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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatcccctctaagaaaattttcttatagttgctcaattgctataggtttaattgtttaaactacagctttgctagggtactgacagttgtggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTGAACCGGTTTCAACATTCAGCGATGGTGATCAGCCTTTATCTACGCCAAG

Basic information

species Oryza sativa
transcript LOC_Os02g43500.1
intron # 6
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|33798152|gb|CF324935.1|CF324935
EST:     AGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: AGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|88587786|gb|CI705560.1|CI705560
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|29661124|gb|CB657399.1|CB657399
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|218495170|gb|FG957512.1|FG957512
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|29619334|gb|CB624346.1|CB624346
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|58608739|gb|CK036772.1|CK036772
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGGGAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|88661720|gb|CI458736.1|CI458736
EST:     AGCAGGAGCATAANCGGGGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: AGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|40491369|gb|BX901479.1|BX901479
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|88468873|gb|CI696875.1|CI696875
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|29684684|gb|CB680959.1|CB680959
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|218483643|gb|FG955539.1|FG955539
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|218480294|gb|FG954453.1|FG954453
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|29643098|gb|CB648105.1|CB648105
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTTTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|88372136|gb|CI641771.1|CI641771
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|66914797|gb|CX101645.1|CX101645
EST:     ATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: ATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|218491083|gb|FG953112.1|FG953112
EST:     AATGTCAAACAGCAGGAGCATAAGCGGTGCCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCCGCTGTCCA-GTACCGGAACTCTGGTGC
genomic: AATGTCAAACAGCAGGAGCATAAGCGGTGC-AAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTC-GCTGTTCAAGTACCGGAACTCTGGTGC
EST: gi|29660129|gb|CB656404.1|CB656404
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|29661191|gb|CB657466.1|CB657466
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|88448624|gb|CI694015.1|CI694015
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|88993265|gb|CI257693.1|CI257693
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|95101156|gb|CI692891.1|CI692891
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|29660498|gb|CB656773.1|CB656773
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTTTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|88852606|gb|CI008799.1|CI008799
EST:     AATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: AATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|29660247|gb|CB656522.1|CB656522
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|38480918|gb|CF965007.1|CF965007
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|29667086|gb|CB663361.1|CB663361
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|29687907|gb|CB684182.1|CB684182
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
EST: gi|29684442|gb|CB680717.1|CB680717
EST:     CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTG                         GATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG
genomic: CAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTG

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), 75 (downstream exon)
Score: 42

TCAGGTGGAGCAGTTGGAGTTATCTCCGCTCTAATGGTTGTTGAGATCAACAATGTCAAACAGCAGGAGCATAAGCGGTGCAAATATTGTTTAGGAACTGgtacttattt ... tggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTGAACCGGTTTCAACATTCAGCGATGGTGATCAGCCTTTATCTACGCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttaattgtttaaactacagctttgctagggtactgacagttgtggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTGAACCGGTTTCAACATTCAGCGATGGTGATCAGCCTTTATCTACGCCAAG
                                 tactgac  putative branch site (score: 42)
     aattgtttaaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatcccctctaagaaaattttcttatagttgctcaattgctataggtttaattgtttaaactacagctttgctagggtactgacagttgtggcttgtagGATACCTGGCCTGTGCTCGCTGTTCAAGTACCGGAACTCTGGTGCTTACTGAACCGGTTTCAACATTCAGCGATGGTGATCAGCCTTTATCTACGCCAAG

- - - - - -aagaaaa
- - - - - - - - - - - - - -agttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtactg