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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcataactgatcttctatgaagttctgatgtctattttaaattcattattggaattcttctgcacctaacataatggtggctcttttaccttgatcagAGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGTTACCAGAGGTTGTTGCAGATGGTGGGGCAGGCTCATCCAGAGAACATAAAATAC

Basic information

species Oryza sativa
transcript LOC_Os11g05930.1
intron # 4
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|29630671|gb|CB635680.1|CB635680
EST:     GTAATGGGTCAAAGACAGGAGAACACAGCGATGAGGAAAGTGATGCTCAG                         AGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGTTACCA
genomic: GTAATGGGTCAAAGACAGGAGAACACAGCGATGAGGAAAGTGATGCTCAGgtgagcatgt ... ccttgatcagAGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGTTACCA
EST: gi|33674795|gb|CF303034.1|CF303034
EST:     GTAATGGGTCAAAGACAGGAGAACACAGCGATGAGGAAAGTGATGCTCAG                         AGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGT-ACCA
genomic: GTAATGGGTCAAAGACAGGAGAACACAGCGATGAGGAAAGTGATGCTCAGgtgagcatgt ... ccttgatcagAGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGTTACCA
EST: gi|29638597|gb|CB643606.1|CB643606
EST:     GTAATGGGTCAAAGACAGGAGAACACAGCGATGAGGAAAGTGATGCTCAG                         AGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGTTACCA
genomic: GTAATGGGTCAAAGACAGGAGAACACAGCGATGAGGAAAGTGATGCTCAGgtgagcatgt ... ccttgatcagAGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGTTACCA
EST: gi|33678541|gb|CF306780.1|CF306780
EST:     GTAATGGGTCAAAGACAGGAGAACACAGCGATGAGGAAAGTGATGCTCAG                         AGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGT-ACCA
genomic: GTAATGGGTCAAAGACAGGAGAACACAGCGATGAGGAAAGTGATGCTCAGgtgagcatgt ... ccttgatcagAGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGTTACCA
EST: gi|5803459|gb|AI978429.1|AI978429
EST:     GTAATGGGTCAAAGACAGGAGAACACAGCGATGAGGAAAGTGATGCTCAG                         AGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGTTACCA
genomic: GTAATGGGTCAAAGACAGGAGAACACAGCGATGAGGAAAGTGATGCTCAGgtgagcatgt ... ccttgatcagAGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGTTACCA
EST: gi|58680467|gb|CK069154.1|CK069154
EST:     GTAATGGGTCAAAGACAGGAGAACACAGCGATGAGGAAAGTGATGCTCAG                         AGTTCTGGTAGCAAAAGGGA
genomic: GTAATGGGTCAAAGACAGGAGAACACAGCGATGAGGAAAGTGATGCTCAGgtgagcatgt ... ccttgatcagAGTTCTGGTAGCAAAAGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattattggaattcttctgcacctaacataatggtggctcttttaccttgatcagAGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGTTACCAGAGGTTGTTGCAGATGGTGGGGCAGGCTCATCCAGAGAACATAAAATAC
                    acctaac  putative branch site (score: 2)
                                     ctcttttacctt  putative PPT
                       taacataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcataactgatcttctatgaagttctgatgtctattttaaattcattattggaattcttctgcacctaacataatggtggctcttttaccttgatcagAGTTCTGGTAGCAAAAGGGAGGTTGAAATTCAAAGTGCTGAAAAGTTACCAGAGGTTGTTGCAGATGGTGGGGCAGGCTCATCCAGAGAACATAAAATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG