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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtcaatgacagggggacgatttccaagtgcatttatccttttataacctttccttataacatattacatgcgtatatacttcctttttttttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG

Basic information

species Oryza sativa
transcript LOC_Os10g10170.2
intron # 14
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|25803304|gb|CA759265.1|CA759265
EST:     ATACCCGTATTCTTGTTGATGCCCGAAAGACAAAGATCTACACTGGGGAG                         GTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATTGACTAGCTGCAG
genomic: ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtattttgct ... tttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
EST: gi|58693842|gb|CK082529.1|CK082529
EST:     ATGCCCGAAAGTCAAAGATCTACACTGCAGAG                         GTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
genomic: ATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtattttgct ... tttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
EST: gi|29678934|gb|CB675209.1|CB675209
EST:     ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAG                         GTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
genomic: ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtattttgct ... tttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
EST: gi|29614516|gb|CB619529.1|CB619529
EST:     ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCAGAG                         GTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
genomic: ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtattttgct ... tttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
EST: gi|58692218|gb|CK080905.1|CK080905
EST:     ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCAGAG                         GTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
genomic: ATACCCGTATTCTTGTTGATGCCCGAAAGTCAAAGATCTACACTGCGGAGgtattttgct ... tttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctttccttataacatattacatgcgtatatacttcctttttttttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG
         ttataac  putative branch site (score: 2)
                            tatatacttccttttt  putative PPT
                            tatatacttccttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtcaatgacagggggacgatttccaagtgcatttatccttttataacctttccttataacatattacatgcgtatatacttcctttttttttttgacagGTTTCAGTTCTTACAACATTGAGGTCTTTAAAGCATCGACTAGCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG