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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAACCAAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaactttgaagtgttctagtccatatagggggagagcttattaccattttatttagatagaacaaggtcgtcctatttaggggtgaaaacggtc...

Basic information

species Oryza sativa
transcript LOC_Os04g23890.2
intron # 22
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|29685192|gb|CB681467.1|CB681467
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         ---A--TCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|86860599|gb|CI324891.1|CI324891
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29618297|gb|CB623309.1|CB623309
EST:     AAAAGCGAAGCCTGACGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29619193|gb|CB624205.1|CB624205
EST:     AAAAGCGAAGCCTGACGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29679663|gb|CB675938.1|CB675938
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|88523276|gb|CI451086.1|CI451086
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGGGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|86870343|gb|CI319449.1|CI319449
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29680790|gb|CB677065.1|CB677065
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29626656|gb|CB631667.1|CB631667
EST:     AAAAGCGAAGCCTGACGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|86861209|gb|CI326647.1|CI326647
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29615866|gb|CB620878.1|CB620878
EST:     AAAAGCGAAGCCTGACGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29685421|gb|CB681696.1|CB681696
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|25806004|gb|CA761965.1|CA761965
EST:     AAAAGCGAAGCCTGACGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|88253359|gb|CI351985.1|CI351985
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|86853887|gb|CI329333.1|CI329333
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCACTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29612811|gb|CB617824.1|CB617824
EST:     AAAAGCGAAGCCTGACGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29630592|gb|CB635601.1|CB635601
EST:     AAAAGCGAAGCCTGACGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29620201|gb|CB625213.1|CB625213
EST:     AAAAGCGAAGCCTGACGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|88517987|gb|CI445540.1|CI445540
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCGTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29619194|gb|CB624206.1|CB624206
EST:     AAAAGCGAAGCCTGACGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|86903055|gb|CI324525.1|CI324525
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29613428|gb|CB618441.1|CB618441
EST:     AAAAGCGAAGCCTGACGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|88531053|gb|CI459492.1|CI459492
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|86481914|gb|CI124547.1|CI124547
EST:     AAAAGCGAAGCCTGATGAAGACGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|88906896|gb|CI375968.1|CI375968
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29618974|gb|CB623986.1|CB623986
EST:     AAAAGCGAAGCCTGACGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|29646470|gb|CB651477.1|CB651477
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|38478618|gb|CF962751.1|CF962751
EST:     AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
EST: gi|38480878|gb|CF964967.1|CF964967
EST:     CAAAGCGAAGCCTGACGAAGATGTTCCCCTAAATCTTGATACATTTTAAG                         GGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC
genomic: AAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTC

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: 73 (upstream exon), 60 (downstream exon)
Score: 6

CCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAACCAAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaac ... atttttgcagGGTAGATCAAACTGGAGCAGTTCTTTTTCCTGTATAGTAATAAGAGGCTTCATGTGATGTTAGCATTGTTGAGTGTTTTCAGTCTGAGCTGCCTCAAAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCCTGAACTAGATGTTCCTCTGAAACTAATTGGCAAGGAAACTCAACCAAAAGCGAAGCCTGATGAAGATGTTCCCCTAAATCTTGATACATTTTAAGgtgaggcaactttgaagtgttctagtccatatagggggagagcttattaccattttatttagatagaacaaggtcgtcctatttaggggtgaaaacggtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG