714.1|CI162714
EST:     TTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCAGTCATCCAAGGCTGTAGGAGAGCCA
genomic: TTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|88451228|gb|CI534221.1|CI534221
EST:     ATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGNTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: ATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|218479236|gb|FG969139.1|FG969139
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTCGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|88830955|gb|CI080379.1|CI080379
EST:     TGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|29624755|gb|CB629766.1|CB629766
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTCGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|29675057|gb|CB671332.1|CB671332
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|88255785|gb|CI353656.1|CI353656
EST:     TAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGG                         GGCCTTTTGAATCCAAAGGTCATTCAATCATCCAAGGCTGTAGGAGAACC
genomic: TAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAA-Ggtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCC
EST: gi|5002750|gb|AU067859.1|AU067859
EST:     CCCTCTGTAAATGGATATACCTCTAAACTTCCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: CCCTCTGTAAAT-GATATACCTCTAAACTT-CAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|89176226|gb|CI043247.1|CI043247
EST:     TCTCACTTTTGAAG                         GGCGTTTTGAATCCCAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|86884878|gb|CI314454.1|CI314454
EST:     AAATCATATACCTGTAAAGTTCAAGGTCTCACTTTTGAA-                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCC-AGGCTGTAGGAGAGCCA
genomic: AAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|86862634|gb|CI345638.1|CI345638
EST:     TACCCTCTGTAAATGATATACCTGTAAACTTCAA-GTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|88840156|gb|CI079610.1|CI079610
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAACCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|89188109|gb|CI115358.1|CI115358
EST:     AGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCCAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: AGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|86833694|gb|CI337268.1|CI337268
EST:     TAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|86871944|gb|CI332116.1|CI332116
EST:     GGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: GGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|86431544|gb|CI085155.1|CI085155
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|25806372|gb|CA762333.1|CA762333
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTCGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|88831031|gb|CI080455.1|CI080455
EST:     CCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: CCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|86862997|gb|CI331790.1|CI331790
EST:     CCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTTTAGGAGAGCCA
genomic: CCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|88971940|gb|CI390523.1|CI390523
EST:     CACTTTTGAAG                         GGCGTTGTGAATCCAAAGGTCATTCACTCATCCAA-GCTGTAGGAGAGCCA
genomic: CACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|88834515|gb|CI077798.1|CI077798
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
EST: gi|86430841|gb|CI083264.1|CI083264
EST:     TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAG                         GGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA
genomic: TACCCTCTGTAAATGATATACCTCTAAACTTCAAGGTCTCACTTTTGAAGgtaaacttca ... ttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacatttatctatcctacatctcgattcacagttgttttttcttttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCACCGTTTTTCCTCGGTTCAGCCGTCTTGTTTGCCATAAAGGATGCGATAT
                                 ttgttttttcttttcg  CT-rich tract
                                 ttgttttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatctaaaaattaatttaccagaaacgctcctgaattgtttcaatgacatttatctatcctacatctcgattcacagttgttttttcttttcgttacagGGCGTTTTGAATCCAAAGGTCATTCACTCATCCAAGGCTGTAGGAGAGCCACCGTTTTTCCTCGGTTCAGCCGTCTTGTTTGCCATAAAGGATGCGATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG