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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgaattgctgcagctattttgtcaatcgtttatatcatacttattgtaagaaagttctttgttgttttcacgtttttcgacttttgaactttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG

Basic information

species Oryza sativa
transcript LOC_Os09g24200.1
intron # 2
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|88410051|gb|CI573290.1|CI573290
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|58672603|gb|CK061289.1|CK061289
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|88400724|gb|CI596145.1|CI596145
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|33691318|gb|CF319557.1|CF319557
EST:     ATGAAAACAAAGTTCTTGANAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCANAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|56157493|gb|D24336.3|D24336
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|88317010|gb|CI625647.1|CI625647
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|88316529|gb|CI622775.1|CI622775
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|58686007|gb|CK074694.1|CK074694
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|88377574|gb|CI605409.1|CI605409
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|88717896|gb|CI739408.1|CI739408
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|58602384|gb|CK012912.1|CK012912
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|86884299|gb|CI311704.1|CI311704
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|88693324|gb|CI736899.1|CI736899
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|29678389|gb|CB674664.1|CB674664
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|88399554|gb|CI583288.1|CI583288
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|88346546|gb|CI623003.1|CI623003
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|88405923|gb|CI591318.1|CI591318
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|58609238|gb|CK037271.1|CK037271
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
EST: gi|88571905|gb|CI663278.1|CI663278
EST:     ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAG                         GGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT
genomic: ATGAAAACAAAGTTCTTGAAAACAGCTTCCTTGTTATAATGCTTAGACAGgtgggtacag ... actttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtaagaaagttctttgttgttttcacgtttttcgacttttgaactttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG
                                              ctttcac  CT-rich tract
                   ttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgaattgctgcagctattttgtcaatcgtttatatcatacttattgtaagaaagttctttgttgttttcacgtttttcgacttttgaactttcacagGGTAAGGGCTCATCAAGTTCAGCTCCTGCTACATCTAAGGCACCCTCAAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC