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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTAGTTTATTTGGTGCAAAGATAACTGGTGGAGGATCTGGGGGCTCGGTTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcgacatcgttttttattgtcagttgtacacaatggatgaccataactacaaagatccaagataaaccctccaagagagttgtgattcaccataatgtttgcattttcatggtattgcatgctaacaaaatatcatttgttttcag

Basic information

species Oryza sativa
transcript LOC_Os02g04840.1
intron # 27
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|18386011|gb|BM419210.1|BM419210
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGTAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGA
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAG-AAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGA
EST: gi|87030698|gb|CI361912.1|CI361912
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|88471515|gb|CI408786.1|CI408786
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|86885994|gb|CI319842.1|CI319842
EST:     TTGGGAAAAAGTGGCTTGAAAACCACTCAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTGGGAAAAA-TTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|86831406|gb|CI299464.1|CI299464
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|86908654|gb|CI318973.1|CI318973
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|88266562|gb|CI377464.1|CI377464
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAACCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|88487497|gb|CI424768.1|CI424768
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|88222831|gb|CI220896.1|CI220896
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|88547409|gb|CI477699.1|CI477699
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|88849379|gb|CI089287.1|CI089287
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAGGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|86430531|gb|CI082954.1|CI082954
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTACTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|86889196|gb|CI315807.1|CI315807
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTG-TTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|38475023|gb|CF959156.1|CF959156
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|88274276|gb|CI394682.1|CI394682
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|86871147|gb|CI328349.1|CI328349
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|88298302|gb|CI561095.1|CI561095
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|88558417|gb|CI488901.1|CI488901
EST:     TGAANAGATTTTTGAG                         ATTCAGAAGAGATACAGAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|86873058|gb|CI328438.1|CI328438
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|88298112|gb|CI558517.1|CI558517
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
EST: gi|88995251|gb|CI036826.1|CI036826
EST:     TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAG                         ATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG
genomic: TTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcga ... ttgttttcagATTCAGAAGAGATACAAAGCTGCTACCGGGTACCTACCAATTGTTTTCGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTAGTTTATTTGGTGCAAAGATAACTGGTGGAGGATCTGGGGGCTCGGTTTGTGTCATTGGGAAAAATTGCTTGAAAAGCAGTGAAGAGATTTTTGAGgtattttcgacatcgttttttattgtcagttgtacacaatggatgaccataactacaaagatccaagataaaccctccaagagagttgtgattcaccataatgtttgcattttcatggtattgcatgctaacaaaatatcatttgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA