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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattattttgcagtaatagtccatattttgtttcctgtttcttgtctagaactaattttaaggttataaatcgactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGGCAGTTCACAGCACGAATCTTGGGAGATAATCCGGAGTCACCAGGAACTA

Basic information

species Oryza sativa
transcript LOC_Os02g44510.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM5G846198_T02 (Zea mays), 3'ss of exon 9
gtaaaattattttgcagtaatagtccatattttgtttcctgtttcttgtctagaactaattttaaggttataaatcgactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGGCAGTTCACAGCACGAATCTTGGGAGATAATCCGGAGTCACCAGGAACTA
|||||||||| |  ||||          |||||        ||| |||||| || ||     |||  || ||   |  ||||| ||||||| | |||||| ||||| ||||||  || |||||||||||||||| |||||||||| |||||||||||||| ||| ||   ||| |  |||   | |
gtaaaattatgtaccagtgg--------atttt--------ttttttgtcttgatctg---ctaaacttgtactgcctctttccagGGTGCTAGAAGAATAGTTCCGGAGTGGACTGGTCTTGACAGTGAAGCACGGCAGTTCACTGCACGAATCTTGGGTGATGATGTCGAGCCTGCAGATGCCA
















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|29624545|gb|CB629556.1|CB629556
EST:     AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
genomic: AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... gactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
EST: gi|428266|gb|D24414.1|D24414
EST:     AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGT
genomic: AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... gactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGT
EST: gi|29641327|gb|CB646334.1|CB646334
EST:     AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
genomic: AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... gactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
EST: gi|29676304|gb|CB672579.1|CB672579
EST:     AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
genomic: AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... gactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
EST: gi|29629314|gb|CB634325.1|CB634325
EST:     AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
genomic: AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... gactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
EST: gi|38483289|gb|CF967091.1|CF967091
EST:     AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
genomic: AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... gactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
EST: gi|58594812|gb|CF993120.1|CF993120
EST:     AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
genomic: AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... gactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
EST: gi|218480649|gb|FG956875.1|FG956875
EST:     AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCCAAAAGAATTGTT
genomic: AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... gactttctagGGTGCCAAAAGAATTGTT
EST: gi|58692422|gb|CK081109.1|CK081109
EST:     AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
genomic: AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... gactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
EST: gi|218479382|gb|FG952388.1|FG952388
EST:     AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCCAAAAGAATTGTTCCAGAGTGGGTTGGATCTTGACAGTGAAGCAAG
genomic: AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... gactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTT-GATCTTGACAGTGAAGCAAG
EST: gi|218505372|gb|FG952963.1|FG952963
EST:     AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
genomic: AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... gactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
EST: gi|27545628|gb|CA767112.2|CA767112
EST:     AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAG                         GGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG
genomic: AAACCATTGATCTTTGCAACAACCCAATGACAAAGGAGCCAAAGCTTCAGgtaaaattat ... gactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtttcctgtttcttgtctagaactaattttaaggttataaatcgactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGGCAGTTCACAGCACGAATCTTGGGAGATAATCCGGAGTCACCAGGAACTA
                      aactaat  putative branch site (score: 2)
                                               ctttct  putative PPT
                      aactaattttaaggtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaattattttgcagtaatagtccatattttgtttcctgtttcttgtctagaactaattttaaggttataaatcgactttctagGGTGCCAAAAGAATTGTTCCAGAGTGGGTTGATCTTGACAGTGAAGCAAGGCAGTTCACAGCACGAATCTTGGGAGATAATCCGGAGTCACCAGGAACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT