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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttttacattgcactgtacatatcatgtgttgttcctgtgcttcctagttaacacgtacatcttttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAAAGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACT

Basic information

species Oryza sativa
transcript LOC_Os02g47440.1
intron # 5
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|86500468|gb|CI143101.1|CI143101
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|58606351|gb|CK034384.1|CK034384
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCGGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|29638446|gb|CB643455.1|CB643455
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|86505518|gb|CI148151.1|CI148151
EST:     TAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACCATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: TAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|29646264|gb|CB651271.1|CB651271
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|25806896|gb|CA762857.1|CA762857
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|58667527|gb|CK056213.1|CK056213
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
EST: gi|86421015|gb|CI057004.1|CI057004
EST:     AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCG                         AGGAAATCGATACCAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA
genomic: AGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAA

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: 50 (upstream exon), 72 (downstream exon)
Score: 32

AGGGAGCAAGCTATTCAAGATATTCAACAACAGATTGGTGAAGTACATGAAGCATTTAAGGATCTTGCTACACTTGTGCATATTCAAGGAGTTACAATCGgcaagtttta ... tttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAAAGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatcatgtgttgttcctgtgcttcctagttaacacgtacatcttttattacagAGGAAATCGATACAAACATTGAGAATTCTGCAGCAGCAACCAAAGAGGCAAAGACAGAACTCGCGAAAGCGTCCAAGACTCAGAAATCGAATTCATCACT
                            agttaac  putative branch site (score: 32)
                                          tcttttatt  putative PPT
                                      tacatcttttatta  TA-rich tract