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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGATTCCCTGCTCGCCCATAATTATTCCAAGAGCACTGGAGCCTGTTGATCTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggctccagattctttgatcccaccagagagaaaaaaaagggtcgttttttaatgctccttcggacccggtttgcggcggtttggacccaatta...

Basic information

species Oryza sativa
transcript LOC_Os03g62500.1
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|58612230|gb|CK039942.1|CK039942
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCGGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|58655908|gb|CK044588.1|CK044588
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|29633183|gb|CB638192.1|CB638192
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|58683314|gb|CK072001.1|CK072001
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|29633212|gb|CB638221.1|CB638221
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|58600090|gb|CK010618.1|CK010618
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|29633151|gb|CB638160.1|CB638160
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|29633239|gb|CB638248.1|CB638248
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|58608773|gb|CK036806.1|CK036806
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|58680835|gb|CK069522.1|CK069522
EST:     CTGCTTGCTCCAAGAA-TTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|29633152|gb|CB638161.1|CB638161
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|88731129|gb|CI754742.1|CI754742
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|58663686|gb|CK052372.1|CK052372
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|29633190|gb|CB638199.1|CB638199
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
EST: gi|88694028|gb|CI738066.1|CI738066
EST:     CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAG                         CTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC
genomic: CTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATC

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: 70 (upstream exon), 75 (downstream exon)
Score: 39

CGATTCCCTGCTCGCCCATAATTATTCCAAGAGCACTGGAGCCTGTTGATCTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggc ... gtgtatgcagCTGTTGCTGAAGTGATGCTGGAGGAAACGGCATTGCAATGGCGGGCTGATCTTCTGCAAGCAATGGAGTGAATACTGGTCTGTTTTTCTTGTCCTGACCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGATTCCCTGCTCGCCCATAATTATTCCAAGAGCACTGGAGCCTGTTGATCTGCTTGCTCCAAGAATTTTTCTTTCATCTCTGTGGGATTTTGGCTCCAGgtactgtggctccagattctttgatcccaccagagagaaaaaaaagggtcgttttttaatgctccttcggacccggtttgcggcggtttggacccaatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcccacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcggcg