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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGTGCCAATCCTTTAGCAAAGGAACTAAACATCAAGGAGCTTTACAATTTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgctaatctcattgacatcatcacctattaatagaattatcgtttatataaattcttactccctccattccacaaacctaggactggatatgac...

Basic information

species Oryza sativa
transcript LOC_Os03g08270.3
intron # 5
splice site 5'
intron type U2

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|86429806|gb|CI082229.1|CI082229
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|88845205|gb|CI084130.1|CI084130
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|4715235|gb|AU056352.1|AU056352
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|88847048|gb|CI001320.1|CI001320
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|88265557|gb|CI376459.1|CI376459
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|44670645|gb|CR284079.1|CR284079
EST:     TGGCAAACCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|66921841|gb|CX108689.1|CX108689
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|88969239|gb|CI382788.1|CI382788
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|88441892|gb|CI557545.1|CI557545
EST:     CTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: CTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|86260890|gb|CI066565.1|CI066565
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|86908615|gb|CI318954.1|CI318954
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAAGTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|29615641|gb|CB620653.1|CB620653
EST:     TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: TTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
EST: gi|86884922|gb|CI314498.1|CI314498
EST:     GCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAG                         ATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT
genomic: GCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgct ... gctttaccagATTTCAAATGCCAGAATTTCAAGGCCTGGTTCAGGAGCAAAATACCCCAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGTGCCAATCCTTTAGCAAAGGAACTAAACATCAAGGAGCTTTACAATTTGCAAAGCAGACTAGCTCAGGAAAAGGCTAGAGATGTATATCGCCAAAGgttagacgctaatctcattgacatcatcacctattaatagaattatcgtttatataaattcttactccctccattccacaaacctaggactggatatgac

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG