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 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACTCTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctcatctctctcgcaatcctctcctcctcttccaaatccctcgccctcctcctcgccttcgaaaatcgaggcccgattttttttttttgttcttcctcgcag

Basic information

species Oryza sativa
transcript LOC_Os05g48960.1
intron # 1
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|88761779|gb|CI771335.1|CI771335
EST:     TCTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: TCTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
EST: gi|88589118|gb|CI706972.1|CI706972
EST:     GATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: GATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
EST: gi|86850550|gb|CI309362.1|CI309362
EST:     CTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: CTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
EST: gi|29686176|gb|CB682451.1|CB682451
EST:     CCCAACTCGGCGTCTCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: CCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
EST: gi|2312597|gb|C28752.1|C28752
EST:     CCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGNGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: CCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
EST: gi|88395759|gb|CI590774.1|CI590774
EST:     TCTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: TCTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
EST: gi|88593254|gb|CI709416.1|CI709416
EST:     GATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: GATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
EST: gi|88314829|gb|CI608288.1|CI608288
EST:     TCTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: TCTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
EST: gi|88851921|gb|CI679479.1|CI679479
EST:     GATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: GATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
EST: gi|86847645|gb|CI288750.1|CI288750
EST:     GATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: GATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
EST: gi|86830466|gb|CI291944.1|CI291944
EST:     CTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: CTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
EST: gi|88361273|gb|CI626377.1|CI626377
EST:     TCTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: TCTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
EST: gi|86876913|gb|CI309724.1|CI309724
EST:     CTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAG                         GAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC
genomic: CTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTC

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: 47 (upstream exon), 56 (downstream exon)
Score: 38

GGACTCTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctca ... ttcctcgcagGAGCAAAGCGGGGATTCAGAACGGGAAGGAGAAGGTCCGGTTCGTCCGCTCTCGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACTCTCCCGATCCTTCCCCAACTCGGCGTCGCGCCGCCTCAACCGAAGCAAGgtgcgtctcatctctctcgcaatcctctcctcctcttccaaatccctcgccctcctcctcgccttcgaaaatcgaggcccgattttttttttttgttcttcctcgcag

- - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - AGCAAG