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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttcctcttttgactcttttacccattgctgtctgcctttatagtttcttgttggacatgttgatagatgattttcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTTTCATGAAAGGTCGTCTTTTTGTTGAATTCAACGTGGAGTTTCCTGAGCC

Basic information

species Oryza sativa
transcript LOC_Os02g43930.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g43930.3 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 7
----------gtatgctttcctcttttgactcttttacccatt--------gctgtctgcctttatagtttcttg---ttggacatgttgatag-atgattttcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTTTCATGAAAGGTCGTCTTTTTGTTGAATTCAACGTGGAGTTTCCTGAGCC
           | |  | || | |||||  |  | || || ||         || ||       |||   |||      || |     |||||  ||| |||  | | |||||||||||||||||||| || |||||||| ||||| ||||||||||| ||||||||||| || ||||| ||||||||||||||||||| |||||| |||||
gtaggatatatttttttctctttttttgcttgctatatccctttgagctcaactatcctatccaataaaatctcagttctgcatgcactgatattatgttttgttggaatagGTCAACACAAGGCCATTAACGATGAAGGTATGCCTCAGCATGGCCGTCCTTTCATGAAGGGCCGTCTGTTTGTTGAATTCAACGTGGTGTTTCCCGAGCC
















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|29665502|gb|CB661777.1|CB661777
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|86428175|gb|CI074856.1|CI074856
EST:     GGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: GGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|218503180|gb|FG945924.1|FG945924
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|396941261|gb|HO188470.1|HO188470
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCTATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|218484817|gb|FG946762.1|FG946762
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|58684540|gb|CK073227.1|CK073227
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCTATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|88216845|gb|CI216447.1|CI216447
EST:     AGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: AGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|33795096|gb|CF323421.1|CF323421
EST:     GGTCGGCAACTCCTAATCAAATCTAATCCAGGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: GGTCGGCAACTCCTAATCAAATCTAATCCAGGGG-AGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|29686473|gb|CB682748.1|CB682748
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|29627564|gb|CB632575.1|CB632575
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|88677265|gb|CI729923.1|CI729923
EST:     GGTCGGCAACTCCTAATCAAATCTAATCCAGGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: GGTCGGCAACTCCTAATCAAATCTAATCCA-GGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|58679665|gb|CK068352.1|CK068352
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCTATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|33658616|gb|CF281229.1|CF281229
EST:     TCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|29665503|gb|CB661778.1|CB661778
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|58598357|gb|CK008885.1|CK008885
EST:     TTATAAAACCTG                         GTCAACACAAGGCTATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|218482248|gb|FG968976.1|FG968976
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|3767212|gb|AU031322.1|AU031322
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|33658615|gb|CF281228.1|CF281228
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|87018980|gb|CI256865.1|CI256865
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|33808760|gb|CF330265.1|CF330265
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|29686472|gb|CB682747.1|CB682747
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|116875639|gb|EC366147.1|EC366147
EST:     TGGTCGGCAACTCCTAATCAAATTTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCTATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|58602870|gb|CK013398.1|CK013398
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCTATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|14571405|gb|BI118773.1|BI118773
EST:     GGTCGGGCAACTCCTAATCAGATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: GGTC-GGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|33796344|gb|CF324039.1|CF324039
EST:     GGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: GGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|218499207|gb|FG956931.1|FG956931
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCTATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|29683464|gb|CB679739.1|CB679739
EST:     TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TGGTCGGCAACTCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
EST: gi|89165412|gb|CI102502.1|CI102502
EST:     TCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTG                         GTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT
genomic: TCCTAATCAAATCTAATCCAGGGGAGGTTATAAAACCTGgtatgctttc ... tcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctgcctttatagtttcttgttggacatgttgatagatgattttcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTTTCATGAAAGGTCGTCTTTTTGTTGAATTCAACGTGGAGTTTCCTGAGCC
                             tgttgat  putative branch site (score: 4)
                                          ttttctt  putative PPT
        tttatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctttcctcttttgactcttttacccattgctgtctgcctttatagtttcttgttggacatgttgatagatgattttcttggatagGTCAACACAAGGCCATCAATGATGAAGGCATGCCCCAGCATGGCCGCCCTTTCATGAAAGGTCGTCTTTTTGTTGAATTCAACGTGGAGTTTCCTGAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG