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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATCCTCCCTCCGACCACTGCTTCCTCCCACCTGCGGAGACGGAACCCTAAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgctacttctcctcaaatttctaatctgctcatggcgggggcgggcgggtgtgcatgcgtttccgttgtgaataagtccccgcgctcctgttg...

Basic information

species Oryza sativa
transcript LOC_Os12g05410.1
intron # 1
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|55411448|gb|CV723824.1|CV723824
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|88739860|gb|CI761370.1|CI761370
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|88351073|gb|CI620733.1|CI620733
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|25801397|gb|CA757358.1|CA757358
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|29626505|gb|CB631516.1|CB631516
EST:     CAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|88570606|gb|CI661979.1|CI661979
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|186892847|gb|FG124515.1|FG124515
EST:     GGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: GGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|88587103|gb|CI704831.1|CI704831
EST:     AGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|186892850|gb|FG124518.1|FG124518
EST:     GGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: GGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|186892849|gb|FG124517.1|FG124517
EST:     GGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: GGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|88404303|gb|CI578180.1|CI578180
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCT-A-                         --AGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|88760081|gb|CI769637.1|CI769637
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|29626506|gb|CB631517.1|CB631517
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|58590796|gb|CF989104.1|CF989104
EST:     GCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: GCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|186893023|gb|FG124708.1|FG124708
EST:     GGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAGACAAGTGGTGTGAAATATCCCG
genomic: GGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|218483294|gb|FG957299.1|FG957299
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCT-A-                         --AGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|186892846|gb|FG124514.1|FG124514
EST:     GGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: GGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|88343583|gb|CI622958.1|CI622958
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|88732031|gb|CI757208.1|CI757208
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|33811912|gb|CF331845.1|CF331845
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|88732753|gb|CI755930.1|CI755930
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|87007984|gb|CI296962.1|CI296962
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|33659786|gb|CF282399.1|CF282399
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCT
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|88573909|gb|CI665678.1|CI665678
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGCGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|88827096|gb|CI777661.1|CI777661
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
EST: gi|88347614|gb|CI634299.1|CI634299
EST:     AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAG                         CCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG
genomic: AAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 74 (downstream exon)
Score: 52

CGATCCTCCCTCCGACCACTGCTTCCTCCCACCTGCGGAGACGGAACCCTAAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgc ... ccatatgcagCCAGAAGAAGCATCATGCCTAAGATAAAAACAAGTGGTGTGAAATATCCCGATGGGTGGGAGCTTATAGAACCCACCCTCTCAGAGCTCCATTCCAAGAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGATCCTCCCTCCGACCACTGCTTCCTCCCACCTGCGGAGACGGAACCCTAAAAAATTTCTTCTTCCCCTTCTCGTCCGGGCAGCGGAAGGAGCTCTAAGgtgatgctgctacttctcctcaaatttctaatctgctcatggcgggggcgggcgggtgtgcatgcgtttccgttgtgaataagtccccgcgctcctgttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggcgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcgggcg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccccgc