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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACATTGGTCTTCCTGGAACAAAGCTTGGATGTGGTGAAGGTGGCTGTGGAGCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaactacatcccttcaacaaaccatgttatgcagtttttatccaactacaatgaaatcactgtatcatgcagtattagaatgaatattgcaccacc...

Basic information

species Oryza sativa
transcript LOC_Os03g31550.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g31550.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G888877_T01 (Zea mays), 5'ss of exon 1
ACATTGGTCTTCCTGGAACAAAGCTTGGATGTGGTGAAGGTGGCTGTGGAGCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaactacatcccttcaacaaaccatgttatgcagtttttatccaactac-aatgaaatcactgtatcatgcagtattagaatgaatattgcaccacc
     || ||||  || |||||||||||||||||||||||||| |||||||| |||||||| |||||||| |||||||| | || |||||||||  ||| || |||||||||| |||  |   |   ||||| || |   | | ||      | ||   ||| |  ||  || |    |  ||||   ||||| ||     
-----GGCCTTCGAGGGACAAAGCTTGGATGTGGTGAAGGTGGTTGTGGAGCTTGCACTGTCATGGTCTCTTGCTATGACCGAATTACAAAGAAATCACTgtaagaactacattcctgtactgactaatgttctgaatgctctctcttctgcctaaaccaattaaagtgacaggtgacaacagaa-atatatttcaatgtt
















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|88403382|gb|CI573105.1|CI573105
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
EST: gi|88366478|gb|CI610623.1|CI610623
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
EST: gi|88364694|gb|CI612509.1|CI612509
EST:     CCTGCACTTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAATCAACGCATGCTTGGCTCCGGTTTATTCTTGTGGAAGGAA
genomic: CCTGCACT-GTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCT-GTGGAAGGAA
EST: gi|88404507|gb|CI580943.1|CI580943
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAACTCAACGCATGCCTTGGCTCGGCTTTATTCTGTGGAAGGA
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAA-TCAACGCATGC-TTGGCTCCGCTTTATTCTGTGGAAGGA
EST: gi|88299845|gb|CI577347.1|CI577347
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAATCAACGCATGCTTGGCTCCG
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCG
EST: gi|88367173|gb|CI563937.1|CI563937
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
EST: gi|88314018|gb|CI600020.1|CI600020
EST:     GCCTGGACTGTGATGGTCTCATGCTATGATCAAAATACAAAGAAGACACA                         GCATTTTGCAATCAAGGCATGGTTGGCTCCGCTTTATTCTGTGGAAGG
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGG
EST: gi|88368103|gb|CI574985.1|CI574985
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
EST: gi|88728262|gb|CI751772.1|CI751772
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAACCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
EST: gi|88421291|gb|CI569136.1|CI569136
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
EST: gi|88410918|gb|CI578724.1|CI578724
EST:     GCCTGGACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGAAACA                         GCATTTTGCAATCAACGCATGCTTGGGTCCG
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCG
EST: gi|88430101|gb|CI565114.1|CI565114
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
EST: gi|88692572|gb|CI736147.1|CI736147
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GNATTTGGCAATCAACGCA
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCA
EST: gi|88694482|gb|CI738520.1|CI738520
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAA
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAA
EST: gi|88353883|gb|CI634674.1|CI634674
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAA
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGC-ATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAA
EST: gi|88423734|gb|CI617086.1|CI617086
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GGATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
EST: gi|88395413|gb|CI611330.1|CI611330
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAATCAACGCATGTTTGGCTCCGCTTTATTCTGTGGAAGGAAT
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
EST: gi|88350340|gb|CI623278.1|CI623278
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTAAAAAGAAGACACA                         GCATTTTGCAATCAACGCATGCTTGGCTCCGCCTTTATTCTGTGGAAGGAA
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGC-TTTATTCTGTGGAAGGAA
EST: gi|88398129|gb|CI585632.1|CI585632
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
EST: gi|88411227|gb|CI564348.1|CI564348
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAAT
EST: gi|88391562|gb|CI600751.1|CI600751
EST:     GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACA                         GCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAG
genomic: GCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAG

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: 56 (upstream exon), 74 (downstream exon)
Score: 43

ACATTGGTCTTCCTGGAACAAAGCTTGGATGTGGTGAAGGTGGCTGTGGAGCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaacta ... acttcatcagGCATTTTGCAATCAACGCATGCTTGGCTCCGCTTTATTCTGTGGAAGGAATGCACATAATCACAGTAGAGGGAATTGGGAATCGTCAGCGAGGTTTGCAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACATTGGTCTTCCTGGAACAAAGCTTGGATGTGGTGAAGGTGGCTGTGGAGCCTGCACTGTGATGGTCTCATGCTATGATCAAACTACAAAGAAGACACAgtgagaactacatcccttcaacaaaccatgttatgcagtttttatccaactacaatgaaatcactgtatcatgcagtattagaatgaatattgcaccacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG