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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGGATCGCAGGGAACTGGAAAATATCTTATTCAAGCTTTTTGAGAGGCAGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttctcaagttatcctaattatgccgagggtggagcatttgttaagaaattgctagcaccaactctagttattgcatgttctgatatcaaagcctcaactctcccggcttgtttctgtgcag

Basic information

species Oryza sativa
transcript LOC_Os01g56550.3
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|13807678|gb|AU182044.1|AU182044
EST:     TAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: TAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|29687102|gb|CB683377.1|CB683377
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|5003585|gb|AU068734.1|AU068734
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|88247838|gb|CI247687.1|CI247687
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|89180162|gb|CI044441.1|CI044441
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|88209380|gb|CI209229.1|CI209229
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|86602342|gb|CI262811.1|CI262811
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|88244723|gb|CI243845.1|CI243845
EST:     ATCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|89179034|gb|CI043539.1|CI043539
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|88274430|gb|CI394836.1|CI394836
EST:     GTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: GTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|86254112|gb|CI058839.1|CI058839
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|87007171|gb|CI277246.1|CI277246
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|86908622|gb|CI318957.1|CI318957
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|89198476|gb|CI007536.1|CI007536
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|15854620|gb|BI807432.1|BI807432
EST:     A-CCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGA-                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAAACACAAAGGG
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTAC-AACA-AAAGGG
EST: gi|88220668|gb|CI220228.1|CI220228
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
EST: gi|89187624|gb|CI115070.1|CI115070
EST:     AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAG                         CAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT
genomic: AGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttc ... ttctgtgcagCAATTCTTGAAGGAGATATTGAATGATCTGTGTTTCTACAACAAAAGGGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGGATCGCAGGGAACTGGAAAATATCTTATTCAAGCTTTTTGAGAGGCAGCCGAATTGGTCTCTTAAGAATCTCATGCAAGAAACTGATCAACCAGAGgtattttttctcaagttatcctaattatgccgagggtggagcatttgttaagaaattgctagcaccaactctagttattgcatgttctgatatcaaagcctcaactctcccggcttgtttctgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA