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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatgtaaacaagtaaaaaaaaagaagtaacttttattttctctttgctggtctctattctctagttagtcatctcaggtcattttatctcgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGGAGCTCTGACGACTCGGATGCATTCTTCTGCCATCAATCAATTGATCCAA

Basic information

species Oryza sativa
transcript LOC_Os03g47740.2
intron # 1
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|88740038|gb|CI763546.1|CI763546
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88452896|gb|CI574443.1|CI574443
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88696270|gb|CI739845.1|CI739845
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATAAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88693943|gb|CI737981.1|CI737981
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88742178|gb|CI765686.1|CI765686
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88388095|gb|CI590371.1|CI590371
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88735320|gb|CI758828.1|CI758828
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88825079|gb|CI775644.1|CI775644
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|29644388|gb|CB649395.1|CB649395
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88739888|gb|CI761398.1|CI761398
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88430485|gb|CI569508.1|CI569508
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|66915032|gb|CX101880.1|CX101880
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|38473104|gb|CF957236.1|CF957236
EST:     TGCCTCCCATGA-GAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCT-AGCTGATGAAGG
genomic: TGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|29646229|gb|CB651236.1|CB651236
EST:     AGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCACG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAG
genomic: AGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCA-Ggtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAG
EST: gi|88729066|gb|CI752576.1|CI752576
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88734602|gb|CI758110.1|CI758110
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88735112|gb|CI758620.1|CI758620
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88426412|gb|CI576654.1|CI576654
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88301197|gb|CI594723.1|CI594723
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88456124|gb|CI567690.1|CI567690
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88371271|gb|CI600119.1|CI600119
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGAAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
EST: gi|88371465|gb|CI602643.1|CI602643
EST:     CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAG                         TGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG
genomic: CAGCAATCTCTGCTGCTTGGTTCTGCCTCCCATGAGGAGCACACCATCAGgtctcccttc ... cgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctggtctctattctctagttagtcatctcaggtcattttatctcgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGGAGCTCTGACGACTCGGATGCATTCTTCTGCCATCAATCAATTGATCCAA
                                     ttttatctcgtctttc  CT-rich tract
                                  tcattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatgtaaacaagtaaaaaaaaagaagtaacttttattttctctttgctggtctctattctctagttagtcatctcaggtcattttatctcgtctttcagTGTGATTACAAAGCAAGGAACCCTCCTACCGCGTCGCTGAGCTGATGAAGGAGCTCTGACGACTCGGATGCATTCTTCTGCCATCAATCAATTGATCCAA

- - -taaacaa
- - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - -tttgctg