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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAGgtcagagccgcaaccttggttgggagaacgttcctgcattattatttgctcgttataaatgcttacaacccaatattgtaaaaaccgttctctgcag

Basic information

species Oryza sativa
transcript LOC_Os02g56850.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56850.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G806449_T01 (Zea mays), 5'ss of exon 4
GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAGgtca-----gagccgcaaccttggttgggagaacgttcctgcattattatttgctcgttataaatgct-tacaacccaatattgtaaaaaccg----ttctctgcag
||| | ||||||||||||||||| || || || || ||||||||||| ||||||| |||  |||||||||||||||      |  | | ||| ||  || ||| | ||||   |   | |  |  | |   |  |||    ||   |||||  |  |||          |||||| |||
GATTCGAAGAATTTTGGGTGGGAGATTAACGGAGATATTAACTTCAATTGGAAAACGCTATTGGAAAATAAGgtcatgtttaaatctctaccatgactgtgagcatgttctc-cgcaactgctgaccctgaaggaatatcatattgcccaaggtcctaattttttcttcttctcttcag
















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|88433133|gb|CI569802.1|CI569802
EST:     AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAG                         ACTCAAGAAATTGTTAGACTAAATGGAGTATACCAGAGGATTCTTGGCAAT
genomic: AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAGgtcagagccg ... ttctctgcagACTCAAGAAATTGTTAGACTAAATGGAGTATACCAGAGGATTCTTGGCAAT
EST: gi|88416046|gb|CI594158.1|CI594158
EST:     AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAG                         ACTCAAGAAATTGTTAG
genomic: AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAGgtcagagccg ... ttctctgcagACTCAAGAAATTGTTAG
EST: gi|88392434|gb|CI612908.1|CI612908
EST:     AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAG                         ACTCAAGAAATTGTTAGACTAAATGGAGTATACCAGAGGATTCTTGGCAAT
genomic: AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAGgtcagagccg ... ttctctgcagACTCAAGAAATTGTTAGACTAAATGGAGTATACCAGAGGATTCTTGGCAAT
EST: gi|58586132|gb|CF984440.1|CF984440
EST:     ATTAACTTCAACTGGAAAAAGCTGCTGGAAAATAAG                         ACTCAAGAAATGGTGAGACTAAATGGAGTATACCAGAGGATTCTTGGCAAT
genomic: ATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAGgtcagagccg ... ttctctgcagACTCAAGAAATTGTTAGACTAAATGGAGTATACCAGAGGATTCTTGGCAAT
EST: gi|117220740|gb|CT845514.1|CT845514
EST:     AAATCAATGGGGACATTAACTTCAACTGGAAAAAGCTGCTGGAAAATAAG                         ACTCAAGAAATTGTTAGACTAAATGGAGTATACCAGAGGATTCTTGGCAAT
genomic: AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAGgtcagagccg ... ttctctgcagACTCAAGAAATTGTTAGACTAAATGGAGTATACCAGAGGATTCTTGGCAAT
EST: gi|29675048|gb|CB671323.1|CB671323
EST:     AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAG                         ACTCAAGAAATTGTTAGACTAAATGGAGTATACCAGAGGATTCTTGGCAAT
genomic: AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAGgtcagagccg ... ttctctgcagACTCAAGAAATTGTTAGACTAAATGGAGTATACCAGAGGATTCTTGGCAAT
EST: gi|88407233|gb|CI583691.1|CI583691
EST:     AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAC                         ACTAAAGAAATTGTTAGACTAAATGGAGTATACCAGAGGATTCTTGGAAAT
genomic: AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAGgtcagagccg ... ttctctgcagACTCAAGAAATTGTTAGACTAAATGGAGTATACCAGAGGATTCTTGGCAAT
EST: gi|88417209|gb|CI576283.1|CI576283
EST:     AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAG                         ACTCAAGAAATTG
genomic: AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAGgtcagagccg ... ttctctgcagACTCAAGAAATTG
EST: gi|2443112|gb|C74883.1|C74883
EST:     AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAG                         ACTCAAGAAATTGTTAGACTAAAT
genomic: AAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAGgtcagagccg ... ttctctgcagACTCAAGAAATTGTTAGACTAAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAGgtcagagccgcaaccttggttgggagaacgttcctgcattattatttgctcgttataaatgcttacaacccaatattgtaaaaaccgttctctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA