Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacaatggagtaatcatagcgctccaatagattgcctttgctgatgaagttcaacacgcaactctccagaaaaaggaactattcatttttccttgtgatcttatgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGGGAAAAGATGGTTTGTAATGCCCAGAACATTCACCATTCTTCCTGATAAT

Basic information

species Oryza sativa
transcript LOC_Os02g49800.1
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|29658893|gb|CB655168.1|CB655168
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|29642626|gb|CB647633.1|CB647633
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|29645619|gb|CB650626.1|CB650626
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|29633919|gb|CB638928.1|CB638928
EST:     TATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: TATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|29675851|gb|CB672126.1|CB672126
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|66916872|gb|CX103720.1|CX103720
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|29618914|gb|CB623926.1|CB623926
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|86858875|gb|CI275099.1|CI275099
EST:     TTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: TTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|89186040|gb|CI047909.1|CI047909
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|86504446|gb|CI147079.1|CI147079
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|27576286|gb|CA998980.1|CA998980
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGTAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|86859086|gb|CI277012.1|CI277012
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|87015957|gb|CI279709.1|CI279709
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|29631316|gb|CB636325.1|CB636325
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|29669337|gb|CB665612.1|CB665612
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|29669338|gb|CB665613.1|CB665613
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|27577711|gb|CB000406.1|CB000406
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGTAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|89189608|gb|CI049147.1|CI049147
EST:     ATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: ATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|29664922|gb|CB661197.1|CB661197
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|29664382|gb|CB660657.1|CB660657
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|29644454|gb|CB649461.1|CB649461
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
EST: gi|25806578|gb|CA762539.1|CA762539
EST:     AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAG                         GTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG
genomic: AGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGG

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: 99

ATCAAATATGCCTACCCAAATTTTGTCCAAGATAGTTCAGATCGTACATTACCTTTATGCTTGGCAACTGATTTTCCTGTGAGgtaaaacaat ... tgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGGGAAAAGATGGTTTGTAATGCCCAGAACATTCACCATTCTTCCTGATAAT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caactctccagaaaaaggaactattcatttttccttgtgatcttatgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGGGAAAAGATGGTTTGTAATGCCCAGAACATTCACCATTCTTCCTGATAAT
                  aactattcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacaatggagtaatcatagcgctccaatagattgcctttgctgatgaagttcaacacgcaactctccagaaaaaggaactattcatttttccttgtgatcttatgatatccagGTATTTGGAAGATGTCAAACAGCTCTTCAAGCCCTTGAATCTTCATTTTGGGAAAAGATGGTTTGTAATGCCCAGAACATTCACCATTCTTCCTGATAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG