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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtcctctcccatgtggcaatccccattccgcatagtgctcatcgttttgtgaaattattaaatacatatttgttattcatttatttgtgtgtgtatatatgctcatggaaatatgtcgtgttcctgtgatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGGGGTGGCAGCCAGCTGCGCCGCAGCGGCAGCTGCATGTGGTGAAACGGGC

Basic information

species Oryza sativa
transcript LOC_Os01g64000.1
intron # 3
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|25806940|gb|CA762901.1|CA762901
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|86492277|gb|CI134910.1|CI134910
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGGATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|5701698|gb|AU063505.2|AU063505
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|86497616|gb|CI140249.1|CI140249
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|88964713|gb|CI070059.1|CI070059
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|89189330|gb|CI048869.1|CI048869
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|27548974|gb|CA766860.2|CA766860
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCNAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|86601832|gb|CI258508.1|CI258508
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|88481991|gb|CI419262.1|CI419262
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|88841546|gb|CI080802.1|CI080802
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|9457318|gb|AU063339.2|AU063339
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCA
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCA
EST: gi|88842196|gb|CI081452.1|CI081452
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|8527686|gb|AU092501.1|AU092501
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|8528101|gb|AU092916.1|AU092916
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|86522773|gb|CI162979.1|CI162979
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|8528266|gb|AU093081.1|AU093081
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|86435385|gb|CI106618.1|CI106618
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
EST: gi|87029252|gb|CI276520.1|CI276520
EST:     AAGACGGTTCTACTGACAAAGAAGCAAATG                         CTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG
genomic: AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGG

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: 30 (upstream exon), 55 (downstream exon)
Score: 12

AAGACGGTTCTACTGACAAAGAAGCAAATGgtattgtcct ... gatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGGGGTGGCAGCCAGCTGCGCCGCAGCGGCAGCTGCATGTGGTGAAACGGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtgtgtgtatatatgctcatggaaatatgtcgtgttcctgtgatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGGGGTGGCAGCCAGCTGCGCCGCAGCGGCAGCTGCATGTGGTGAAACGGGC
                                               tttttc  CT-rich tract
         tgtatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtcctctcccatgtggcaatccccattccgcatagtgctcatcgttttgtgaaattattaaatacatatttgttattcatttatttgtgtgtgtatatatgctcatggaaatatgtcgtgttcctgtgatttttcagCTGGTTGAGAAAATGATGGAGCAGTCCAAGGAGAAGATGAATGCAAATAGGGGTGGCAGCCAGCTGCGCCGCAGCGGCAGCTGCATGTGGTGAAACGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC