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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccatattcagaacaagatatatcactaaatgccctaatgtacacctatggtgctttctcaaacagttcccccatgttgatataatacgcactaaggcactaagcacattcaaaacaatttctaagtacagacagcttctcatatttgttttctgacgctcttatatttcctttctaatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT

Basic information

species Oryza sativa
transcript LOC_Os04g56480.1
intron # 11
splice site 3'
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|89182762|gb|CI114131.1|CI114131
EST:     ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAG                         GTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
genomic: ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
EST: gi|88224189|gb|CI224038.1|CI224038
EST:     ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAG                         GTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
genomic: ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
EST: gi|86505661|gb|CI148294.1|CI148294
EST:     ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAG                         GTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
genomic: ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
EST: gi|87006648|gb|CI295031.1|CI295031
EST:     ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAG                         GTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAATGA
genomic: ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAATGA
EST: gi|88227542|gb|CI227022.1|CI227022
EST:     AGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAG                         GTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
genomic: AGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
EST: gi|86854586|gb|CI258879.1|CI258879
EST:     ATAGCCCAAGTGTGATGACCCTAATAAAAGATACAAAGGCGGCGCAGGAG                         GTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
genomic: ATAGCCCAAGTGTGATGACACTAATAAAAGATACAAAGGCGGCGCAGGAGgtaagccata ... taatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacagcttctcatatttgttttctgacgctcttatatttcctttctaatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT
                                          ttctaat  putative branch site (score: 2)
                            ctcttatatttccttt  CT-rich tract
           atatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagccatattcagaacaagatatatcactaaatgccctaatgtacacctatggtgctttctcaaacagttcccccatgttgatataatacgcactaaggcactaagcacattcaaaacaatttctaagtacagacagcttctcatatttgttttctgacgctcttatatttcctttctaatttgcagGTCCAAGCTTTGAAGGACTTCTTCAACATGCTTACAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG