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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacagtccatttttaacatgaaaaaggaattattccttaatgtgctttgttaatggaatgcttactttgcgttgcaataccaaagtaccaaactg...

Basic information

species Oryza sativa
transcript LOC_Os03g12370.4
intron # 3
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|88852467|gb|CI374235.1|CI374235
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTCCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|29667708|gb|CB663983.1|CB663983
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|88250928|gb|CI248779.1|CI248779
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|27554416|gb|CA998316.1|CA998316
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATC
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATC
EST: gi|89163938|gb|CI101026.1|CI101026
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|88508192|gb|CI435698.1|CI435698
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTGTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|87033388|gb|CI188012.1|CI188012
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|88245332|gb|CI245181.1|CI245181
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|12404781|gb|AU166382.1|AU166382
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATNTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|86828647|gb|CI278720.1|CI278720
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|88961046|gb|CI096449.1|CI096449
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|29671629|gb|CB667904.1|CB667904
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|88366596|gb|CI556380.1|CI556380
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCNGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|89169618|gb|CI109977.1|CI109977
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|88996490|gb|CI259994.1|CI259994
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|86413300|gb|CI067705.1|CI067705
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|86594995|gb|CI258249.1|CI258249
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|88206077|gb|CI205926.1|CI205926
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|86431737|gb|CI085348.1|CI085348
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|86495289|gb|CI137922.1|CI137922
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|86825574|gb|CI361750.1|CI361750
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGATCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|88968188|gb|CI098430.1|CI098430
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|86497061|gb|CI139694.1|CI139694
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
EST: gi|218482494|gb|FG954955.1|FG954955
EST:     ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAG                         TTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT
genomic: ATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAAT

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: 50 (upstream exon), 70 (downstream exon)
Score: 15

CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacag ... acatctgcagTTCTTCGGTGACCAACCTCCGGGCGCATCTGCACCATTGGCATCCCGAAATGGCGTCCTCAGGGTGTACCGATGAATTATGCTAACACAGAAGAAGATAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGATGTCATTACCGAAGCTTGATTGGTGGTCCAGGAGCATACTTGCAGTAACATTAGgtgggtacagtccatttttaacatgaaaaaggaattattccttaatgtgctttgttaatggaatgcttactttgcgttgcaataccaaagtaccaaactg

- - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - GGAGCA