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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAAACAGTAACAGGTTTTGCACCCTGGTTCTTCAAGAAGGCGTCGTGCCACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtattataatcttgtttcctaaaactgacaagctcatttctatcctaaaacttccttcaaacctatacgtatttatgcgcag

Basic information

species Oryza sativa
transcript LOC_Os01g66130.1
intron # 4
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|88506051|gb|CI433557.1|CI433557
EST:     CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAG                         GCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
genomic: CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtatta ... ttatgcgcagGCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
EST: gi|88507523|gb|CI435029.1|CI435029
EST:     CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAG                         GCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
genomic: CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtatta ... ttatgcgcagGCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
EST: gi|88841863|gb|CI081119.1|CI081119
EST:     CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAG                         GCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
genomic: CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtatta ... ttatgcgcagGCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
EST: gi|88488222|gb|CI425493.1|CI425493
EST:     CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAG                         GCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
genomic: CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtatta ... ttatgcgcagGCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
EST: gi|88508292|gb|CI435798.1|CI435798
EST:     CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAG                         GCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
genomic: CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtatta ... ttatgcgcagGCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
EST: gi|87031033|gb|CI362247.1|CI362247
EST:     CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAG                         GCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
genomic: CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtatta ... ttatgcgcagGCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
EST: gi|88413214|gb|CI523775.1|CI523775
EST:     CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAG                         GCTCAGGTTCTTTTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
genomic: CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtatta ... ttatgcgcagGCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
EST: gi|86413454|gb|CI067859.1|CI067859
EST:     CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAG                         GCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
genomic: CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtatta ... ttatgcgcagGCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
EST: gi|88507667|gb|CI435173.1|CI435173
EST:     CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAG                         GCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
genomic: CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtatta ... ttatgcgcagGCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
EST: gi|87014006|gb|CI273196.1|CI273196
EST:     CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAG                         GCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
genomic: CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtatta ... ttatgcgcagGCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
EST: gi|88509000|gb|CI436506.1|CI436506
EST:     CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAG                         GCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG
genomic: CACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtatta ... ttatgcgcagGCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGG

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: 42 (upstream exon), 67 (downstream exon)
Score: 5

CACAAACAGTAACAGGTTTTGCACCCTGGTTCTTCAAGAAGGCGTCGTGCCACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtatta ... ttatgcgcagGCTCAGGTTCTTCTAAGCTATTTTCGCAACCAGCGCCACGTCAGGGTTGGGAGAGGGTAAGTCTACGCAATTAAGCAGCAATGCGGCGGTCTGATTATTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAAACAGTAACAGGTTTTGCACCCTGGTTCTTCAAGAAGGCGTCGTGCCACCTTTGGTTGCATTGTCGCAATCAGGCACAGCCCGTGCAAGAGAGAAGgttagtattataatcttgtttcctaaaactgacaagctcatttctatcctaaaacttccttcaaacctatacgtatttatgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA